Mercurial > public > atmospheric_lidar / changeset
changeset
Improved documentation and clean-up of BaseLidarMeasurement class.
Wed, 06 Dec 2017 13:36:42 +0200
- author
- Iannis <ulalume3@yahoo.com>
- date
- Wed, 06 Dec 2017 13:36:42 +0200
- changeset 92
- 6d26002aaeed
- parent 91
- f9d9d3ea8edb
- child 93
- c352254b4650
Improved documentation and clean-up of BaseLidarMeasurement class.
--- a/atmospheric_lidar/generic.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/generic.py Wed Dec 06 13:36:42 2017 +0200 @@ -1,7 +1,6 @@ -# General imports import datetime +import logging from operator import itemgetter -import logging import matplotlib as mpl import netCDF4 as netcdf @@ -9,24 +8,30 @@ from matplotlib import pyplot as plt from matplotlib.ticker import ScalarFormatter -netcdf_format = 'NETCDF3_CLASSIC' # choose one of 'NETCDF3_CLASSIC', 'NETCDF3_64BIT', 'NETCDF4_CLASSIC' and 'NETCDF4' +NETCDF_FORMAT = 'NETCDF4' # choose one of 'NETCDF3_CLASSIC', 'NETCDF3_64BIT', 'NETCDF4_CLASSIC' and 'NETCDF4' class BaseLidarMeasurement(object): - """ This is the general measurement object. - It is meant to become a general measurement object - independent of the input files. + """ + This class represents a general measurement object, independent of the input files. Each subclass should implement the following: - * the import_file method. - * set the "extra_netcdf_parameters" variable to a dictionary that includes the appropriate parameters. + * the _import_file method; + * set the "extra_netcdf_parameters" variable to a dictionary that includes the appropriate parameters; + + You can override the set_PT method to define a custom procedure to get ground temperature and pressure. - You can override the get_PT method to define a custom procedure to get ground temperature and pressure. - The one implemented by default is by using the MILOS meteorological station data. - + The class assumes that the input files are consequtive, i.e. there are no measurements gaps. """ - - def __init__(self, filelist=None): + def __init__(self, file_list=None): + """ + This is run when creating a new object. + + Parameters + ---------- + file_list : list + A list of the full paths to the input file. + """ self.info = {} self.dimensions = {} self.variables = {} @@ -34,27 +39,47 @@ self.attributes = {} self.files = [] self.dark_measurement = None + self.extra_netcdf_parameters = None - if filelist: - self.import_files(filelist) + if file_list: + self._import_files(file_list) - def import_files(self, filelist): - for f in filelist: - self.import_file(f) + def _import_files(self, file_list): + """ + Imports a list of files, and updates the object parameters. + + Parameters + ---------- + file_list : list + A list of the full paths to the input file. + """ + for f in file_list: + self._import_file(f) self.update() - def import_file(self, filename): + def _import_file(self, filename): + """ + Reads a single lidar file. + + This method should be overwritten at all subclasses. + + Parameters + ---------- + filename : str + Path to the lidar file. + """ raise NotImplementedError('Importing files should be defined in the instrument-specific subclass.') def update(self): - ''' - Update the the info, variables and dimensions of the lidar measurement based - on the information found in the channels. + """ + Update the info dictionary, variables, and dimensions of the measurement object + based on the information found in the channels objects. + Note + ---- Reading of the scan_angles parameter is not implemented. - ''' + """ # Initialize - start_time = [] stop_time = [] points = [] @@ -86,67 +111,90 @@ # Update the variables dictionary # Write time scales in seconds - raw_Data_Start_Time = [] - raw_Data_Stop_Time = [] + raw_data_start_time = [] + raw_data_stop_time = [] for current_time_scale in list(time_scales): raw_start_time = np.array(current_time_scale) - min(start_time) # Time since start_time raw_start_in_seconds = np.array([t.seconds for t in raw_start_time]) # Convert in seconds - raw_Data_Start_Time.append(raw_start_in_seconds) # And add to the list - # Check if this time scale has measurements every 30 or 60 seconds. + raw_data_start_time.append(raw_start_in_seconds) # And add to the list duration = self._get_duration(raw_start_in_seconds) + # TODO: Define stop time for each measurement based on real data raw_stop_in_seconds = raw_start_in_seconds + duration - raw_Data_Stop_Time.append(raw_stop_in_seconds) + raw_data_stop_time.append(raw_stop_in_seconds) - self.variables['Raw_Data_Start_Time'] = raw_Data_Start_Time - self.variables['Raw_Data_Stop_Time'] = raw_Data_Stop_Time + self.variables['Raw_Data_Start_Time'] = raw_data_start_time + self.variables['Raw_Data_Stop_Time'] = raw_data_stop_time # Make a dictionary to match time scales and channels channel_timescales = [] for (channel_name, current_time_scale) in zip(channel_name_list, all_time_scales): - # The following lines are PEARL specific. The reason they are here is not clear. - # if channel_name =='1064BLR': - # channel_name = '1064' for (ts, n) in zip(time_scales, range(len(time_scales))): if current_time_scale == ts: channel_timescales.append([channel_name, n]) self.variables['id_timescale'] = dict(channel_timescales) def _get_duration(self, raw_start_in_seconds): - ''' Return the duration for a given time scale. In some files (e.g. Licel) this - can be specified from the files themselves. In others this must be guessed. - - ''' - # The old method, kept here for reference - # dt = np.mean(np.diff(raw_start_in_seconds)) - # for d in duration_list: - # if abs(dt - d) <15: #If the difference of measurements is 10s near the(30 or 60) seconds - # duration = d - + """ + Return the duration for a given time scale. + + In some files (e.g. Licel) this can be specified from the files themselves. + In others this must be guessed. + + Parameters + ---------- + raw_start_in_seconds : array + An array of floats, representing the start time of each measurement profile. + + Returns + ------- + duration : float + Guess of the duration of each bin in the timescale + """ duration = np.diff(raw_start_in_seconds)[0] return duration def subset_by_channels(self, channel_subset): - ''' Get a measurement object containing only the channels with names - contained in the channel_sublet list ''' + """ + Create a measurement object containing only a subset of channels. + + Parameters + ---------- + channel_subset : list + A list of channel names (str) to be included in the new measurement object. + + Returns + ------- + m : BaseLidarMeasurements object + A new measurements object + """ m = self.__class__() # Create an object of the same type as this one. m.channels = dict([(channel, self.channels[channel]) for channel in channel_subset]) - + m.files = self.files - + m.update() - + return m def subset_by_scc_channels(self): """ - Subset the measurement based on the channels provided in the extra_netecdf_parameter file. + Subset the measurement based on the channels provided in the + extra_netecdf_parameter file. + + Returns + ------- + m : BaseLidarMeasurements object + A new measurements object """ + if self.extra_netcdf_parameters is None: + raise RuntimeError("Extra netCDF parameters not defined, cannot subset measurement.") + scc_channels = self.extra_netcdf_parameters.channel_parameters.keys() common_channels = list(set(scc_channels).intersection(self.channels.keys())) @@ -158,6 +206,21 @@ return self.subset_by_channels(common_channels) def subset_by_time(self, start_time, stop_time): + """ + Subset the measurement for a specific time interval + + Parameters + ---------- + start_time : datetime + The starting datetime to subset. + stop_time : datetime + The stopping datetime to subset. + + Returns + ------- + m : BaseLidarMeasurements object + A new measurements object + """ if start_time > stop_time: raise ValueError('Stop time should be after start time') @@ -168,14 +231,29 @@ m = self.__class__() # Create an object of the same type as this one. for (channel_name, channel) in self.channels.items(): m.channels[channel_name] = channel.subset_by_time(start_time, stop_time) + m.update() return m def subset_by_bins(self, b_min=0, b_max=None): - """Remove some height bins from the file. This could be needed to - remove aquisition artifacts at the start or the end of the files. """ - + Remove some height bins from the file. + + This could be needed to remove acquisition artifacts at + the first or last bins of the profiles. + + Parameters + ---------- + b_min : int + The fist valid data bin + b_max : int or None + The last valid data bin. If equal to None, all bins are used. + + Returns + ------- + m : BaseLidarMeasurements object + A new measurements object + """ m = self.__class__() # Create an object of the same type as this one. for (channel_name, channel) in self.channels.items(): @@ -185,12 +263,17 @@ return m - def rename_channel(self, prefix="", suffix=""): - """ Add a prefix and a suffix in a channel name. - - :param prefix: A string for the prefix - :param suffix: A string for the suffix - :return: Nothing + def rename_channels(self, prefix="", suffix=""): + """ Add a prefix and a suffix to all channel name. + + This is uses when processing Delta90 depolarization calibration measurements. + + Parameters + ---------- + prefix : str + The prefix to add to channel names. + suffix : str + The suffix to add to channel names. """ channel_names = self.channels.keys() @@ -198,16 +281,27 @@ new_name = prefix + channel_name + suffix self.channels[new_name] = self.channels.pop(channel_name) - def get_PT(self): - ''' Sets the pressure and temperature at station level . - The results are stored in the info dictionary. - ''' - - self.info['Temperature'] = 10.0 - self.info['Pressure'] = 930.0 + def set_PT(self): + """ + Sets the pressure and temperature at station level at the info dictionary . + + In this method, default values are used. It can be overwritten by subclasses + to define more appropriate values for each system. + """ + self.info['Temperature'] = 15.0 # Temperature in degC + self.info['Pressure'] = 1013.15 # Pressure in hPa def subtract_dark(self): - + """ + Subtract dark measurements from the raw lidar signals. + + This method is here just for testing. + + Note + ---- + This method should not be called if processing the data with the SCC. The SCC + performs this operations anyway. + """ if not self.dark_measurement: raise IOError('No dark measurements have been imported yet.') @@ -228,10 +322,10 @@ ---------- measurement_id: str A measurement id with the format YYYYMMDDccNN, where YYYYMMDD the date, - cc the earlinet call sign and NN a number between 00 and 99. + cc the EARLiNet call sign and NN a number between 00 and 99. measurement_number: str If measurement id is not provided the method will try to create one - based on the input dete. The measurement number can specify the value + based on the input date. The measurement number can specify the value of NN in the created ID. """ if measurement_id is None: @@ -244,10 +338,15 @@ self.info['Measurement_ID'] = measurement_id - def save_as_netcdf(self, filename=None): - """Saves the measurement in the netcdf format as required by the SCC. - Input: filename. If no filename is provided <measurement_id>.nc will - be used. + def save_as_SCC_netcdf(self, filename=None): + """Saves the measurement in the netCDF format as required by the SCC. + + If no filename is provided <measurement_id>.nc will be used. + + Parameters + ---------- + filename : str + Output file name. If None, <measurement_id>.nc will be used. """ params = self.extra_netcdf_parameters @@ -260,7 +359,7 @@ stored_value = self.info.get(parameter, None) if stored_value is None: try: - self.get_PT() + self.set_PT() except: raise ValueError('A value needs to be specified for %s' % parameter) @@ -308,128 +407,127 @@ input_values['Latitude_degrees_north'] = params.general_parameters['Latitude_degrees_north'] input_values['Longitude_degrees_east'] = params.general_parameters['Longitude_degrees_east'] input_values['Altitude_meter_asl'] = params.general_parameters['Altitude_meter_asl'] - - # Override general paremeters with those provided by any subclass + + # Override general parameters with those provided by any subclass # in a custom fashion - for param in self.getCustomGeneralParameters(): - input_values[ param["name"] ] = param["value"] + for param in self.get_custom_general_parameters(): + input_values[param["name"]] = param["value"] - # Open a netCDF4 file - f = netcdf.Dataset(filename, 'w', format=netcdf_format) # the format is specified in the begining of the file + # Open a netCDF file. The format is specified in the beginning of this module. + with netcdf.Dataset(filename, 'w', format=NETCDF_FORMAT) as f: + + # Create the dimensions in the file + for (d, v) in dimensions.iteritems(): + v = input_values.pop(d, v) + f.createDimension(d, v) - # Create the dimensions in the file - for (d, v) in dimensions.iteritems(): - v = input_values.pop(d, v) - f.createDimension(d, v) + # Create global attributes + for (attrib, value) in global_att.iteritems(): + val = input_values.pop(attrib, value) + if val: + setattr(f, attrib, val) + + # Variables - # Create global attributes - for (attrib, value) in global_att.iteritems(): - val = input_values.pop(attrib, value) - if val: - setattr(f, attrib, val) + # Write either channel_id or string_channel_id in the file + first_channel_keys = params.channel_parameters.items()[0][1].keys() + if "channel_ID" in first_channel_keys: + channel_var = 'channel_ID' + variable_type = 'i' + elif "channel string ID" in first_channel_keys: + channel_var = 'channel string ID' + variable_type = str + else: + raise ValueError('Channel parameters should define either "chanel_id" or "channel_string_ID".') - """ Variables """ - # Write either channel_id or string_channel_id in the file - first_channel_keys = params.channel_parameters.items()[0][1].keys() - if "channel_ID" in first_channel_keys: - channel_var = 'channel_ID' - variable_type = 'i' - elif "channel string ID" in first_channel_keys: - channel_var = 'channel string ID' - variable_type = str - else: - raise ValueError('Channel parameters should define either "chanel_id" or "channel_string_ID".') + 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 custom subclass parameters: + for param in self.get_custom_channel_parameters(): + temp_v = f.createVariable(param["name"], param["type"], param["dimensions"]) + + for (value, n) in zip(param["values"], range(len(param["values"]))): + temp_v[n] = value - 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 custom subclass parameters: - for param in self.getCustomChannelParameters(): - temp_v = f.createVariable(param["name"], param["type"], param["dimensions"]) - - for (value, n) in zip(param["values"], range(len(param["values"]))): - temp_v[n] = value - - # Write the values of fixed channel parameters: - fill_value = -9999 - for param in self._get_provided_extra_parameters(): - if param in channel_variables.keys(): - try: - temp_v = f.createVariable(param, channel_variables[param][1], channel_variables[param][0]) - except RuntimeError: - logging.warning("NetCDF variable \"%s\" ignored because it was read from the input files!" % param) - continue - else: - try: - temp_v = f.createVariable(param, 'd', ('channels',), fill_value = fill_value) - except RuntimeError: - logging.warning("NetCDF variable \"%s\" ignored because it was read from the input files!" % param) - continue - + # Write the values of fixed channel parameters: + fill_value = -9999 + for param in self._get_provided_extra_parameters(): + if param in channel_variables.keys(): + try: + temp_v = f.createVariable(param, channel_variables[param][1], channel_variables[param][0]) + except RuntimeError: + logging.warning("NetCDF variable \"%s\" ignored because it was read from the input files!" % param) + continue + else: + try: + temp_v = f.createVariable(param, 'd', ('channels',), fill_value=fill_value) + except RuntimeError: + logging.warning("NetCDF variable \"%s\" ignored because it was read from the input files!" % param) + continue + + for (channel, n) in zip(channels, range(len(channels))): + try: + temp_v[n] = params.channel_parameters[channel][param] + except KeyError: # The parameter was not provided for this channel so we mask the value. + temp_v[n] = fill_value + + # Write the id_timescale values + temp_id_timescale = f.createVariable('id_timescale', 'i', ('channels',)) for (channel, n) in zip(channels, range(len(channels))): - try: - temp_v[n] = params.channel_parameters[channel][param] - except KeyError: # The parameter was not provided for this channel so we mask the value. - temp_v[n] = fill_value + temp_id_timescale[n] = self.variables['id_timescale'][channel] - # Write the id_timescale values - temp_id_timescale = f.createVariable('id_timescale', 'i', ('channels',)) - for (channel, n) in zip(channels, range(len(channels))): - temp_id_timescale[n] = self.variables['id_timescale'][channel] + # Laser pointing angle + temp_v = f.createVariable('Laser_Pointing_Angle', 'd', ('scan_angles',)) + temp_v[:] = params.general_parameters['Laser_Pointing_Angle'] + + # Molecular calculation + temp_v = f.createVariable('Molecular_Calc', 'i') + temp_v[:] = params.general_parameters['Molecular_Calc'] - # Laser pointing angle - temp_v = f.createVariable('Laser_Pointing_Angle', 'd', ('scan_angles',)) - temp_v[:] = params.general_parameters['Laser_Pointing_Angle'] + # Laser pointing angles of profiles + temp_v = f.createVariable('Laser_Pointing_Angle_of_Profiles', 'i', ('time', 'nb_of_time_scales')) + for (time_scale, n) in zip(self.variables['Raw_Data_Start_Time'], + range(len(self.variables['Raw_Data_Start_Time']))): + temp_v[:len(time_scale), n] = 0 # The lidar has only one laser pointing angle - # Molecular calculation - temp_v = f.createVariable('Molecular_Calc', 'i') - temp_v[:] = params.general_parameters['Molecular_Calc'] - - # Laser pointing angles of profiles - temp_v = f.createVariable('Laser_Pointing_Angle_of_Profiles', 'i', ('time', 'nb_of_time_scales')) - for (time_scale, n) in zip(self.variables['Raw_Data_Start_Time'], - range(len(self.variables['Raw_Data_Start_Time']))): - temp_v[:len(time_scale), n] = 0 # The lidar has only one laser pointing angle + # Raw data start/stop time + temp_raw_start = f.createVariable('Raw_Data_Start_Time', 'i', ('time', 'nb_of_time_scales')) + temp_raw_stop = f.createVariable('Raw_Data_Stop_Time', 'i', ('time', 'nb_of_time_scales')) + for (start_time, stop_time, n) in zip(self.variables['Raw_Data_Start_Time'], + self.variables['Raw_Data_Stop_Time'], + range(len(self.variables['Raw_Data_Start_Time']))): + temp_raw_start[:len(start_time), n] = start_time + temp_raw_stop[:len(stop_time), n] = stop_time - # Raw data start/stop time - temp_raw_start = f.createVariable('Raw_Data_Start_Time', 'i', ('time', 'nb_of_time_scales')) - temp_raw_stop = f.createVariable('Raw_Data_Stop_Time', 'i', ('time', 'nb_of_time_scales')) - for (start_time, stop_time, n) in zip(self.variables['Raw_Data_Start_Time'], - self.variables['Raw_Data_Stop_Time'], - range(len(self.variables['Raw_Data_Start_Time']))): - temp_raw_start[:len(start_time), n] = start_time - temp_raw_stop[:len(stop_time), n] = stop_time - - # Laser shots - try: - temp_v = f.createVariable('Laser_Shots', 'i', ('time', 'channels')) - for (channel, n) in zip(channels, range(len(channels))): - time_length = len(self.variables['Raw_Data_Start_Time'][self.variables['id_timescale'][channel]]) - # Array slicing stoped working as usual ex. temp_v[:10] = 100 does not work. ??? np.ones was added. - temp_v[:time_length, n] = np.ones(time_length) * params.channel_parameters[channel]['Laser_Shots'] - except RuntimeError: - logging.warning("NetCDF variable \"%s\" ignored because it was read from the input files!" % "LaserShots") + # Laser shots + try: + temp_v = f.createVariable('Laser_Shots', 'i', ('time', 'channels')) + for (channel, n) in zip(channels, range(len(channels))): + time_length = len(self.variables['Raw_Data_Start_Time'][self.variables['id_timescale'][channel]]) + # Array slicing stoped working as usual ex. temp_v[:10] = 100 does not work. ??? np.ones was added. + temp_v[:time_length, n] = np.ones(time_length) * params.channel_parameters[channel]['Laser_Shots'] + except RuntimeError: + logging.warning("NetCDF variable \"%s\" ignored because it was read from the input files!" % "LaserShots") + # Raw lidar data + temp_v = f.createVariable('Raw_Lidar_Data', 'd', ('time', 'channels', 'points')) + for (channel, n) in zip(channels, range(len(channels))): + c = self.channels[channel] + temp_v[:len(c.time), n, :c.points] = c.matrix - # Raw lidar data - temp_v = f.createVariable('Raw_Lidar_Data', 'd', ('time', 'channels', 'points')) - for (channel, n) in zip(channels, range(len(channels))): - c = self.channels[channel] - temp_v[:len(c.time), n, :c.points] = c.matrix - - self.add_dark_measurements_to_netcdf(f, channels) + self.add_dark_measurements_to_netcdf(f, channels) - # Pressure at lidar station - temp_v = f.createVariable('Pressure_at_Lidar_Station', 'd') - temp_v[:] = self.info['Pressure'] + # Pressure at lidar station + temp_v = f.createVariable('Pressure_at_Lidar_Station', 'd') + temp_v[:] = self.info['Pressure'] - # Temperature at lidar station - temp_v = f.createVariable('Temperature_at_Lidar_Station', 'd') - temp_v[:] = self.info['Temperature'] + # Temperature at lidar station + temp_v = f.createVariable('Temperature_at_Lidar_Station', 'd') + temp_v[:] = self.info['Temperature'] - self.save_netcdf_extra(f) - f.close() + self.save_netcdf_extra(f) def _get_scc_mandatory_channel_variables(self): channel_variables = \ @@ -439,37 +537,46 @@ 'DAQ_Range': (('channels',), 'd'), } return channel_variables - + def _get_provided_extra_parameters(self): # When looking for non-mandatory channel parameters, ignore the following parameter names: ignore = ['channel_ID', 'channel string ID', 'Depolarization_Factor', 'Laser_Shots'] - + channels = self.channels.keys() params = self.extra_netcdf_parameters.channel_parameters mandatory = self._get_scc_mandatory_channel_variables() - + # Get all the provided extra parameters (both mandatory and optional): provided_extra_parameters = [] for (channel, n) in zip(channels, range(len(channels))): # Check all the mandatory parameters are provided for each of the channels: for var in mandatory.keys(): if var not in params[channel].keys(): - raise ValueError ("Mandatory parameter '{0}' not provided for channel {1}!".format( + raise ValueError("Mandatory parameter '{0}' not provided for channel {1}!".format( var, channel )) - + provided_extra_parameters.extend(params[channel].keys()) - + provided_extra_parameters = set(provided_extra_parameters) # Discard certain parameter names: for param in ignore: provided_extra_parameters.discard(param) - + return provided_extra_parameters def add_dark_measurements_to_netcdf(self, f, channels): - + """ + Adds dark measurement variables and properties to an open netCDF file. + + Parameters + ---------- + f : netcdf Dataset + A netCDF Dataset, open for writing. + channels : list + A list of channels names to consider when adding dark measurements. + """ # Get dark measurements. If it is not given in self.dark_measurement # try to get it using the get_dark_measurements method. If none is found # return without adding something. @@ -509,12 +616,12 @@ f.RawBck_Stop_Time_UT = dark_measurement.info['stop_time'].strftime('%H%M%S') def save_netcdf_extra(self, f): + """ Save extra netCDF parameters to an open netCDF file. + + If required, this method should be overwritten by subclasses of BaseLidarMeasurement. + """ pass - def _gettime(self, date_str, time_str): - t = datetime.datetime.strptime(date_str + time_str, '%d/%m/%Y%H.%M.%S') - return t - def plot(self): for channel in self.channels: self.channels[channel].plot(show_plot=False) @@ -522,32 +629,24 @@ def get_dark_measurements(self): return None - - def getCustomGeneralParameters(self): - """ - Abstract method to provide custom NetCDF parameters - that should be included in the final NetCDF file. - This method should be implemented by subclasses of - BaseLidarMeasurement. + + def get_custom_general_parameters(self): """ - return [] + Abstract method to provide custom NetCDF parameters that should be included + in the final NetCDF file. - def getCustomChannelParameters(self): - """ - Abstract method to provide custom NetCDF parameters - for the channels in this measurement that should be - included in the final NetCDF file. This method should - be implemented by subclasses of BaseLidarMeasurement. + If required, this method should be implemented by subclasses of BaseLidarMeasurement. """ return [] - @property - def mean_time(self): - start_time = self.info['start_time'] - stop_time = self.info['stop_time'] - dt = stop_time - start_time - t_mean = start_time + dt / 2 - return t_mean + def get_custom_channel_parameters(self): + """ + Abstract method to provide custom NetCDF parameters for the channels in this + measurement that should be included in the final NetCDF file. + + If required, this method should be implemented by subclasses of BaseLidarMeasurement. + """ + return [] class LidarChannel: @@ -616,7 +715,7 @@ def subset_by_bins(self, b_min=0, b_max=None): """Remove some height bins from the file. This could be needed to - remove aquisition artifacts at the start or the end of the files. + remove acquisition artifacts at the start or the end of the files. """ subset_data = {} @@ -704,7 +803,7 @@ else: data = self.matrix - hmax_idx = self.index_at_height(zoom[1]) + hmax_idx = self._index_at_height(zoom[1]) # If z0 is given, then the plot is a.s.l. if z0: @@ -770,8 +869,8 @@ else: data = self.matrix - hmax_idx = self.index_at_height(zoom[1]) - hmin_idx = self.index_at_height(zoom[0]) + hmax_idx = self._index_at_height(zoom[1]) + hmin_idx = self._index_at_height(zoom[0]) # If z0 is given, then the plot is a.s.l. if z0: @@ -785,7 +884,6 @@ # dateFormatter = mpl.dates.DateFormatter('%H.%M') # hourlocator = mpl.dates.HourLocator() - if date_labels: dayFormatter = mpl.dates.DateFormatter('%H:%M\n%d/%m/%Y') daylocator = mpl.dates.AutoDateLocator(minticks=3, maxticks=8, interval_multiples=True) @@ -835,17 +933,8 @@ ticklabels.set_fontsize(cb_font_size) cb1.ax.yaxis.get_offset_text().set_fontsize(cb_font_size) - def index_at_height(self, height): + def _index_at_height(self, height): idx = np.array(np.abs(self.z - height).argmin()) if idx.size > 1: idx = idx[0] return idx - - -def netcdf_from_files(LidarClass, filename, files, channels, measurement_ID): - # Read the lidar files and select channels - temp_m = LidarClass(files) - m = temp_m.subset_by_channels(channels) - m.get_PT() - m.info['Measurement_ID'] = measurement_ID - m.save_as_netcdf(filename)
--- a/atmospheric_lidar/licel.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/licel.py Wed Dec 06 13:36:42 2017 +0200 @@ -197,11 +197,11 @@ durations = {} # Keep the duration of the files laser_shots = [] - def __init__(self, filelist=None, use_id_as_name=False): + def __init__(self, file_list=None, use_id_as_name=False): self.use_id_as_name = use_id_as_name - super(LicelLidarMeasurement, self).__init__(filelist) + super(LicelLidarMeasurement, self).__init__(file_list) - def import_file(self, filename): + def _import_file(self, filename): if filename in self.files: logging.warning("File has been imported already: %s" % filename) else: @@ -229,10 +229,10 @@ channel.append(other.channels[channel_name]) def _get_duration(self, raw_start_in_seconds): - ''' Return the duration for a given time scale. If only a single + """ Return the duration for a given time scale. If only a single file is imported, then this cannot be guessed from the time difference and the raw_info of the file are checked. - ''' + """ if len(raw_start_in_seconds) == 1: # If only one file imported duration = self.durations.itervalues().next() # Get the first (and only) raw_info @@ -242,7 +242,7 @@ return duration_sec - def getCustomChannelParameters(self): + def get_custom_channel_parameters(self): params = [{ "name": "DAQ_Range", "dimensions": ('channels',), @@ -263,7 +263,7 @@ return params - def getCustomGeneralParameters(self): + def get_custom_general_parameters(self): params = [{ "name": "Altitude_meter_asl", "value": self.raw_info[ self.files[0] ]["Altitude"]
--- a/atmospheric_lidar/licel_depol.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/licel_depol.py Wed Dec 06 13:36:42 2017 +0200 @@ -40,10 +40,10 @@ # Read plus and minus 45 measurements self.plus45_measurement = LicelLidarMeasurement(self.plus45_files, self.use_id_as_name) - self.plus45_measurement.rename_channel(suffix='_p45') + self.plus45_measurement.rename_channels(suffix='_p45') self.minus45_measurement = LicelLidarMeasurement(self.minus45_files, self.use_id_as_name) - self.minus45_measurement.rename_channel(suffix='_m45') + self.minus45_measurement.rename_channels(suffix='_m45') # Combine them in this object self.channels = {}
--- a/atmospheric_lidar/scripts/licel2scc.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/scripts/licel2scc.py Wed Dec 06 13:36:42 2017 +0200 @@ -38,10 +38,10 @@ class CustomLidarMeasurement(LicelLidarMeasurement): extra_netcdf_parameters = custom_netcdf_parameters - def __init__(self, filelist=None): - super(CustomLidarMeasurement, self).__init__(filelist, use_id_as_name) + def __init__(self, file_list=None): + super(CustomLidarMeasurement, self).__init__(file_list, use_id_as_name) - def get_PT(self): + def set_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). @@ -147,6 +147,6 @@ # Save the netcdf logger.info("Saving netcdf") measurement.set_measurement_id(args.measurement_id, args.measurement_number) - measurement.save_as_netcdf() + measurement.save_as_SCC_netcdf() logger.info("Created file %s" % measurement.scc_filename)
--- a/atmospheric_lidar/scripts/licel2scc_depol.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/scripts/licel2scc_depol.py Wed Dec 06 13:36:42 2017 +0200 @@ -41,7 +41,7 @@ def __init__(self, plus45_files=None, minus45_files=None): super(CustomLidarMeasurement, self).__init__(plus45_files, minus45_files, use_id_as_name) - def get_PT(self): + def set_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). @@ -136,5 +136,5 @@ # Save the netcdf logger.info("Saving netcdf") measurement.set_measurement_id(args.measurement_id, args.measurement_number) - measurement.save_as_netcdf() + measurement.save_as_SCC_netcdf() logger.info("Created file %s" % measurement.scc_filename)
--- a/atmospheric_lidar/systems/eole/eole.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/systems/eole/eole.py Wed Dec 06 13:36:42 2017 +0200 @@ -5,7 +5,7 @@ class EoleLidarMeasurement(LicelLidarMeasurement): extra_netcdf_parameters = eole_netcdf_parameters - def get_PT(self): + def set_PT(self): ''' Sets the pressure and temperature at station level . The results are stored in the info dictionary. '''
--- a/atmospheric_lidar/systems/ipral/ipral.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/systems/ipral/ipral.py Wed Dec 06 13:36:42 2017 +0200 @@ -5,10 +5,10 @@ class IpralLidarMeasurement(LicelLidarMeasurement): extra_netcdf_parameters = ipral_netcdf_parameters - def __init__(self, filelist=None, use_id_as_name=True): - super(IpralLidarMeasurement, self).__init__(filelist, use_id_as_name) + def __init__(self, file_list=None, use_id_as_name=True): + super(IpralLidarMeasurement, self).__init__(file_list, use_id_as_name) - def get_PT(self): + def set_PT(self): ''' Sets the pressure and temperature at station level . The results are stored in the info dictionary. '''
--- a/atmospheric_lidar/systems/lilas/lilas.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/systems/lilas/lilas.py Wed Dec 06 13:36:42 2017 +0200 @@ -5,7 +5,7 @@ class LilasLidarMeasurement(LicelLidarMeasurement): extra_netcdf_parameters = lilas_netcdf_parameters - def get_PT(self): + def set_PT(self): ''' Sets the pressure and temperature at station level . The results are stored in the info dictionary. '''
--- a/atmospheric_lidar/systems/pearl/pearl.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/systems/pearl/pearl.py Wed Dec 06 13:36:42 2017 +0200 @@ -18,14 +18,14 @@ extra_netcdf_parameters = pearl_netcdf_parameters - def import_file(self,filename): + def _import_file(self, filename): ''' Import a pearl file. ''' if filename in self.files: print "File has been imported already:" + filename else: parameters, channels_dict = self.read_pearl_data(filename) - start_time = self._gettime(parameters['Acq_date'],parameters['Acq_start_time']) + start_time = self._get_time(parameters['Acq_date'], parameters['Acq_start_time']) for channel_info in channels_dict.itervalues(): @@ -81,6 +81,9 @@ f.close() return parameters,channels + def _get_time(self, date_str, time_str): + t = datetime.datetime.strptime(date_str + time_str, '%d/%m/%Y%H.%M.%S') + return t def get_measurement_for_interval(start_time, stop_time): ''' Searches for a pearl measurement based on a time interval
--- a/atmospheric_lidar/systems/rali/rali.py Wed Dec 06 11:50:41 2017 +0200 +++ b/atmospheric_lidar/systems/rali/rali.py Wed Dec 06 13:36:42 2017 +0200 @@ -7,7 +7,7 @@ class RaliLidarMeasurement(LicelLidarMeasurement): extra_netcdf_parameters = rali_netcdf_parameters - def get_PT(self): + def set_PT(self): ''' Gets the pressure and temperature from Radiometer data. If no data file is found, mean values from past measurements are used.
--- a/example_scripts/convert_ipral.py Wed Dec 06 11:50:41 2017 +0200 +++ b/example_scripts/convert_ipral.py Wed Dec 06 13:36:42 2017 +0200 @@ -68,7 +68,7 @@ #Save the netcdf print "Saving netcdf." measurement.set_measurement_id(args.measurement_id, args.measurement_number) - measurement.save_as_netcdf() + measurement.save_as_SCC_netcdf() print "Created file ", measurement.scc_filename else: print "No files found when searching for ", search_str \ No newline at end of file
--- a/example_scripts/convert_lilas.py Wed Dec 06 11:50:41 2017 +0200 +++ b/example_scripts/convert_lilas.py Wed Dec 06 13:36:42 2017 +0200 @@ -68,7 +68,7 @@ #Save the netcdf print "Saving netcdf." measurement.set_measurement_id(args.measurement_id, args.measurement_number) - measurement.save_as_netcdf() + measurement.save_as_SCC_netcdf() print "Created file ", measurement.scc_filename else: print "No files found when searching for ", search_str \ No newline at end of file
--- a/readme.rst Wed Dec 06 11:50:41 2017 +0200 +++ b/readme.rst Wed Dec 06 13:36:42 2017 +0200 @@ -176,6 +176,6 @@ .. code-block:: python - my_measurement.save_as_netcdf("filename") + my_measurement.save_as_SCC_netcdf("filename") where you change the output filename to the filename you want to use. \ No newline at end of file
