Dear All,
I would like to add Charles SUN in the mailing list,
<charles.sun at noaa.gov>, from NOAA/NODC, the GTSPP Chair, and include
the GTSPP netCDFF format issues in the discussions.
Regards, -Sissy
On 04/04/2012 03:06, andrew walsh wrote:
> Hi Thierry,
>
> Thank you for this information. These netCDF examples and documentation
> are excellent. I was able to visualise (vertical cross section of
> Temperature ,Salinity)
> the Pheidippides glider netCDF data with the ncBrowse tool OK.
>
> Regards,
>
> Andrew
>
> ----- Original Message ----- From: "Thierry Carval"
> <Thierry.Carval at ifremer.fr>
> To: "'Lowry, Roy K.'" <rkl at bodc.ac.uk>
> Cc: "'Luke Callcut'" <luke at metoc.gov.au>; <cf-metadata at cgd.ucar.edu>;
> "'Upendra Dadi'" <Upendra.Dadi at noaa.gov>; <sdn2-tech at seadatanet.org>;
> <greg at metoc.gov.au>; "'andrew walsh'" <awalsh at metoc.gov.au>
> Sent: Wednesday, April 04, 2012 4:31 AM
> Subject: TR: [CF-metadata] Ocean CTD data following CF Conventions v1.6
>
>
> Hello Roy and All,
>
> I am involved in Argo data-management, OceanSITES and the MyOcean EU
> project.
>
> These 3 projects are intensive users of NetCDF CTD data files.
>
>
>
> Within these communities :
>
> ? The natural vertical reference for a CTD is pressure. This is
> also true for Argo floats, gliders or sea-mammals.
>
> ? The natural vertical reference for XBTs, moorings and buoys is
> depth.
>
> So the NetCDF files vertical reference can be either pressure or
> depth, but
> not both.
>
>
>
> If another community wants an homogeneous vertical reference, a
> profile with
> additional data (pressure or depth) "could" be provided, as a product.
>
> BUT, this adds complexity; I feel more comfortable with data reported as
> naturally as possible :
>
> ? If you add a vertical reference, you have to decide which
> one is
> the Z axis (PRES:axis = "Z" or DEPH:axis = "Z" attribute).
>
> ? All the QC flags assigned to pressure should be transferred to
> depth; but this is not straightforward.
> If the salinity is bad or spiky, from a good pressure you will have a bad
> depth.
>
>
>
> Here are links to different NetCDF user's manual managing vertical
> profiles
> with pressure or depth (but not both) vertical axes:
>
> ? Argo documentation <http://www.argodatamgt.org/Documentation> ,
> the user's manual
> <http://www.argodatamgt.org/content/download/12096/80327/file/argo-dm-user-m
>
> anual.pdf> : we are heading toward 1 million profiles
>
> ? OceanSITES <http://www.oceansites.org/data/index.html> , the
> user's manual
> <http://www.oceansites.org/docs/oceansites_user_manual_version1.2.pdf> :
> 1400 long time-series from mooring sites
>
>
>
> The EU MyOcean project <http://www.myocean.eu.org/> adopted the
> OceanSITES
> implementation of NetCDF CF for oceanographic in-situ data.
>
> The last 3 years of in-situ observations are available in OceanSITES
> NetCDF
> CF files (see attached map of 3.3 million vertical profiles).
>
>
>
> This format is also used for EGO gliders
> <http://ego.dt.insu.cnrs.fr/dokuwiki/doku.php?id=start> , where
> pressure is
> the vertical axis.
>
> Example : Pheidippides glider data
> <http://www.ifremer.fr/co/ego/ego/pheidippides/> (NetCDF OceanSITES
> vertical profiles) operating now around Cyprus island.
>
>
>
> The above user's manuals for NetCDF-CF CTDs (and others) files may be
> enhanced with this ongoing v1.6 proposal.
>
> Best regards,
>
>
>
> Thierry
>
>
>
>
>
> -----Message d'origine-----
> De : cf-metadata-bounces at cgd.ucar.edu
> [mailto:cf-metadata-bounces at cgd.ucar.edu] De la part de Lowry, Roy K.
> Envoy? : mardi 3 avril 2012 12:56
> ? : Lowry, Roy K.; andrew walsh
> Cc : Luke Callcut; cf-metadata at cgd.ucar.edu; Upendra Dadi;
> sdn2-tech at seadatanet.org; greg at metoc.gov.au
> Objet : Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
>
>
>
> Hello again,
>
>
>
> It has been pointed out to me that in the current SeaDataNet format
> specification (written and updated by me!) that the initial position of
> insisting upon depth for the z co-ordinate was relaxed to allow either
> pressure or depth. So, I guess we need to be relaxed and leave z
> co-ordinate
> harmonisation to the the application tools.
>
>
>
> Yet another 'senior moment'......
>
>
>
> Cheers, Roy.
>
>
>
> ________________________________________
>
> From: cf-metadata-bounces at cgd.ucar.edu
> [cf-metadata-bounces at cgd.ucar.edu] On
> Behalf Of Lowry, Roy K. [rkl at bodc.ac.uk]
>
> Sent: 03 April 2012 06:46
>
> To: andrew walsh
>
> Cc: cf-metadata at cgd.ucar.edu; sdn2-tech at seadatanet.org;
> greg at metoc.gov.au;
> Luke Callcut; Upendra Dadi
>
> Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
>
>
>
> Hi again,
>
>
>
> The reason that I prefer depth to pressure as the dimension for CTD is
> that
> the information required for pressure to depth conversion is virtually
> always present in the CTD data. However, in other oceanographic
> profiles -
> say nutrient bottle data - it is quite possible to have depth present
> without temperature and salinity, making the conversion to pressure
> impossible. Calculating depth from pressure at the time of standardised
> formatting of CTD data is as you say is trivial. So, why not make the
> CTD
> data more compatible with bottle data for very little cost?
>
>
>
> SeaDataNet already mandate inclusion of depth in their other data formats
> for CTD data delivery and so I can't see them switching to pressure
> for the
> dimension in NetCDF.
>
>
>
> Cheers, Roy.
>
>
>
> ________________________________________
>
> From: andrew walsh [awalsh at metoc.gov.au]
>
> Sent: 03 April 2012 06:15
>
> To: Lowry, Roy K.
>
> Cc: Jim Biard; Upendra Dadi; cf-metadata at cgd.ucar.edu; Luke Callcut;
> greg at metoc.gov.au; sdn2-tech at seadatanet.org
>
> Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
>
>
>
> Hi Roy/All,
>
>
>
> Agree totally it would be good to get this CTD netCDF done in an
> interoperable way.
>
>
>
> Regarding having pressure vs. depth. We liked to use pressure because:
>
>
>
> 1) It is the thing that is measured, let us store just that and calculate
> depth if needed.
>
>
>
> 2) Depth can later be easily be calculated on the fly using the
> 'Pressure to
> Depth' algorithm in "UNESCO (1983) Techinical Papers in Marine
> Science 44,
> Algorithms for Computation of fundamental properties of Seawater. One can
> use the python seawater library (see
> http://packages.python.org/seawater/ )
> and seawater.csiro.depth(p, lat) to get depth from pressure and
> seawater.csiro.pres(depth, lat) to get pressure from depth.
>
>
>
> 3) I noted that the ARGO project (10000's CTD like profiles) and
> others like
> CSIRO Oceanography in Aust. make data available with just pressure.
>
>
>
> 4) It makes our processing and QC a whole lot simpler. We don't have to
> worry about calculating and managing the extra 'depth' variable.
>
>
>
> Is there any problem with having the "pressure" as a co-ordinate which
> isn't really a "dimensional"
>
> quantity like depth (z) in the 4-D sense i.e x,y,z,t ?
>
>
>
> However I note that pressure (decibar) is allowed as a vertical axis
> e.g see
> section 4.3. Vertical (Height or Depth) Coordinate of CF v1.6 conventions
> document which
>
> says:
>
>
>
> "A vertical coordinate will be identifiable by:
>
>
>
> . units of pressure; or
>
> . the presence of the positive attribute with a value of up or down (case
> insensitive).
>
> "
>
>
>
> AND
>
>
>
> section 4.3.1. "Dimensional Vertical Coordinate" which says:
>
>
>
> "The units attribute for dimensional coordinates will be a string
> formatted
> as per the udunits.dat3 file. The acceptable units for vertical (depth or
> height) coordinate variables are:
>
>
>
> . units of pressure as listed in the file udunits.dat. For vertical
> axes the
> most commonly used of these include include bar, millibar, decibar,
> atmosphere (atm), pascal (Pa), and hPa.
>
> ...
>
> ..."?
>
>
>
>
>
> Regards,
>
>
>
> Andrew
>
>
>
> ----- Original Message -----
>
> From: Lowry, Roy K.
>
> To: andrew walsh
>
> Cc: Jim Biard ; Upendra Dadi ; cf-metadata at cgd.ucar.edu ; Luke Callcut ;
> greg at metoc.gov.au ; sdn2-tech at seadatanet.org
>
> Sent: Tuesday, April 03, 2012 2:16 PM
>
> Subject: RE: [CF-metadata] Ocean CTD data following CF Conventions v1.6
>
>
>
>
>
> 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/>
> 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.
>
> To: Upendra Dadi ; andrew walsh
>
> Cc: Luke Callcut ; cf-metadata at cgd.ucar.edu ; 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
> [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 <
> <mailto:awalsh at metoc.gov.au>
> 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--
>
> snip ....
>
--
--------------------------------------------------
Sissy IONA,
JCOMM/DMPA Coordinator, IOC/IODE Co-Chair,
Head, Hellenic National Oceanographic Data Centre-HNODC,
Hellenic Centre for Marine Research-HCMR,
Institute of Oceanography,
P.O. Box 712, 190 13 Anavyssos,
GREECE.
Email: sissy at hnodc.hcmr.gr
Phone: +30-22910-76367
Fax: +30-22910-76323-347
http://www.hcmr.gr
http://hnodc.hcmr.gr
--
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