def modify_faimms_netcdf(netcdf_file_path, channel_id_info):
""" Modify the downloaded netCDF file so it passes both CF and IMOS checker
input:
netcdf_file_path(str) : path of netcdf file to modify
channel_id_index(tupple) : information from xml for the channel
"""
modify_aims_netcdf(netcdf_file_path, channel_id_info)
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
netcdf_file_obj.aims_channel_id = int(channel_id_info['channel_id'])
if not (channel_id_info['metadata_uuid'] == 'Not Available'):
netcdf_file_obj.metadata_uuid = channel_id_info['metadata_uuid']
# some weather stations channels don't have a depth variable if sensor above water
if 'depth' in netcdf_file_obj.variables.keys():
var = netcdf_file_obj.variables['depth']
var.long_name = 'nominal depth'
var.positive = 'down'
var.axis = 'Z'
var.reference_datum = 'sea surface'
var.valid_min = -10.0
var.valid_max = 30.0
netcdf_file_obj.renameVariable('depth', 'NOMINAL_DEPTH')
if 'DEPTH' in netcdf_file_obj.variables.keys():
var = netcdf_file_obj.variables['DEPTH']
var.coordinates = "TIME LATITUDE LONGITUDE NOMINAL_DEPTH"
var.long_name = 'actual depth'
var.reference_datum = 'sea surface'
var.positive = 'down'
var.valid_min = -10.0
var.valid_max = 30.0
netcdf_file_obj.close()
netcdf_file_obj = Dataset(
netcdf_file_path, 'a', format='NETCDF4'
) # need to close to save to file. as we call get_main_netcdf_var just after
main_var = get_main_netcdf_var(netcdf_file_path)
# DEPTH, LATITUDE and LONGITUDE are not dimensions, so we make them into auxiliary cooordinate variables by adding this attribute
if 'NOMINAL_DEPTH' in netcdf_file_obj.variables.keys():
netcdf_file_obj.variables[
main_var].coordinates = "TIME LATITUDE LONGITUDE NOMINAL_DEPTH"
else:
netcdf_file_obj.variables[
main_var].coordinates = "TIME LATITUDE LONGITUDE"
netcdf_file_obj.close()
if not convert_time_cf_to_imos(netcdf_file_path):
return False
remove_dimension_from_netcdf(
netcdf_file_path) # last modification to do in this order!
return True
def modify_faimms_netcdf(netcdf_file_path, channel_id_info):
""" Modify the downloaded netCDF file so it passes both CF and IMOS checker
input:
netcdf_file_path(str) : path of netcdf file to modify
channel_id_index(tupple) : information from xml for the channel
"""
modify_aims_netcdf(netcdf_file_path, channel_id_info)
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
netcdf_file_obj.aims_channel_id = int(channel_id_info['channel_id'])
if not (channel_id_info['metadata_uuid'] == 'Not Available'):
netcdf_file_obj.metadata_uuid = channel_id_info['metadata_uuid']
# some weather stations channels don't have a depth variable if sensor above water
if 'depth' in netcdf_file_obj.variables.keys():
var = netcdf_file_obj.variables['depth']
var.long_name = 'nominal depth'
var.positive = 'down'
var.axis = 'Z'
var.reference_datum = 'sea surface'
var.valid_min = -10.0
var.valid_max = 30.0
netcdf_file_obj.renameVariable('depth', 'NOMINAL_DEPTH')
if 'DEPTH' in netcdf_file_obj.variables.keys():
var = netcdf_file_obj.variables['DEPTH']
var.coordinates = "TIME LATITUDE LONGITUDE NOMINAL_DEPTH"
var.long_name = 'actual depth'
var.reference_datum = 'sea surface'
var.positive = 'down'
var.valid_min = -10.0
var.valid_max = 30.0
netcdf_file_obj.close()
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4') # need to close to save to file. as we call get_main_faimms_var just after
main_var = get_main_faimms_var(netcdf_file_path)
# DEPTH, LATITUDE and LONGITUDE are not dimensions, so we make them into auxiliary cooordinate variables by adding this attribute
if 'NOMINAL_DEPTH' in netcdf_file_obj.variables.keys():
netcdf_file_obj.variables[main_var].coordinates = "TIME LATITUDE LONGITUDE NOMINAL_DEPTH"
else:
netcdf_file_obj.variables[main_var].coordinates = "TIME LATITUDE LONGITUDE"
netcdf_file_obj.close()
if not convert_time_cf_to_imos(netcdf_file_path):
return False
remove_dimension_from_netcdf(netcdf_file_path) # last modification to do in this order!
return True
def modify_soop_trv_netcdf(netcdf_file_path, channel_id_info):
"""
Modify the downloaded NetCDF file so it passes both CF and IMOS checker
input:
netcdfFile_path(str) : path of netcdf file to modify
channel_id_index(tupple) : information from xml for the channel
"""
logger = logging_aims()
modify_aims_netcdf(netcdf_file_path, channel_id_info)
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
ship_code = netcdf_file_obj.platform_code
vessel_name = ship_callsign(ship_code)
if vessel_name is None:
logger.error(' UNKNOWN SHIP - channel %s' % str(channel_id_info['channel_id']))
netcdf_file_obj.close()
return False
# add gatts to net_cDF
netcdf_file_obj.cdm_data_type = 'Trajectory'
netcdf_file_obj.vessel_name = vessel_name
netcdf_file_obj.trip_id = channel_id_info['trip_id']
netcdf_file_obj.cdm_data_type = "Trajectory"
coordinates_att = "TIME LATITUDE LONGITUDE DEPTH"
# depth
depth = netcdf_file_obj.variables['depth']
depth.positive = 'down'
depth.axis = 'Z'
depth.reference_datum = 'sea surface'
depth.valid_max = 30.0
depth.valid_min = -10.0
netcdf_file_obj.renameVariable('depth', 'DEPTH')
# latitude longitude
latitude = netcdf_file_obj.variables['LATITUDE']
latitude.ancillary_variables = 'LATITUDE_quality_control'
longitude = netcdf_file_obj.variables['LONGITUDE']
longitude.ancillary_variables = 'LONGITUDE_quality_control'
latitude_qc = netcdf_file_obj.variables['LATITUDE_quality_control']
latitude_qc.long_name = 'LATITUDE quality control'
latitude_qc.standard_name = 'latitude status_flag'
longitude_qc = netcdf_file_obj.variables['LONGITUDE_quality_control']
longitude_qc.long_name = 'LONGITUDE quality control'
longitude_qc.standard_name = 'longitude status_flag'
netcdf_file_obj.close()
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
main_var = get_main_soop_trv_var(netcdf_file_path)
netcdf_file_obj.variables[main_var].coordinates = coordinates_att
netcdf_file_obj.close()
if not convert_time_cf_to_imos(netcdf_file_path):
return False
remove_dimension_from_netcdf(netcdf_file_path) # last modification to do !
return True
def modify_soop_trv_netcdf(netcdf_file_path, channel_id_info):
"""
Modify the downloaded NetCDF file so it passes both CF and IMOS checker
input:
netcdfFile_path(str) : path of netcdf file to modify
channel_id_index(tupple) : information from xml for the channel
"""
modify_aims_netcdf(netcdf_file_path, channel_id_info)
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
ship_code = netcdf_file_obj.platform_code
vessel_name = ship_callsign(ship_code)
if vessel_name is None:
logger.error(' UNKNOWN SHIP - channel %s' %
str(channel_id_info['channel_id']))
netcdf_file_obj.close()
return False
# add gatts to net_cDF
netcdf_file_obj.cdm_data_type = 'Trajectory'
netcdf_file_obj.vessel_name = vessel_name
netcdf_file_obj.trip_id = channel_id_info['trip_id']
netcdf_file_obj.cdm_data_type = "Trajectory"
coordinates_att = "TIME LATITUDE LONGITUDE DEPTH"
# depth
depth = netcdf_file_obj.variables['depth']
depth.positive = 'down'
depth.axis = 'Z'
depth.reference_datum = 'sea surface'
depth.valid_max = 30.0
depth.valid_min = -10.0
netcdf_file_obj.renameVariable('depth', 'DEPTH')
# latitude longitude
latitude = netcdf_file_obj.variables['LATITUDE']
latitude.ancillary_variables = 'LATITUDE_quality_control'
longitude = netcdf_file_obj.variables['LONGITUDE']
longitude.ancillary_variables = 'LONGITUDE_quality_control'
latitude_qc = netcdf_file_obj.variables['LATITUDE_quality_control']
latitude_qc.long_name = 'LATITUDE quality control'
latitude_qc.standard_name = 'latitude status_flag'
longitude_qc = netcdf_file_obj.variables['LONGITUDE_quality_control']
longitude_qc.long_name = 'LONGITUDE quality control'
longitude_qc.standard_name = 'longitude status_flag'
netcdf_file_obj.close()
netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
main_var = get_main_soop_trv_var(netcdf_file_path)
netcdf_file_obj.variables[main_var].coordinates = coordinates_att
netcdf_file_obj.close()
if not convert_time_cf_to_imos(netcdf_file_path):
return False
remove_dimension_from_netcdf(netcdf_file_path) # last modification to do !
return True