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Hi José, Once again, sorry for the delay. I've modified my last example to incorporate the changes you requested [1]. A few things to note: 1. The "Other" dimension is now shared instead of private. NetcdfFileWriter.addDimension creates a dimension and adds it to a Group. When Dimensions are contained by Groups, they should *always* be shared. In fact, NetcdfFileWriter.addDimension shouldn't even have the isShared parameter, as it is confusing and error-prone. In v5.0.0, it won't [2]. Thanks for bringing this to my attention! 2. In the first example, the Date1 and Date2 variables use *anonymous dimensions*. Anonymous dimensions are both private (i.e. contained by a Variable, not a Group) and nameless. NetcdfFileWriter does not provide a direct way to create them, so you'll have to do a little more work, as I've shown. 3. In the first example, it looks like the "CHANGELOG=2" snippet may indicate a private, *named* dimension. If that's the case, create it the same way you did the anonymous dimensions but just – you know – give it a name. Cheers, Christian [1] https://gist.github.com/cwardgar/35427c2e245ec0157416 [2] https://github.com/Unidata/thredds/pull/326 On Tue, Nov 24, 2015 at 1:23 AM, José Évora <jose.evora@xxxxxxxx> wrote: > Hi Christian, > > Thank you very much, it worked perfectly!. However, I'm trying to > replicate the output as expected for a netcdf reader of a specific kind of > data. When I read a netcdf that is accepted by the specific reader using > the netcdf java library, this is what I obtain (I've have adapted the > content to our toy case, but it can be extrapolated to the real case): > > netcdf res/in original.nc { >> dimensions: > > City = 1; > > Other = UNLIMITED; // (2 currently) >> ... >> variables: > > String City(City=1); > > > > Structure { >> char Date1(30); >> char Date2(53); >> } CHANGELOG(CHANGELOG=2); >> :_ChunkSizes = 1; // int >> } > > > With the code you provided me, I obtain: > > netcdf res/mockSimulation2.nc { >> dimensions: >> City = 1; >> Other-Entry_Dim0 = 1; >> Other = 1; >> strlen = 30; >> variables: >> String City(City=1); >> Structure { >> char Date1(30); >> char Date2(30); >> } Other-Entry(Other-Entry_Dim0=1); >> >> } > > > I only did one change to what you sent me at line 26: > > Structure otherVar = (Structure) ncFile.addVariable(root, "Other-Entry", >> STRUCTURE, singletonList(other)); > > > I don't know how I can: > > 1) Avoid having a dimension strlen > 2) Avoid having Other-Entry_Dim0 > > Thanks in advance! > > José Évora Gómez > Instituto Universitario SIANI > Universidad de Las Palmas de GC > @j_evora > > 2015-11-23 6:59 GMT+00:00 Christian Ward-Garrison <cwardgar@xxxxxxxx>: > >> Hi José, >> >> Sorry for the late response—hopefully this is still useful to you. >> >> Writing structures to NetCDF-4 is a recent addition to our library and >> hasn't been tested as comprehensively as we'd like, especially since most >> of our users that are writing NetCDF-4 are only utilizing the classic data >> model (i.e. no structures). Your example uncovered multiple bugs [1][2][3], >> so thank you for that! >> >> That said, it is still possible to make your example work, although the >> admittedly limited documentation makes it tricky to get right. I've >> corrected your NetCdfCreatorLite2 class and posted it here [4]. Notice that >> the "Other" dimension is no longer unlimited and that I'm recalculating the >> structure's size after adding members to it. >> >> Also, for future reference, the latest versions of our library artifacts >> are not available on Maven Central. Instead, grab them from our >> organization's repository, as described here [5]. >> >> Cheers, >> Christian >> >> [1] https://github.com/Unidata/thredds/issues/296 >> [2] https://github.com/Unidata/thredds/issues/298 >> [3] https://github.com/Unidata/thredds/issues/299 >> [4] https://gist.github.com/cwardgar/7aa866886468e97c8eea >> [5] >> https://www.unidata.ucar.edu/software/thredds/current/netcdf-java/reference/BuildDependencies.html >> >> On Thu, Nov 5, 2015 at 8:01 AM, José Évora <jose.evora@xxxxxxxx> wrote: >> >>> The dependency is being taken from Maven central. However, I have tried >>> this jar instead of maven: >>> >>> ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v4.6/netcdfAll-4.6.jar >>> >>> And I get exactly the same problems in both java files. >>> >>> José Évora Gómez >>> Instituto Universitario SIANI >>> Universidad de Las Palmas de GC >>> @j_evora >>> >>> 2015-11-05 14:09 GMT+00:00 John Caron <jcaron1129@xxxxxxxxx>: >>> >>>> what repo is >>>> >>>> <dependency> >>>> <groupId>edu.ucar</groupId> >>>> <artifactId>netcdf4</artifactId> >>>> <version>LATEST</version> >>>> </dependency> >>>> >>>> coming from? >>>> >>>> >>>> >>>> On Thu, Nov 5, 2015 at 12:13 AM, José Évora <jose.evora@xxxxxxxx> >>>> wrote: >>>> >>>>> When maven resolves the code quoted, this is the library that >>>>> downloads: >>>>> >>>>> Maven: edu.ucar:netcdf4:4.5.5 >>>>> >>>>> >>>>> Version seems to be 4.5.5 for the netcdf java library. For the netcdf >>>>> C libraries, I downloaded and installed: netCDF 4.3.3.1. Specifically, >>>>> this >>>>> file: >>>>> >>>>> >>>>> http://www.unidata.ucar.edu/downloads/netcdf/ftp/netCDF4.3.3.1-NC4-DAP-64.exe >>>>> >>>>> Thanks, >>>>> >>>>> José Évora Gómez >>>>> Instituto Universitario SIANI >>>>> Universidad de Las Palmas de GC >>>>> @j_evora >>>>> >>>>> 2015-11-04 23:33 GMT+00:00 John Caron <jcaron1129@xxxxxxxxx>: >>>>> >>>>>> Hi Jose, what version of netcdf-java and netcdf C libraries are you >>>>>> using? John >>>>>> >>>>>> On Wed, Nov 4, 2015 at 12:54 AM, José Évora <jose.evora@xxxxxxxx> >>>>>> wrote: >>>>>> >>>>>>> Hi everyone, >>>>>>> >>>>>>> I'm trying to create a structure (also know compounded type). In >>>>>>> this email I attach two different ways I've tried to do it and their >>>>>>> respective error message. This is the dependency I'm using >>>>>>> >>>>>>> <dependency> >>>>>>>> <groupId>edu.ucar</groupId> >>>>>>>> <artifactId>netcdf4</artifactId> >>>>>>>> <version>LATEST</version> >>>>>>>> </dependency> >>>>>>> >>>>>>> >>>>>>> *1) NetCdfCreatorLite.java* >>>>>>> >>>>>>> The execution throws a NullPointerException at >>>>>>> >>>>>>> Structure otherVar = ncFile.addStructure(root, >>>>>>>> root.getParentStructure(), "Other", singletonList(other)); >>>>>>> >>>>>>> >>>>>>> Exception in thread "main" java.lang.NullPointerException >>>>>>>> at ucar.nc2.NetcdfFileWriter.addStructure(NetcdfFileWriter.java:584) >>>>>>>> at org.mock.NetCdfCreatorLite.main(NetCdfCreatorLite.java:27) >>>>>>> >>>>>>> >>>>>>> *2) NetCdfCreatorLite2.java* >>>>>>> >>>>>>> According to the java doc, the method addstructure shouldn't be >>>>>>> used. Then, in this second version, I uses a addVariable method to >>>>>>> create >>>>>>> the structure: >>>>>>> >>>>>>> Structure otherVar = (Structure) ncFile.addVariable(root, "Other", >>>>>>>> STRUCTURE, singletonList(other)); >>>>>>> >>>>>>> >>>>>>> The exeception given this time is: >>>>>>> >>>>>>> Exception in thread "main" java.io.IOException: nc_put_vars: -49: >>>>>>>> NetCDF: Variable not found grpid=65536 objid=1 >>>>>>>> at ucar.nc2.jni.netcdf.Nc4Iosp.writeCompoundData(Nc4Iosp.java:2895) >>>>>>>> at ucar.nc2.jni.netcdf.Nc4Iosp.writeData(Nc4Iosp.java:2839) >>>>>>>> at ucar.nc2.jni.netcdf.Nc4Iosp.writeData(Nc4Iosp.java:2721) >>>>>>>> at ucar.nc2.NetcdfFileWriter.write(NetcdfFileWriter.java:934) >>>>>>>> at ucar.nc2.NetcdfFileWriter.write(NetcdfFileWriter.java:918) >>>>>>>> at org.mock.NetCdfCreatorLite2.main(NetCdfCreatorLite2.java:46) >>>>>>> >>>>>>> >>>>>>> At line: >>>>>>> >>>>>>> ncFile.write(otherVar, otherStructure); >>>>>>> >>>>>>> >>>>>>> If I comment the creation of structures, the application executes >>>>>>> perfectly. Even more, by only adding the addVariable of a structure >>>>>>> line, I >>>>>>> get this exception, even though I only write the cityVar at line 50 . >>>>>>> >>>>>>> What is wrong? Can you please provide me with an example of use of >>>>>>> the structures?. >>>>>>> >>>>>>> Best regards, thank you very much, >>>>>>> >>>>>>> José Évora Gómez >>>>>>> Instituto Universitario SIANI >>>>>>> Universidad de Las Palmas de GC >>>>>>> @j_evora >>>>>>> >>>>>>> _______________________________________________ >>>>>>> netcdf-java mailing list >>>>>>> netcdf-java@xxxxxxxxxxxxxxxx >>>>>>> For list information or to unsubscribe, visit: >>>>>>> http://www.unidata.ucar.edu/mailing_lists/ >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> netcdf-java mailing list >>> netcdf-java@xxxxxxxxxxxxxxxx >>> For list information or to unsubscribe, visit: >>> http://www.unidata.ucar.edu/mailing_lists/ >>> >> >> >
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