Hi Heiko:
It was indeed a bug in the CDM. Now fixed with a pull request on 4.6.
Thanks for reporting.
John
On Fri, Aug 28, 2015 at 2:56 AM, Heiko Klein <Heiko.Klein@xxxxxx> wrote:
> Hi Bob,
>
> I totally agree that our files must be CF-compliant. But we want to be
> able to read the files with most programs, and the whole CF can be
> difficult to implement. The change I made is still CF compliant and it
> works with the netcdf-java, too. Yes, netcdf-java only implements a
> subset of CF, but since I'm not funding them, I can live with that subset.
>
> Writing a special format is usually simple (and we have some flexibility
> within CF), reading all formats is hard, so we're trying to find a
> compromise.
>
>
> BTW since you have a NOAA email address: we started from the NOAA
> templates:
>
> https://geo-ide.noaa.gov/wiki/index.php?title=NODC_NetCDF_Trajectory_Template
> (and eliminated some conflicts with CF from them, e.g. axis)
>
>
> Best regards,
>
> Heiko
>
>
> On 2015-08-27 21:21, Bob Simons - NOAA Federal wrote:
> > I'm not following this closely, but I was bothered by "we now know how
> > to create a netcdf-java compliant trajectory file". netcdf-java is just
> > one tool. There are other tools now, and there will be more in the
> > future. netcdf-java probably supports a subset/superset of the file
> > types defined by the CF DSG standard (which allows a huge number of
> > minor variations).
> >
> > I think a far better goal is to seek to make files which are compliant
> > with the CF DSG standard, and thus with any tool that follows the CF DSG
> > standard. If a given tool (e.g., netcdf-java) can't deal with a valid CF
> > DSG file, then it is a bug in that tool and you can
> > legitimately/reasonably ask the developer to fix the bug.
> >
> > On Thu, Aug 27, 2015 at 12:01 PM, Heiko Klein <Heiko.Klein@xxxxxx
> > <mailto:Heiko.Klein@xxxxxx>> wrote:
> >
> > Hi Kyle,
> >
> > I made now the time-dimension 2-dimensional, i.e. time(obs,
> trajectory),
> > removing the one simplification made below. netcdf-java seems now to
> be
> > able to read the trajectories. Since the page:
> >
> http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/reference/FeatureDatasets/CFpointImplement.html
> > already mentions differences from CF, maybe this one could be entered
> > there, too? (Or maybe it's easy to extend the cdm to support
> > one-dimensional time-axes?)
> >
> >
> >
> > I wasn't able to plot trajectories as seen in netcdf-java 2.2. Is it
> > just me not finding the right buttons or was this feature removed?
> This
> > is not critical, but would be nice for debugging.
> >
> >
> > But the most important point is that we now know how to create a
> > netcdf-java compliant trajectory file. Thanks for your help.
> >
> > Heiko
> >
> >
> > On 2015-08-27 20:17, Heiko Klein wrote:
> > > Hi Kyle,
> > >
> > > we're trying to use quite strictly H.4.1 here, with one addition:
> > >
> > > Since all trajectories have the same timesteps we use 'time'='obs'
> and
> > > we don't have a special obs dimension. According to CF, this is
> > allowed:
> > > (Chapter H.4.1: "If the trajectories all have the same set of
> > times, the
> > > time auxiliary coordinate variable could be one-dimensional
> time(obs),
> > > or replaced by a one-dimensional coordinate variable time(time),
> > where
> > > the size of the time dimension is now equal to the number of
> > elements of
> > > each trajectory. In the latter case, listing the time coordinate
> > > variable in the coordinates attribute is optional.")
> > >
> > > Best regards,
> > >
> > > Heiko
> > >
> > >
> > > On 2015-08-27 16:22, Kyle Wilcox wrote:
> > >> Hi Heiko,
> > >>
> > >> At first glace, I can't figure out which CF specification you were
> > >> trying to adhere to: H.4.1, H.4.2, H.4.3, or H.4.4. It appears
> > you may
> > >> have tried to adopt H.4.2 to use multiple trajectories, which I'm
> not
> > >> sure is supported in NetCDF-Java.
> > >>
> > >> Take a look at these Trajectory
> > >> examples:
> >
> https://github.com/asascience-open/CFPointConventions/tree/master/trajectory
> .
> > >> Each folder contains a .cdl, .nc (that will load into
> > NetCDF-Java), and
> > >> an .ncml file.
> > >>
> > >> Hope that helps,
> > >> Kyle
> > >>
> > >>
> > >> On Thu, Aug 27, 2015 at 4:21 AM, Heiko Klein <Heiko.Klein@xxxxxx
> > <mailto:Heiko.Klein@xxxxxx>
> > >> <mailto:Heiko.Klein@xxxxxx <mailto:Heiko.Klein@xxxxxx>>> wrote:
> > >>
> > >> Hi,
> > >>
> > >> I'm trying to read trajectory data with netcdf-java. I've
> > seen figures
> > >> of this with netcdf-java 2.2 at
> > >>
> > >>
> >
> https://www.unidata.ucar.edu/software/thredds/v4.3/netcdf-java/tutorial/PointDatatype.html
> > >>
> > >> but both netcdf-4.6 and CF-1.6 have a different layout for
> > >> trajectory data.
> > >>
> > >>
> > >>
> > >> I've tried now to generate a netcdf/CF file following the
> > guidelines at
> > >>
> >
> http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/reference/FeatureDatasets/CFpointImplement.html
> > >> (see attached file).
> > >>
> > >>
> > >> ToolsUI gives me a 'CoordSys' with trajectory, time, lat, lon
> and
> > >> time,lat,lon have the expected axisTypes. Using FeatureScan,
> > I get a
> > >> coverage of 'Swath(T,Y,X): trajectory', which looks ok, but I
> > get also
> > >> an error message:
> > >>
> > >> ---------
> > >> /home/heikok/openoil2.nc4
> > >> NetCDF-4
> > >> map = 'f:D(2)->R(4)'
> > >>
> > >> null
> > >>
> > >> CoverageFactory for '/home/heikok/openoil2.nc4'
> > >> coverage = Swath
> > >> FeatureDatasetFactoryManager errlog = Table
> > >> PsuedoStructure(trajectory)/MultidimPseudo(trajectory,time)
> > featureType
> > >> TRAJECTORY: lat/lon/time coord not found
> > >> **Failed to find FeatureDatasetFactory for=
> > /home/heikok/openoil2.nc4
> > >> datatype=TRAJECTORY
> > >> ----------
> > >>
> > >>
> > >> According to 'CoordSys', lat/lon/time are availble.
> > >>
> > >> The PointFeature/TRAJECTORY wasn't then able to plot the
> > data. Any idea
> > >> how I can correct my data to enable plotting in netcdf-java
> UI?
> > >>
> > >>
> > >> Best regards,
> > >>
> > >> Heiko
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> netcdf-java mailing list
> > >> netcdf-java@xxxxxxxxxxxxxxxx
> > <mailto:netcdf-java@xxxxxxxxxxxxxxxx>
> > <mailto:netcdf-java@xxxxxxxxxxxxxxxx
> > <mailto:netcdf-java@xxxxxxxxxxxxxxxx>>
> > >> For list information or to unsubscribe, visit:
> > >> http://www.unidata.ucar.edu/mailing_lists/
> > >>
> > >>
> > >
> >
> > _______________________________________________
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> >
> >
> >
> >
> > --
> > Sincerely,
> >
> > Bob Simons
> > IT Specialist
> > Environmental Research Division
> > NOAA Southwest Fisheries Science Center
> > 99 Pacific St., Suite 255A (New!)
> > Monterey, CA 93940 (New!)
> > Phone: (831)333-9878 (New!)
> > Fax: (831)648-8440
> > Email: bob.simons@xxxxxxxx <mailto:bob.simons@xxxxxxxx>
> >
> > The contents of this message are mine personally and
> > do not necessarily reflect any position of the
> > Government or the National Oceanic and Atmospheric Administration.
> > <>< <>< <>< <>< <>< <>< <>< <>< <><
> >
>
> --
> Dr. Heiko Klein Norwegian Meteorological Institute
> Tel. + 47 22 96 32 58 P.O. Box 43 Blindern
> http://www.met.no 0313 Oslo NORWAY
>
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