[netCDFJava #GGL-730752]: OpenDAP URL works okay in ncks, ncdump, but not in NetCDF-Java

It might be helpful to see what it looks like opening the file (not opendap 
URL) directly in ToolsUI; if differrent, that may indicate something funny in 
opendap or las.

john 

> Roland
> 
> Thanks much for this.  I knew there had to be a way to get a better plot
> out of ferret.
> 
> BTW: I had another look at the unmasked data and the masking is
> definitely doing something. One interesting thing is that even in the
> masked off areas, it's  clear that the magnitudes don't entirely match.
> Look around the entrance to the bay in particular.  I've got no
> explanation for that, but I suspect, again, that the underlying grid is
> to blame.
> 
> Here's the ferret image on the unmasked data.  Compare it to the image
> of the masked data Roland sent.
> 
> yes?  use
> "http://testbedapps.sura.org/threddsdev/dodsC/estuarine_hypoxia/cbofs2/agg-masked.nc";
> *** NOTE: If no missing_value or _FillValue attribute on variables,
> will use NaN
> yes? shade/l=1/k=1 temp,lon_rho,lat_rho
> yes? go land_detail
> 
> 
> 
> 
> Howard
> On 3/23/11 4:59 PM, Roland Schweitzer wrote:
> > For fun, here it is again in Ferret using this:
> >
> > yes? shade/l=1/k=1 temp_masked,lon_rho,lat_rho
> > yes? go land_detail
> >
> > to get the lat/lon lookups working to orient the plot in space.
> >
> > Roland
> >
> >
> >
> >
> > On 03/23/2011 03:37 PM, Howard wrote:
> >> On 3/23/11 4:14 PM, Rich Signell wrote:
> >> >  Howard&   Kyle,
> >> >
> >> >  Actually, we now HAVE moved forward!   Upgrading to TDS 4.2.5
> >> >  apparently fixed the problem we were having with OpenDAP, and I can
> >> >  now open the OpenDAP Data URL
> >> >  
> >> > <http://testbedapps.sura.org/threddsdev/dodsC/estuarine_hypoxia/cbofs2/agg-masked.nc>
> >> >    in ToolsUI.
> >> >
> >> >  After adding "Conventions = CF-1.0" in the NcML (it was incorrectly
> >> >  "COARDS" in the original NetCDF File), I can now plot your new F-TDS
> >> >  generated "temp_masked" variable.   See attached!
> >> That's pretty cool. Thanks for adding the conventions. The downside, 
> >> though, is
> >> that the graph looks about the same as the other one. We were hoping using 
> >> the
> >> mask would fix the problem. It's interesting that the graph ferret produced
> >> doesn't seem to have the same issues. I think it needs the equivalent of 
> >> axeq in
> >> matlab. Speaking of matlab, I note that I can now read the URL, so that's 
> >> more
> >> evidence of improvement.
> >>
> >>
> >>
> >> >  Note that there are some white regions in the plot where there should
> >> >  be data.   I think this is because the lon/lat values for this grid do
> >> >  not describe a continuous surface.   The lon/lat values over land are
> >> >  really whacky (see 2nd attached plot).
> >> I think we are going to have to talk to the scientist again and try to
> >> understand their data.
> >>
> >> Howard
> >>
> >> >  This could also be why the WMS doesn't work. Looks like it's bombing
> >> >  when trying to figure out how to best read the data:
> >> >
> >> >  The threddsServlet.log says:
> >> >
> >> >  2011-03-23T16:04:47.039 -0400 [    827407][     131] ERROR -
> >> >  thredds.server.wms.ThreddsWmsController - dispatchWmsRequest():
> >> >  Exception:
> >> >  java.lang.NullPointerException
> >> >       at 
> >> > uk.ac.rdg.resc.ncwms.cdm.CdmUtils.getOptimumDataReadingStrategy(CdmUtils.java:221)
> >> >       at 
> >> > thredds.server.wms.ThreddsDataset.<init>(ThreddsDataset.java:102)
> >> >
> >> >  -Rich
> >> >
> >> >  On Wed, Mar 23, 2011 at 2:15 PM, Howard<address@hidden>   wrote:
> >> >>  On 3/23/11 1:40 PM, Rich Signell wrote:
> >> >>
> >> >>  Howard
> >> >>
> >> >>  So this is a bit confusing. For some reason now in
> >> >>  /var/www/tomcat-threddsdev/content we have both thredds and 
> >> >> threddsdev.    I'm
> >> >>  pretty sure that the threddsdev is what was already there.    Rich: is 
> >> >> this
> >> >>  what you added today?
> >> >>
> >> >>  Blow away content/thredds.   This got created when I deployed thredds
> >> >>  the first time, before I edited the configuration using these
> >> >>  instructions:
> >> >>  
> >> >> http://www.unidata.ucar.edu/projects/THREDDS/tech/tds4.1/reference/InstallOptions.html
> >> >>
> >> >>  -Rich
> >> >>
> >> >>  Right.    I blew away content thredds.    The opendap access to is 
> >> >> restored.
> >> >>  See
> >> >>
> >> >>  
> >> >> http://testbedapps.sura.org/threddsdev/dodsC/estuarine_hypoxia/cbofs2/agg-masked.nc.html
> >> >>
> >> >>  Now back to the original problem ...
> >> >>
> >> >>  From
> >> >>
> >> >>  /var/www/tomcat-threddsdev/content/threddsdev/logs/threddsServlet.log
> >> >>
> >> >>  2011-03-23T13:50:14.705 -0400 [        115653][            35] INFO    
> >> >> -
> >> >>  thredds.server.wms.ThreddsWmsController - Remote host: 152.54.8.78 -
> >> >>  Request: "GET
> >> >>  
> >> >> /threddsdev/wms/estuarine_hypoxia/cbofs2/agg-masked.nc?service=WMS&version=1.3.0&request=GetCapabilities
> >> >>  HTTP/1.1"
> >> >>  2011-03-23T13:50:14.796 -0400 [        115744][            35] ERROR -
> >> >>  thredds.server.wms.ThreddsWmsController - dispatchWmsRequest(): 
> >> >> Exception:
> >> >>  java.lang.NullPointerException
> >> >>          at
> >> >>  
> >> >> uk.ac.rdg.resc.ncwms.cdm.CdmUtils.getOptimumDataReadingStrategy(CdmUtils.java:221)
> >> >>          at 
> >> >> thredds.server.wms.ThreddsDataset.<init>(ThreddsDataset.java:102)
> >> >>          at
> >> >>  
> >> >> thredds.server.wms.ThreddsWmsController.dispatchWmsRequest(ThreddsWmsController.java:164)
> >> >>          at
> >> >>  
> >> >> uk.ac.rdg.resc.ncwms.controller.AbstractWmsController.handleRequestInternal(AbstractWmsController.java:195)
> >> >>          at
> >> >>  
> >> >> org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
> >> >>          at
> >> >>  
> >> >> org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
> >> >>          at
> >> >>  
> >> >> org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:875)
> >> >>          at
> >> >>  
> >> >> org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:809)
> >> >>          at
> >> >>  
> >> >> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:571)
> >> >>          at
> >> >>  
> >> >> org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:501)
> >> >>
> >> >>  I think this is why the WMS link gives this
> >> >>
> >> >>  ServiceExceptionReport version="1.3.0"
> >> >>  xsi:schemaLocation="http://www.opengis.net/ogc
> >> >>  
> >> >> http://schemas.opengis.net/wms/1.3.0/exceptions_1_3_0.xsd";><ServiceException>Unexpected
> >> >>  error of type java.lang.NullPointerException:
> >> >>  </ServiceException></ServiceExceptionReport>
> >> >>
> >> >>  but I'm not sure that is the root problem.
> >> >>
> >> >>  Anyone have a suggestion as to how to move forward?
> >> >>
> >> >>  Howard
> >> >>
> >> >>  --
> >> >>
> >> >>  Howard Lander
> >> >>  Senior Research Software Developer
> >> >>  Renaissance Computing Institute (RENCI)
> >> >>  The University of North Carolina at Chapel Hill
> >> >>  Duke University
> >> >>  North Carolina State University
> >> >>  100 Europa Drive
> >> >>  Suite 540
> >> >>  Chapel Hill, NC 27517
> >> >>  919-445-9651
> >> >
> >> >
> >>
> >>
> >> --
> >> Howard Lander<mailto:address@hidden>
> >> Senior Research Software Developer
> >> Renaissance Computing Institute (RENCI)<http://www.renci.org>
> >> The University of North Carolina at Chapel Hill
> >> Duke University
> >> North Carolina State University
> >> 100 Europa Drive
> >> Suite 540
> >> Chapel Hill, NC 27517
> >> 919-445-9651
> >
> 
> 
> --
> Howard Lander <mailto:address@hidden>
> Senior Research Software Developer
> Renaissance Computing Institute (RENCI) <http://www.renci.org>
> The University of North Carolina at Chapel Hill
> Duke University
> North Carolina State University
> 100 Europa Drive
> Suite 540
> Chapel Hill, NC 27517
> 919-445-9651
> 
> 


Ticket Details
===================
Ticket ID: GGL-730752
Department: Support netCDF Java
Priority: Normal
Status: Open