Hi Andrew,
SeaDataNet will very soon be considering how it is going to encode data, including single CTD casts, in CF-compliant NetCDF and so I think the time is ripe for agreeing how the significant numbers of us who indulge in this practice for whatever reason do it. That way we'll end up with interoperable data.
I think there are a number of people on this list who have already encoded single CTDs into NetCDF and so it would be useful to start by asking for descriptions (like Andrew's examples) of how this has been done and what tools are dependent upon that encoding.
The z co-ordinate parameter (pressure/depth) is also an issue worth resolving. Whilst interconversions are relatively straightforward, agreement would make life much easier. My preference leans dowards having depth as the dimension with pressure as an optional variable. That way we interoperate with other kinds of oceanographic profile data such as bottle data.
If we can get that far, we can then look at how to aggregate multiple CTDs into a file according to the CF point data conventions.
Cheers, Roy.
________________________________
From: andrew walsh [awalsh at metoc.gov.au]
Sent: 03 April 2012 04:39
To: Lowry, Roy K.
Cc: Jim Biard; Upendra Dadi; cf-metadata at cgd.ucar.edu; Luke Callcut; greg at metoc.gov.au
Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
Hello Roy, Upendra, Jim and CF list,
Thanks for all your feedbacks.
My proposal relates to single CTD profile data (a vertical profile of pressure, Temp. Salinity)
not a trajectory in x,y,z,t and I have put :featureType = "profile" as recommended in the global
attributes section. As Roy has mentioned to Jim CTD data is usually processed and QC'ed
as a single profile per netCDF file so that's why I am doing it this way.
Aggregations using multiple CTD profiles per netCDF file
may be constructed later at say national/international data centres and these aggregrations
would follow the CF conventions v1.6, Chapter 9 - Discrete Sampling geometries
and also the new netCDF templates provided by NODC, thanks NODC -:)
Roy,
The recent NODC netCDF templates don't have an aggregation example for CTD
however the "Profile/World Ocean Database Observed Level" example comes close
(see
http://www.nodc.noaa.gov/data/formats/netcdf/) and click on
Profile/World Ocean Database Observed Level link. This example appears
to be for ocean station/bottle samples with vertical dimension of depth (z) (m) rather
than case of CTD which would use pressure (dbar) as the vertical (z) dimension.
It would be useful I think to have a NODC netCDF template for an aggregation of
CTD casts.
Upendra,
Based on your responses and what I have seen at NODC and other places
it seems there are 2 methods to do this:
1) You can have dimensions for lat, long time i.e an array
with a single value. That is:
dimensions:
TIME=1
PRESSURE=729
LATITUDE=1
LONGITUDE=1
variables:
double TIME(TIME) ;
+ std. attrs.
double LATITUDE(LATITUDE) ;
+ std. attrs.
double LONGITUDE(LONGITUDE) ;
+ std. attrs.
double PRESSURE(PRESSURE) ;
+ std. attrs.
double TEMPERATURE(PRESSURE) ;
+ std. attrs.
TEMPERATURE:coordinates="TIME LATITUDE LONGITUDE PRESSURE"
double SALINITY(PRESSURE) ;
+ std. attrs.
SALINITY:coordinates="TIME LATITUDE LONGITUDE PRESSURE"
(2) Other way is to have Lat, long and time are single valued scalars:
dimensions:
PRESSURE=729
variables:
double LATITUDE ;
+ std attrs
double LONGITUDE ;
+ std attrs
double TIME ;
+std attrs
double PRESSURE(PRESSURE) ;
+ std. attrs.
double TEMPERATURE(PRESSURE) ;
+ std. attrs.
TEMPERATURE:coordinates="TIME LATITUDE LONGITUDE PRESSURE"
double SALINITY(PRESSURE) ;
+ std. attrs.
SALINITY:coordinates="TIME LATITUDE LONGITUDE PRESSURE"
I can see Method 2 above is much simpler and I would prefer to use
this.
However I have another small concern about all of this. Given there is more than
1 way to treat dimensions does the netCDF plotting and visualising sofware out
there understand both approaches. That is can we expect something like
ncBrowse, IDV or ODV? give me a plot of say salinity vs. pressure
and work OK with BOTH approaches to coding the netCDF?
Thanks and Regards All,
Andrew Walsh
----- Original Message -----
From: Lowry, Roy K.<mailto:rkl at bodc.ac.uk>
To: Upendra Dadi<mailto:upendra.dadi at noaa.gov> ; andrew walsh<mailto:awalsh at metoc.gov.au>
Cc: Luke Callcut<mailto:luke at metoc.gov.au> ; cf-metadata at cgd.ucar.edu<mailto:cf-metadata at cgd.ucar.edu> ; sdn2-tech at seadatanet.org<mailto:sdn2-tech at seadatanet.org>
Sent: Tuesday, April 03, 2012 9:31 AM
Subject: RE: [CF-metadata] Ocean CTD data following CF Conventions v1.6
Hi Upendra,
I like the idea of a station dimension. It goes a long way to resolving the issue raised in my response to Jim which was based on the tunnel vision of having pressure/depth as a dimension. I have yet to look at the recently published NODC NetCDF templates. Is this CTD encoding included in them? If so, I'll bump up looking at them on my 'todo' list. I'd also recommend that Andrew and my colleagues in SeaDataNet take a look.
Cheers, Roy.
________________________________
From: cf-metadata-bounces at cgd.ucar.edu<mailto:cf-metadata-bounces at cgd.ucar.edu> [cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Upendra Dadi [upendra.dadi at noaa.gov]
Sent: 02 April 2012 17:21
To: andrew walsh
Cc: Luke Callcut; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
Hi Andrew,
Either way it should be okay as far as CF compliance is concerned. But the dimensions - latitude, longitude and time are not really required. If it is required to indicate that there is only one station(profile) in the file, there could be a dimension for number of stations instead, with a value of 1. Also, using a station dimension is the way to go if storing a collection of profiles in a single file. Here at NODC, we took the approach that we would use the same consistent representation whether there is a single instance or a collection in a file.
Upendra
On Mon, Apr 2, 2012 at 2:51 AM, andrew walsh <awalsh at metoc.gov.au<mailto:awalsh at metoc.gov.au>> wrote:
Hi CF lis
We are working on coding up some 1000's netCDF files off CTD
instruments and want to make usre we are following the
latest netCDF conventions (v1.6) OK. As background the CTD records
a profile pressure, temperature and salinity.
Here is a summarised CDL version (not all attributes+variables+qc flags there, just majors for now)
of what we propose:
dimensions:
TIME=1
PRESSURE=729
LATITUDE=1
LONGITUDE=1
variables:
double TIME(TIME) ;
TIME:standard_name = "time" ;
TIME:units = "days since 1950-01-01 00:00:00Z" ;
TIME:axis = "T" ;
TIME:valid_min = 0. ;
TIME:valid_max = 999999. ;
double LATITUDE(LATITUDE) ;
LATITUDE:standard_name = "latitude" ;
LATITUDE:units = "degrees_north" ;
LATITUDE:axis = "Y" ;
LATITUDE:valid_min = -90. ;
LATITUDE:valid_max = 90. ;
double LONGITUDE(LONGITUDE) ;
LONGITUDE:standard_name = "longitude" ;
LONGITUDE:units = "degrees_east" ;
LONGITUDE:axis = "X" ;
LONGITUDE:valid_min = -180. ;
LONGITUDE:valid_max = 180. ;
double PRESSURE(PRESSURE) ;
PRESSURE:standard_name = "sea_water_pressure" ;
PRESSURE:units = "decibars" ;
PRESSURE:axis = "Z" ;
PRESSURE:valid_min = 0. ;
PRESSURE:valid_max = 12000. ;
PRESSURE:positive = "down" ;
double TEMPERATURE(PRESSURE) ;
TEMPERATURE:standard_name = "sea_water_temperature" ;
TEMPERATURE:units = "degrees_C" ;
TEMPERATURE:_FillValue = -99.99 ;
TEMPERATURE:valid_min = -2. ;
TEMPERATURE:valid_max = 40. ;
TEMPERATURE:coordinates="TIME LATITUDE LONGITUDE PRESSURE"
double SALINITY(PRESSURE) ;
SALINITY:standard_name = "sea_water_salinity" ;
SALINITY:units = "psu" ;
SALINITY:_FillValue = -99.99 ;
SALINITY:valid_min = 0. ;
SALINITY:valid_max = 40. ;
SALINITY:coordinates="TIME LATITUDE LONGITUDE PRESSURE"
// global attributes:
:conventions = "CF-1.6" ;
:featureType = "profile"
:cdm_data_type = "profile"
+ several other attributes later for ISO19115 metadata generation
I am not sure if I should have TEMPERATURE and SALINITY arrays with 4 dimensions
like TEMPERATURE(TIME,LATITUDE,LONGITUDE,PRESSURE) or just 1 dimension
like I have above i.e. TEMPERATURE(PRESSURE). ?
Any feedback on the above is greatly appreciated.
Andrew Walsh
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