pycnv 0.5.0

Tool to convert Seabird cnv textfiles

Python toolbox to read and process Seabird cnv files.

These text files are the standard output files of the Seabird CTD software.

The main purpose for pycnv is to create a standardised interface for slightly differing naming conventions of sensors in the cnv files and the usage of the Gibb Sea Water Toolbox (gsw) for the calculation of all derived parameters as practical salinity, absolute salinity, potential and conservative temperature or density. For this purpose pycnv does only need pressure, conductivity and temperature, all other properties will be derived from these. Furthermore pycnv will take care for a different absolute salinity computation in the Baltic Sea, by automatically checking of a cast was made in the Baltic Sea and choosing the correct function.

Install

The package was developed using python 3.5+, it might work with earlier versions, but its not supported. The newest Gibb Sea Water Toolbox (gsw) depends also on python 3.5+, pycnv heavily depends on the gsw toolbox. It therefore strongly recommended to use python 3.5+.

User

Install as a user using pip

pip install pycnv

Install as a user from the repository

python setup.py install --user

Uninstall as a user

pip uninstall pycnv

Developer

Install as a developer

python setup.py develop --user

Uninstall as a user

pip uninstall pycnv

FEATURES

• The data can be accessed by the original names defined in the cnv file in the named array called data. E.g. header name “# name 11 = oxsatML/L: Oxygen Saturation, Weiss [ml/l]” can be accessed like this: data[‘oxsatML/L’].

• Standard parameters (Temperature, Conductivity, pressure, oxygen) are mapped to standard names. E.g. data[‘T0’] for the first temperature sensor and data[‘C1’] for the second conductivity sensor.

• If the standard parameters (C0,T0,p), (C1,T1,p) are available the Gibbs Sea water toolbox is used to calculate absolute salinity, SA, conservative temperature, CT, and potential temperature pt. The data is stored in a second field called computed data: cdata. E.g. cdata[‘SA00’]. The code used to compute the properties are

  SP = gsw.SP_from_C(data['C' + isen], T, data['p'])
  SA = gsw.SA_from_SP(SP,data['p'],lon = lon, lat = lat)
  if(baltic == True):
      SA = gsw.SA_from_SP_Baltic(SA,lon = lon, lat = lat)
  
  PT = gsw.pt0_from_t(SA, T, data['p'])
  CT = gsw.CT_from_t(SA, T, data['p'])
  pot_rho = gsw.pot_rho_t_exact(SA, T, data['p'], p_ref)

• The cnv object provides standard entries for pressure (cnv.p), temperature (cnv.T), conservative temperature (cnv.CT), practical salinity (cnv.SP), absolute salinity (cnv.SA), potential density (cnv.pot_rho), oxygen (cnv.oxy). The units have the extension _units, i.e. cnv.p_units

• The module checks if the cast was made in the Baltic Sea, if so, the modified Gibbs sea water functions are automatically used.

• The package provides scripts to search a given folder for cnv files and can create a summary of the folder in a csv format easily readable by python or office programs. The search can be refined by a location or a predefined station.

• Possibility to provide an own function for parsing custom header information.

• Plotting of the profile using matplotlib

USAGE

The package installs the executables:

• pycnv

• pycnv_sum_folder

EXAMPLES

Plot the absolute salinity and oxygen of a CTD cast:

import pycnv
import pylab as pl
fname = 'test.cnv' # Some CTD cast

cnv = pycnv.pycnv(fname)
print('Test if we are in the Baltic Sea (usage of different equation of state): ' + str(cnv.baltic))
print('Position of cast is: Longitude:', cnv.lon,'Latitude:',cnv.lat)
print('Time of cast was:', cnv.date)
print('Number of sensor entries (len(cnv.data.keys())):',len(cnv.data.keys()))
print('Names of sensor entries (cnv.data.keys()):',cnv.data.keys())

# Get data of entry
key0 = list(cnv.data.keys())[0]
data0 = cnv.data[key0]

# Get derived data:
keyd0 = list(cnv.cdata.keys())[0]
datad0 = cnv.cdata[keyd0]
# Get unit of derived data
datad0_unit = cnv.cunits[keyd0]

# Standard names are mapped to
# cnv.p,cnv.CT,cnv.T,cnv.SP,cnv.oxy
# units are _unit, e.g. cnv.p_unit

# Plot standard parameters
pl.figure(1)
pl.clf()
pl.subplot(1,2,1)
pl.plot(cnv.SA,cnv.p)
pl.xlabel('Absolute salinity [' + cnv.SA_unit + ']')
pl.ylabel('Pressure [' + cnv.p_unit + ']')
pl.gca().invert_yaxis()

pl.subplot(1,2,2)
pl.plot(cnv.oxy,cnv.p)
pl.plot(cnv.cdata['oxy0'],cnv.p)
pl.plot(cnv.cdata['oxy1'],cnv.p)
pl.xlabel('Oxygen [' + cnv.oxy_unit + ']')
pl.ylabel('Pressure [' + cnv.p_unit + ']')
pl.gca().invert_yaxis()

pl.show()

Lists all predefined stations (in terminal):

pycnv_sum_folder --list_stations

Makes a summary of the folder called cnv_data of all casts around station TF0271 with a radius of 5000 m, prints it to the terminal and saves it into the file TF271.txt (in terminal):

pycnv_sum_folder --data_folder cnv_data --station TF0271 5000 -p -f TF271.txt

Show and plot conservative temperature, salinity and potential density of a cnv file into a pdf:

pycnv --plot show,save,CT00,SA00,pot_rho00 ctd_cast.cnv

Interpolate all CTD casts on station TF0271 onto the same pressure axis and make a netCDF out of it:

see code pycnv/test/make_netcdf.py

Devices tested

• SEACAT (SBE16) V4.0g

• MICROCAT (SBE37)

• SBE 11plus V 5.1e

• SBE 11plus V 5.1g

• Sea-Bird SBE 9 Software Version 4.206