Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.
Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.
Niels,one thing you could try is to change the Conventions global attribute of these files to "CF-1.6" to see if this changes the way they are handled (if these files are close enough to CF).
Sean, do you expect aggregations to behave the same as single files with the same Conventions? It looks like Niels has identified a difference.
Kind regards, Ben. On 30/08/16 03:29, Sean Arms wrote:
Greetings Niels, The class DefaultConvention is netCDF-Java's way of trying to handle cases in which a convention is not specified. It tries to be pretty forgiving in terms of files where people have tried to be compliant with some convention, but didn't set a convention attribute, or knew enough about some conventions in general to sort of get things in the ball park...for example, setting positive=up on a vertical coordinate, but not getting the rest of the stuff correct (not true for your case, but our code tries to handle the more common case we come across). If a file is actually following CF, netCDF-Java will use the class CF1Convention. Currently we handle (or try to) around 30 specific conventions (not sure all are actually documented conventions), but when all else fails, we go to the default convention. NcML aggregations in general can get pretty gnarly, and are very hard to get correct. Have you looked into using the Forecast Model Run Collection (FMRC) featureCollection element to serve these data? https://www.unidata.ucar.edu/software/thredds/current/tds/tutorial/FmrcFeatureCollectionsTutorial.html Cheers, Sean On Mon, Aug 29, 2016 at 6:11 AM, Niels Charlier <niels@xxxxxxxxx> wrote:Hello, I am currently working on the netcdf extensions of geotools/geoserver, although I should say I am fairly new at netcdf, so I am still learning. I am currently trying to get some particular datasets to work with geoserver, and I think I might have hit against some limitations, perhaps even a bug, in netcdf-java, so I wanted to ask you for advice. We have a .ncml have that aggregate datasets based on 'runtime'. This is an explanation from the client: *"'runtime' is not a first class coordinate in the data produced by our production groups, so the initial approach to solve this using unidata mechanisms is to use NCML to aggregate * *two datasets with different runtimes together using a 'joinNew' aggregation, which adds a new coordinate axis 'runtime' to the dataset * *(this takes place in several of the .ncml files included in the test data). The runtime axis would then be exposed as a custom dimension in geoserver so that it can be used for subsets. This means that a reader would have to be prepared to handle dimension values that are possibly two dimensional(a set of values for each available 'runtime'), which I don't think the current reader can handle? "* My first question is what it would entail for building support for this in netcdf-java? In the meantime I have been extensively debugging what happens when I try to load the aggregation file, and I can give some detailed information about what goes wrong in the code. I think I might have found something else that is going wrong. * as part of the aggregation, the runtime dimension is being added to every other variable of each of the .nc files. * During *CoordSysBuilder.buildCoordinateSystems* some things happen as a consequence of that that is different from when I read the .nc files individually: -> In *makeCoordinateSystemsImplicit*, as a consequence of all variables having an additional dimension, the CRS with lacking runtime dimension is not considered sufficient and is not being set. -> However, in *makeCoordinateSystemsMaximal* the CRS's are being set, except for one variable called "surf_el", because it is being considered an AXIS (see line 873, call to* !vp.isData()*). * During index building (*NetCDFImageReader.init -> initIndex -> getCoordinateSystem*), a runtime exception is thrown because surf_el doesn't have a CRS. The thing is, surf_el is not an axis. The reason it is considered an axis is because it has a "positive" attribute. This happens in *DefaultConvention.findCoordinateAxes -> getAxisType -> getAxisTypeCoards* (see line 297, *positive != null*). To quote my colleague Ben who I asked advice about this: *"surf_el is a time-varying data variable and not any kind of coordinate. Surface elevation looks to me like an output of the HYCOM ocean model **<https://hycom.org/> <https://hycom.org/>**. Any logic that says that a variable is a coordinate if it has attribute "positive"="up" is broken. There is this statement in the CF conventions: * *"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)." * *http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html <http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html>* *There are such things as time-varying multidimensional coordinate variables (think of the lat and lon grids for a satellite swathe), but this is not one of these. * *I think that, to be a coordinate variable, a variable must be mentioned in the "coordinates" attribute of another variable in the same file, or have a name that matches its dimension (i.e. a basic single-dimensional coordinate variable). " * So have I indeed identified a bug here? please advice. Thank you for your help. Kind Regards, Niels _______________________________________________ NOTE: All exchanges posted to Unidata maintained email lists are recorded in the Unidata inquiry tracking system and made publicly available through the web. Users who post to any of the lists we maintain are reminded to remove any personal information that they do not want to be made public. netcdf-java mailing list netcdf-java@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/_______________________________________________ NOTE: All exchanges posted to Unidata maintained email lists are recorded in the Unidata inquiry tracking system and made publicly available through the web. Users who post to any of the lists we maintain are reminded to remove any personal information that they do not want to be made public. netcdf-java mailing list netcdf-java@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/
-- Ben Caradoc-Davies <ben@xxxxxxxxxxxx> Director Transient Software Limited <http://transient.nz/> New Zealand
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