[IDV #RLV-572542]: Error loading .nc files using "Aggregate Grids by Time"

Alexa,

One more thing: We will also be offering this in November of 2014: 
https://github.com/Unidata/tds-python-workshop

Best Wishes,

Unidata IDV Support

> Alexa,
> 
> Unfortunately, strictly speaking we don't really offer help in this area 
> (though I am hoping this will change in the future by offering a cloud based 
> ipython notebook server tailored with Unidata technology including 
> netcdf4-python). You can try the Python Enthought distribution though at the 
> USGS you'll have to pay for a license (I think). I am CCing your colleague 
> Dr. Rich Signell. Rich may have some ideas on getting you going with 
> netcdf4-python at the USGS.
> 
> Best Wishes,
> 
> Unidata IDV Support
> 
> > Thanks again for your helpful reply. I had some trouble running the python
> > script - do I need to have the netCDF version 4 library implemented on top
> > of HDF5? I don't believe I have either of those yet, but could do if it
> > means fixing this problem and not having to re-run the entire simulation(!).
> >
> > All the best
> >
> > Alexa
> >
> >
> > address@hidden> wrote:
> >
> > > Alexa,
> > >
> > > NcML can work a lot of magic, but in your case you may be out of luck. I
> > > noticed the data are not evenly spaced along the grid (is this true?) in
> > > the longitude dimension. If the data had been evenly spaced you could 
> > > maybe
> > > have used
> > > http://www.unidata.ucar.edu/software/thredds/v4.4/netcdf-java/ncml/Cookbook.html#valuesto
> > >  fix the grid values.
> > >
> > > But the root issue is you need to fix the data file. After all, someone
> > > may use your data down the road and get tripped up over this longitude
> > > problem.
> > >
> > > I actually think you can fix these data fairly easily with a bit of
> > > Python. In fact here is that bit of Python:
> > >
> > > import netCDF4
> > > f = netCDF4.Dataset('/tmp/netCDF_PIC_119.nc', 'r+')
> > > lon = f.variables['lon']
> > > lon[:] = lon[:]*-1
> > > f.close()
> > >
> > > When I open your NcML aggregation, the data end up over Kenai, Alaska (Mt.
> > > Redoubt?)
> > >
> > > Best Wishes,
> > >
> > > Unidata IDV Support
> > >
> > > > Thank you so much for your reply. This works perfectly!
> > > >
> > > > I wonder - can I also write a little script in the NCML to read in the
> > > > longtitude as degrees west (instead of the default degrees east)? I
> > > should
> > > > have used a negative number (instead of positive) to specify the 
> > > > latitude
> > > > the Alaskan volcano in my simulation, so now the data are plotting
> > > > somewhere in Russia.
> > > >
> > > > Thanks again - I really appreciate your help, this has opened up so many
> > > > possibilities for our work on eruption dynamics.
> > > >
> > > > All the best
> > > >
> > > > Alexa
> > > >
> > > >
> > > > address@hidden> wrote:
> > > >
> > > > > Alexa,
> > > > >
> > > > > Sorry for the delayed response. We have been short-staffed here on
> > > account
> > > > > of the AGU conference.  The IDV is trying to aggregate the data but
> > > can't
> > > > > find an aggregation dimension of "time". This can be solved fairly
> > > simply
> > > > > by writing your own NcML (
> > > > >
> > > http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/v2.2/Aggregation.html
> > > ).
> > > > > Attached you will find an example NcML file that should work for your
> > > data.
> > > > > Note I replaced the aggregation dimension "dimName" from "time" to
> > > "date".
> > > > > Please give that a try. It looks like you are working with interesting
> > > > > volcanic data.
> > > > >
> > > > > Please keep us up-to-date on your progress.
> > > > >
> > > > > Best Wishes,
> > > > >
> > > > > Unidata IDV Support
> > > > >
> > > > >
> > > > > > Hi there - thanks for your reply.
> > > > > >
> > > > > > I've uploaded two of the NetCDF files I'm been working with. I'm not
> > > > > > actually sure where the NCML is located, however, I'm using the
> > > latest
> > > > > > release of the IDV (v 4.1) so I assume there is a default location
> > > for
> > > > > it?
> > > > > >
> > > > > > All the best
> > > > > >
> > > > > > Alexa
> > > > > >
> > > > > >
> > > > > > address@hidden> wrote:
> > > > > >
> > > > > > > Alexa,
> > > > > > >
> > > > > > > Sorry for the delayed response. Please upload the netCDF sample
> > > data
> > > > > here (
> > > > > > > http://motherlode.ucar.edu/repository/alias/idvupload) along with
> > > the
> > > > > > > NCML. Let us know when it is uploaded by responding to this
> > > message.
> > > > > > >
> > > > > > > Also, I don't know if this is the problem, but you may wish to
> > > > > familiarize
> > > > > > > yourself with the Time Coordinate of the NetCDF Climate and
> > > Forecast
> > > > > (CF)
> > > > > > > Metadata Conventions (
> > > > > > >
> > > > >
> > > http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.0/cf-conventions.html#time-coordinate
> > > > > > > ).
> > > > > > >
> > > > > > > Best Wishes,
> > > > > > >
> > > > > > > Unidata IDV Support
> > > > > > >
> > > > > > >
> > > > > > > > Greetings IDV support,
> > > > > > > >
> > > > > > > > I've just started using IDV to analyze netCDF files from 3d
> > > > > atmospheric
> > > > > > > > simulations and I am very impressed with the program. Thank you
> > > for
> > > > > all
> > > > > > > > your hard work.
> > > > > > > >
> > > > > > > > I have multiple files that vary only by time, and would like to
> > > try
> > > > > to
> > > > > > > load
> > > > > > > > them in using the "Aggregate Grids by Time" option under data
> > > source
> > > > > type
> > > > > > > > (goal = plot the same field at different time steps and generate
> > > an
> > > > > > > > animation). I've gotten the following error:
> > > > > > > >
> > > > > > > > -----------
> > > > > > > > There was an error loading the data:
> > > > > > > > Error creating data source:aggregated.netcdf.grid with:
> > > > > > > > [/home/avaneaton/output/netCDF_PIC_106.nc,
> > > > > > > > /home/avaneaton/output/netCDF_PIC_107.nc]
> > > > > > > > Grid data source failed making data set:
> > > > > > > >
> > > > > > >
> > > > >
> > > /home/avaneaton/.unidata/idv/DefaultIdv/tmp/multigrid_b7c4c046-ee15-428c-9af3-09f0db845a590.ncml
> > > > > > > > AggregationExisting: no coordinate variable for agg
> > > > > > > > dimension= time
> > > > > > > > ------------
> > > > > > > >
> > > > > > > > So it looks like the ncml script does not recognize the time
> > > stamp
> > > > > in my
> > > > > > > > files. Any suggestions for troubleshooting this issue?
> > > > > > > >
> > > > > > > > All the best
> > > > > > > >
> > > > > > > > Alexa
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Ticket Details
> > > > > > > ===================
> > > > > > > Ticket ID: RLV-572542
> > > > > > > Department: Support IDV
> > > > > > > Priority: Normal
> > > > > > > Status: Closed
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Alexa Van Eaton
> > > > > > NSF Postdoctoral Fellow
> > > > > > U.S. Geological Survey
> > > > > > David A. Johnston Cascades Volcano Observatory
> > > > > > 1300 SE Cardinal Court, Bldg 10, Suite 100
> > > > > > Vancouver, Washington 98683 USA
> > > > > > Office (360) 993 8921
> > > > > > Mobile (208) 596 8265
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > > Ticket Details
> > > > > ===================
> > > > > Ticket ID: RLV-572542
> > > > > Department: Support IDV
> > > > > Priority: Normal
> > > > > Status: Closed
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Alexa Van Eaton
> > > > NSF Postdoctoral Fellow
> > > > U.S. Geological Survey
> > > > David A. Johnston Cascades Volcano Observatory
> > > > 1300 SE Cardinal Court, Bldg 10, Suite 100
> > > > Vancouver, Washington 98683 USA
> > > > Office (360) 993 8921
> > > > Mobile (208) 596 8265
> > > >
> > > >
> > >
> > >
> > > Ticket Details
> > > ===================
> > > Ticket ID: RLV-572542
> > > Department: Support IDV
> > > Priority: Normal
> > > Status: Closed
> > >
> > >
> >
> >
> > --
> > Alexa Van Eaton
> > NSF Postdoctoral Fellow
> > U.S. Geological Survey
> > David A. Johnston Cascades Volcano Observatory
> > 1300 SE Cardinal Court, Bldg 10, Suite 100
> > Vancouver, Washington 98683 USA
> > Office (360) 993 8921
> > Mobile (208) 596 8265
> >
> >
> 


Ticket Details
===================
Ticket ID: RLV-572542
Department: Support IDV
Priority: Normal
Status: Closed