oceano2oceansites 
This application read Seabird CTD cnv files, extract data from header files and write result into one ASCII file and NetCDF OceanSITES file.
Binary programs under Windows, Linux and Mac OSX are available from the depot under release:
https://github.com/jgrelet/oceano2oceansites/releases
Code is tested and deploy for Linux and OsX with Travis-CI:
https://travis-ci.org/jgrelet/oceano2oceansites
You can get the latest version by compiling it from the sources for the following OS:
Add some Seabird cnv files under data directory, for example data/csp/*.cnv
Run and test, you can use make or go:
> make
or
> go run *.go --files=data/csp/csp*.cnv -e
Compile it:
> go build
Update go packages:
> go get -u ./...
> go mod tidy
Install binary under go/bin:
> go install
Usage:
> oceano2oceansites -h
Usage: oceano2oceansites.exe [-dehv] [-c value] [-f value] [-m value] [parameters ...]
-c, --config=value
Name of the configuration file to use.
-d debug
-e echo
-f, --files=value files to process ex: data/dfr25*.cnv
-h help
-m, --cycle_mesure=value
Name of cycle_mesure
-v, --version Show version, then exit.
Test binary:
> oceano2oceansites -e --files=data/CTD/csp/csp*.cnv
The program use by default the configuration files oceano2oceansites.toml and the code_roscop.csv in the current directory.
You can set a different location or file name by setting environment variables
OCEANO2OCEANSITES_CFG and ROSCOP_CSV.
Edit toml config file:
[global]
author = "your name"
[cruise]
cycleMesure = "CRUISE_NAME"
plateforme = "SHIP"
callsign = "XXXX"
institute = "IRD"
pi = "PI_NAME"
timezone = "GMT"
beginDate = "18/03/2015"
endDate = "13/04/2015"
creator = "Firstname.Name@domaine.fr"
[ctd]
cruisePrefix = "csp"
stationPrefixLength = 5
titleSummary = "CTD profiles processed during this cruise"
typeInstrument = "SBE911+"
instrumentNumber = "09Pxxxxx-xxx"
split = "PRES,3,DEPTH,4,ETDD,2,TEMP,5,PSAL,22,DENS,24,SVEL,26,DOX2,19,FLU2,14,TUR3,13,LGH3,15,NUMP,18,NAVG,21"
splitAll = "PRES,3,DEPTH,4,ETDD,2,TE01,5,TE02,6,PSA1,22,PSA2,23,DO12,19,DO22,20,DEN1,24,DEN2,25,SVEL,26,CND1,7,CND2,8,DOV1,9,DVT1,10,DOV2,11,DVT2,12,TUR3,13,FLU2,14,LGH3,15,LGHT,16,LGH4,17,NUMP,18,NAVG,21"
split describe the column order of each physical parameter to extract data from seabird cnv files. The order is used also for ASCII file output.
All the physical parameters definition are decribed inside code_roscop.csv.
You can update this file with your own definition.
Example:
TYPE;string;string;float64;float64;string;float64
TEMP;SEA TEMPERATURE;Celsius degree;0;30;%6.3f;1e36
SSTP;SEA SURFACE TEMPERATURE;Celsius degree;-1.5;38;%6.3f;1e36
PSAL;PRACTICAL SALINITY SCALE 1978;P.S.S.78;33;37;%6.3f;1e36
SSPS;SEA SURFACE PRACTICAL SALINITY;P.S.S.78;0;40;%6.3f;1e36
DOX1;DISSOLVED OXYGEN;ml/l;0;10;%5.2f;1e36
DOX2;DISSOLVED OXYGEN;micromole/kg;0;450;%7.3f;1e36
Check data with ncdump:
$ ncdump -v TIME test_ctd.nc
netcdf test_ctd {
dimensions:
TIME = 4 ;
DEPTH = 13 ;
variables:
double PROFILE(TIME) ;
PROFILE:long_name = "PROFILE NUMBER" ;
PROFILE:units = "N/A" ;
PROFILE:valid_min = 1. ;
PROFILE:valid_max = 99999. ;
PROFILE:format = "%5.0f" ;
PROFILE:_FillValue = 1.e+36 ;
double TIME(TIME) ;
TIME:long_name = "TIME" ;
TIME:units = "days since 1950-01-01T00:00:00Z" ;
TIME:valid_min = 0. ;
TIME:valid_max = 90000. ;
TIME:format = "%6.6f" ;
TIME:_FillValue = 1.e+36 ;
double LATITUDE(TIME) ;
LATITUDE:long_name = "LATITUDE" ;
LATITUDE:units = "decimal degree" ;
LATITUDE:valid_min = -90. ;
LATITUDE:valid_max = 90. ;
LATITUDE:format = "%+8.4f" ;
LATITUDE:_FillValue = 1.e+36 ;
double LONGITUDE(TIME) ;
LONGITUDE:long_name = "LONGITUDE" ;
LONGITUDE:units = "decimal degree" ;
LONGITUDE:valid_min = -180. ;
LONGITUDE:valid_max = 180. ;
LONGITUDE:format = "%+9.4f" ;
LONGITUDE:_FillValue = 1.e+36 ;
double BATH(TIME) ;
BATH:long_name = "BATHYMETRIC DEPTH" ;
BATH:units = "meter" ;
BATH:valid_min = 0. ;
BATH:valid_max = 11000. ;
BATH:format = "%6.1f" ;
BATH:_FillValue = 1.e+36 ;
double DEPH(TIME, DEPTH) ;
DEPH:long_name = "DEPTH BELOW SEA SURFACE" ;
DEPH:units = "meter" ;
DEPH:valid_min = 0. ;
DEPH:valid_max = 6000. ;
DEPH:format = "%6.1f" ;
DEPH:_FillValue = 1.e+36 ;
double TEMP(TIME, DEPTH) ;
TEMP:long_name = "SEA TEMPERATURE" ;
TEMP:units = "Celsius degree" ;
TEMP:valid_min = 0. ;
TEMP:valid_max = 30. ;
TEMP:format = "%6.3f" ;
TEMP:_FillValue = 1.e+36 ;
double PRES(TIME, DEPTH) ;
PRES:long_name = "SEA PRESSURE sea surface=0" ;
PRES:units = "decibar=10000 pascals" ;
PRES:valid_min = 0. ;
PRES:valid_max = 6500. ;
PRES:format = "%6.1f" ;
PRES:_FillValue = 1.e+36 ;
double DOX2(TIME, DEPTH) ;
DOX2:long_name = "DISSOLVED OXYGEN" ;
DOX2:units = "micromole/kg" ;
DOX2:valid_min = 0. ;
DOX2:valid_max = 450. ;
DOX2:format = "%7.3f" ;
DOX2:_FillValue = 1.e+36 ;
double PSAL(TIME, DEPTH) ;
PSAL:long_name = "PRACTICAL SALINITY SCALE 1978" ;
PSAL:units = "P.S.S.78" ;
PSAL:valid_min = 33. ;
PSAL:valid_max = 37. ;
PSAL:format = "%6.3f" ;
PSAL:_FillValue = 1.e+36 ;
// global attributes:
:cycle_mesure = "CRUISE" ;
:plateforme = "SHIP" ;
...
data:
TIME = 23820.5651041667, 23821.5832638889, 23823.3512615741, 23826.5581481481 ;
}