m = max(data['pressure'])
if m > max_abs_pressure:
max_abs_pressure = m
m_ind = [i for i, j in enumerate(data['pressure']) if j ==m] # this line finds the index of the max depth
#this loop here will take the readings only when the fish is going down
for j in names:
vars()[j] = []
for i in np.arange(1,float(m_ind[0])):
if data['pressure'][i]-data['pressure'][i-1] >0:
vars()[j].append(data[str(j)][i])
depth = sw.depth(pressure, xyzt['lat_DD.dd'])
c3515 = 42.9140
condr = [x/c3515 for x in cond]
salinity = sw.salt(condr, temp, pressure)
density = sw.dens(salinity, temp,pressure)
griddeddata=[]
for k in names2:
griddeddata = np.interp(grid_depth,depth,vars()[k],right=np.NaN)
griddeddata = griddeddata[0:]
vars()['grid_'+k][:,file[0]] = vars()['griddeddata']
f.close()
except:
failedloadfiles.append(str(file))
print ("Could not process " + file[1])
def write_pctd(self, inFile):
'''
Write lists out as NetCDF using the base name of the file for the .nc file that this creates.
'''
outFile = '.'.join(inFile.split('.')[:-1]) + '.nc'
# Create the NetCDF file
self.ncFile = netcdf_file(outFile, 'w')
# If specified on command line override the default generic title with what is specified
self.ncFile.title = 'Profile CTD cast data'
if self.args.title:
self.ncFile.title = self.args.title
# Combine any summary text specified on commamd line with the generic summary stating the original source file
self.ncFile.summary = 'Observational oceanographic data translated with no modification from original data file %s' % inFile
if self.args.summary:
self.ncFile.summary = self.args.summary
if not self.args.summary.endswith('.'):
self.ncFile.summary += '.'
self.ncFile.summary += ' Translated with no modification from original data file %s' % inFile
# If specified on command line override the default generic license with what is specified
if self.args.license:
self.ncFile.license = self.args.license
# Trajectory dataset, time is the only netCDF dimension
self.ncFile.createDimension('time', len(self.esec_list))
self.time = self.ncFile.createVariable('time', 'float64', ('time',))
self.time.standard_name = 'time'
self.time.units = 'seconds since 1970-01-01'
self.time[:] = self.esec_list
# Record Variables - coordinates for trajectory - save in the instance and use for metadata generation
self.latitude = self.ncFile.createVariable('latitude', 'float64', ('time',))
self.latitude.long_name = 'LATITUDE'
self.latitude.standard_name = 'latitude'
self.latitude.units = 'degree_north'
self.latitude[:] = self.lat_list
self.longitude = self.ncFile.createVariable('longitude', 'float64', ('time',))
self.longitude.long_name = 'LONGITUDE'
self.longitude.standard_name = 'longitude'
self.longitude.units = 'degree_east'
self.longitude[:] = self.lon_list
self.depth = self.ncFile.createVariable('depth', 'float64', ('time',))
self.depth.long_name = 'DEPTH'
self.depth.standard_name = 'depth'
self.depth.units = 'm'
self.depth[:] = csiro.depth(self.pr_list, self.lat_list) # Convert pressure to depth
# Record Variables - Profile CTD Data
temp = self.ncFile.createVariable('TEMP', 'float64', ('time',))
temp.long_name = 'Temperature, [ITS-90, deg C]'
temp.standard_name = 'sea_water_temperature'
temp.coordinates = 'time depth latitude longitude'
temp.units = 'Celsius'
temp[:] = self.t_list
sal = self.ncFile.createVariable('PSAL', 'float64', ('time',))
sal.long_name = 'Salinity, Practical [PSU]'
sal.standard_name = 'sea_water_salinity'
sal.coordinates = 'time depth latitude longitude'
sal[:] = self.sal_list
xmiss = self.ncFile.createVariable('xmiss', 'float64', ('time',))
xmiss.long_name = 'Beam Transmission, Chelsea/Seatech'
xmiss.coordinates = 'time depth latitude longitude'
xmiss.missing_value = self.missing_value
xmiss._FillValue = self._FillValue
xmiss.units = '%'
xmiss[:] = self.xmiss_list
if self.ecofl_list:
ecofl = self.ncFile.createVariable('ecofl', 'float64', ('time',))
ecofl.long_name = 'Fluorescence, WET Labs ECO-AFL/FL'
ecofl.coordinates = 'time depth latitude longitude'
ecofl.units = 'mg/m^3'
ecofl[:] = self.ecofl_list
if self.wetstar_list:
wetstar = self.ncFile.createVariable('wetstar', 'float64', ('time',))
wetstar.long_name = 'Fluorescence, WET Labs WETstar'
wetstar.coordinates = 'time depth latitude longitude'
wetstar.units = 'mg/m^3'
wetstar[:] = self.wetstar_list
if self.oxygen_list:
oxygen = self.ncFile.createVariable('oxygen', 'float64', ('time',))
oxygen.long_name = 'Oxygen, SBE 43'
oxygen.coordinates = 'time depth latitude longitude'
oxygen.units = 'ml/l'
oxygen[:] = self.oxygen_list
if self.args.analog:
if self.analog_list:
analog = self.ncFile.createVariable(self.an_var, 'float64', ('time',))
analog.coordinates = 'time depth latitude longitude'
analog.units = self.an_units
analog[:] = self.analog_list
self.add_global_metadata()
self.ncFile.close()
print 'Wrote ' + outFile
def write_pctd(self, inFile):
'''
Write lists out as NetCDF using the base name of the file for the .nc file that this creates.
'''
outFile = '.'.join(inFile.split('.')[:-1]) + '.nc'
# Create the NetCDF file
self.ncFile = netcdf_file(outFile, 'w')
# If specified on command line override the default generic title with what is specified
self.ncFile.title = 'Profile CTD cast data'
if self.args.title:
self.ncFile.title = self.args.title
# Combine any summary text specified on commamd line with the generic summary stating the original source file
self.ncFile.summary = 'Observational oceanographic data translated with no modification from original data file %s' % inFile
if self.args.summary:
self.ncFile.summary = self.args.summary
if not self.args.summary.endswith('.'):
self.ncFile.summary += '.'
self.ncFile.summary += ' Translated with no modification from original data file %s' % inFile
# If specified on command line override the default generic license with what is specified
if self.args.license:
self.ncFile.license = self.args.license
# Trajectory dataset, time is the only netCDF dimension
self.ncFile.createDimension('time', len(self.esec_list))
self.time = self.ncFile.createVariable('time', 'float64', ('time', ))
self.time.standard_name = 'time'
self.time.units = 'seconds since 1970-01-01'
self.time[:] = self.esec_list
# Record Variables - coordinates for trajectory - save in the instance and use for metadata generation
self.latitude = self.ncFile.createVariable('latitude', 'float64',
('time', ))
self.latitude.long_name = 'LATITUDE'
self.latitude.standard_name = 'latitude'
self.latitude.units = 'degree_north'
self.latitude[:] = self.lat_list
self.longitude = self.ncFile.createVariable('longitude', 'float64',
('time', ))
self.longitude.long_name = 'LONGITUDE'
self.longitude.standard_name = 'longitude'
self.longitude.units = 'degree_east'
self.longitude[:] = self.lon_list
self.depth = self.ncFile.createVariable('depth', 'float64', ('time', ))
self.depth.long_name = 'DEPTH'
self.depth.standard_name = 'depth'
self.depth.units = 'm'
self.depth[:] = csiro.depth(self.pr_list,
self.lat_list) # Convert pressure to depth
# Record Variables - Profile CTD Data
temp = self.ncFile.createVariable('TEMP', 'float64', ('time', ))
temp.long_name = 'Temperature, [ITS-90, deg C]'
temp.standard_name = 'sea_water_temperature'
temp.coordinates = 'time depth latitude longitude'
temp.units = 'Celsius'
temp[:] = self.t_list
sal = self.ncFile.createVariable('PSAL', 'float64', ('time', ))
sal.long_name = 'Salinity, Practical [PSU]'
sal.standard_name = 'sea_water_salinity'
sal.coordinates = 'time depth latitude longitude'
sal[:] = self.sal_list
xmiss = self.ncFile.createVariable('xmiss', 'float64', ('time', ))
xmiss.long_name = 'Beam Transmission, Chelsea/Seatech'
xmiss.coordinates = 'time depth latitude longitude'
xmiss.missing_value = self.missing_value
xmiss._FillValue = self._FillValue
xmiss.units = '%'
xmiss[:] = self.xmiss_list
if self.ecofl_list:
ecofl = self.ncFile.createVariable('ecofl', 'float64', ('time', ))
ecofl.long_name = 'Fluorescence, WET Labs ECO-AFL/FL'
ecofl.coordinates = 'time depth latitude longitude'
ecofl.units = 'mg/m^3'
ecofl[:] = self.ecofl_list
if self.wetstar_list:
wetstar = self.ncFile.createVariable('wetstar', 'float64',
('time', ))
wetstar.long_name = 'Fluorescence, WET Labs WETstar'
wetstar.coordinates = 'time depth latitude longitude'
wetstar.units = 'mg/m^3'
wetstar[:] = self.wetstar_list
if self.oxygen_list:
oxygen = self.ncFile.createVariable('oxygen', 'float64',
('time', ))
oxygen.long_name = 'Oxygen, SBE 43'
oxygen.coordinates = 'time depth latitude longitude'
oxygen.units = 'ml/l'
oxygen[:] = self.oxygen_list
if self.args.analog:
if self.analog_list:
analog = self.ncFile.createVariable(self.an_var, 'float64',
('time', ))
analog.coordinates = 'time depth latitude longitude'
analog.units = self.an_units
analog[:] = self.analog_list
self.add_global_metadata()
self.ncFile.close()
print 'Wrote ' + outFile
def write_pctd(self, inFile):
'''
Write lists out as NetCDF using the base name of the file for the .nc file that this creates.
'''
outFile = '.'.join(inFile.split('.')[:-1]) + '.nc'
# Create the NetCDF file
self.ncFile = netcdf_file(outFile, 'w')
self.outFile = outFile
# Trajectory dataset, time is the only netCDF dimension
self.ncFile.createDimension('time', len(self.esec_list))
self.time = self.ncFile.createVariable('time', 'float64', ('time',))
self.time.standard_name = 'time'
self.time.units = 'seconds since 1970-01-01'
self.time[:] = self.esec_list
# Record Variables - coordinates for trajectory - save in the instance and use for metadata generation
self.latitude = self.ncFile.createVariable('latitude', 'float64', ('time',))
self.latitude.long_name = 'LATITUDE'
self.latitude.standard_name = 'latitude'
self.latitude.units = 'degree_north'
self.latitude[:] = self.lat_list
self.longitude = self.ncFile.createVariable('longitude', 'float64', ('time',))
self.longitude.long_name = 'LONGITUDE'
self.longitude.standard_name = 'longitude'
self.longitude.units = 'degree_east'
self.longitude[:] = self.lon_list
self.depth = self.ncFile.createVariable('depth', 'float64', ('time',))
self.depth.long_name = 'DEPTH'
self.depth.standard_name = 'depth'
self.depth.units = 'm'
self.depth[:] = csiro.depth(self.pr_list, self.lat_list) # Convert pressure to depth
# Record Variables - Profile CTD Data
temp = self.ncFile.createVariable('TEMP', 'float64', ('time',))
temp.long_name = 'Temperature, [ITS-90, deg C]'
temp.standard_name = 'sea_water_temperature'
temp.coordinates = 'time depth latitude longitude'
temp.units = 'Celsius'
temp[:] = self.t_list
sal = self.ncFile.createVariable('PSAL', 'float64', ('time',))
sal.long_name = 'Salinity, Practical [PSU]'
sal.standard_name = 'sea_water_salinity'
sal.coordinates = 'time depth latitude longitude'
sal[:] = self.sal_list
xmiss = self.ncFile.createVariable('xmiss', 'float64', ('time',))
xmiss.long_name = 'Beam Transmission, Chelsea/Seatech'
xmiss.coordinates = 'time depth latitude longitude'
xmiss.units = '%'
xmiss[:] = self.xmiss_list
if self.ecofl_list:
ecofl = self.ncFile.createVariable('ecofl', 'float64', ('time',))
ecofl.long_name = 'Fluorescence, WET Labs ECO-AFL/FL'
ecofl.coordinates = 'time depth latitude longitude'
ecofl.units = 'mg/m^3'
ecofl[:] = self.ecofl_list
if self.wetstar_list:
wetstar = self.ncFile.createVariable('wetstar', 'float64', ('time',))
wetstar.long_name = 'Fluorescence, WET Labs WETstar'
wetstar.coordinates = 'time depth latitude longitude'
wetstar.units = 'mg/m^3'
wetstar[:] = self.wetstar_list
if self.oxygen_list:
oxygen = self.ncFile.createVariable('oxygen', 'float64', ('time',))
oxygen.long_name = 'Oxygen, SBE 43'
oxygen.coordinates = 'time depth latitude longitude'
oxygen.units = 'ml/l'
oxygen[:] = self.oxygen_list
if self.oxyps_list:
oxygen = self.ncFile.createVariable('oxygen_ps', 'float64', ('time',))
oxygen.long_name = 'Oxygen, SBE 43'
oxygen.coordinates = 'time depth latitude longitude'
oxygen.units = '%'
oxygen[:] = self.oxyps_list
self.add_global_metadata()
self.ncFile.close()
