Hi José,
I'm not sure what program that image came from, but when I ncdump the
NetCDF-4 file created after incorporating your changes, I get:
$ ncdump -h foo.nc4
netcdf foo {
types:
compound CHANGELOG_t {
char Date1(30) ;
char Date2(53) ;
}; // CHANGELOG_t
dimensions:
City = 1 ;
CHANGELOG = 1 ;
variables:
string City(City) ;
CHANGELOG_t CHANGELOG(CHANGELOG) ;
}
"CHANGELOG_t" is the name of the compound type. Currently, there is no way
in NetCDF-Java to configure that name; it'll always be
"<structure_name>_t".
Cheers,
Christian
On Fri, Dec 11, 2015 at 3:06 AM, José Évora <jose.evora@xxxxxxxx> wrote:
> Hi Christian!
>
> Thank you very much. It worked perfectly and now the netcdf file is much
> more clean. I just did one change which is calling the dimension
> "changelog" and the structured variable "changelog" too:
>
> structure = (Structure) ncFile.addVariable(null, "CHANGELOG", STRUCTURE,
> singletonList(ncFile.addDimension(null, "CHANGELOG", 1, true, false, false)));
>
> As result I have next file structure:
>
> [image: Imágenes integradas 2]
>
> Is there anyway to have CHANGE-LOG-ENTRY instead of CHANGELOG_t in the
> yellow marked entry?
>
> Thanks in advance, you're helping me alot
>
>
> José Évora Gómez
> Instituto Universitario SIANI
> Universidad de Las Palmas de GC
> @j_evora
>
> 2015-12-08 23:57 GMT+00:00 Christian Ward-Garrison <cwardgar@xxxxxxxx>:
>
>> 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/
>>>>>
>>>>
>>>>
>>>
>>
>
