Re: NetCDF java libraries: versions 1 and 2

I'm using version 1 (not version 2.1).  Perhaps my assumption (that the
version 1 and early version 2.2 exceptions are related) is not true....


On Fri, 2005-11-18 at 09:56, John Caron wrote:
> Scott Neu wrote:
> > Thanks for your email!  The first 4 bytes of the file are "CDF1", so I
> > don't think I am seeing the CDF2 issue.
> > 
> > It doesn't appear to me that I am seeing truncated files, because I can
> > run NCDump using the webstart netcdfTools on the unidata web site and I
> > see a successful output
> 
> the webstart tool uses the latest 2.2 library
> 
> > 
> > But this didn't work on June 22.  On that day the netcdfTools threw an
> > exception:
> > 
> > java.io.IOException: File is truncated calculated size= 23262660 actual
> > = 23262596
> >         at ucar.nc2.N3header.read(N3header.java:236)
> >         at ucar.nc2.N3iosp.open(N3iosp.java:92)
> >         at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:730)
> >         at ucar.nc2.NetcdfFile.open(NetcdfFile.java:329)
> >         at ucar.nc2.NetcdfFile.open(NetcdfFile.java:214)
> >         at ucar.nc2.NetcdfFile.open(NetcdfFile.java:161)
> >         at
> > ucar.nc2.dataset.NetcdfDataset.openFile(NetcdfDataset.java:171)
> >         at ucar.nc2.ui.ToolsUI$NCdumpPanel.run(ToolsUI.java:849)
> >         at ucar.nc2.ui.ToolsUI$GetDataTask.run(ToolsUI.java:1917)
> >         at java.lang.Thread.run(Thread.java:534)
> 
> probably did not have the fix in back then
> 
> > 
> > and now it works fine on the same file (it is a MINC file from the
> > Montreal group).
> 
> 
> so you are using version 1 or version 2.1?
> 
> > 
> > I am willing to go in and patch the version 1 code myself, but it would
> > be helpful if I knew what I was looking for.  Do you think you could
> > lend me some insight as to what the problem/fix was?
> 
> 
> > 
> > Many thanks,
> > Scott
> > 
> > 
> > On Fri, 2005-11-18 at 09:19, John Caron wrote:
> > 
> >>Scott Neu wrote:
> >>
> >>>Hello,
> >>>
> >>>I know I'm somewhat behind the times, but a while ago I downloaded the
> >>>NetCDF java library version 1 and integrated that into my code. 
> >>>Everything has been great up until last July, when I started to receive
> >>>reports that my code was no longer able to parse certain NetCDF files.
> >>>
> >>>The obvious solution is to upgrade to version 2, but the class library
> >>>has changed too much for me to do this quickly (and I just don't have
> >>>the time right now).
> >>>
> >>>My question is:  is there a quick patch I can write to parse these newer
> >>>NetCDF files using the version 1 library? 
> >>
> >>no, im afraid version 1 is no longer maintained.
> >>
> >> Did a substantial change
> >>
> >>>occur in the definition of NetCDF files?
> >>
> >>one  possibility is that you are seeing truncated files. double check with 
> >>the C library ncdump program, and dump the values of the last variable in 
> >>the file. if that fails, you have a truncated file.
> >>
> >>otherwise, maybe you are seeing the "truncated netcdf problem" where the 
> >>writer doesnt write all the bytes to the file. this has always been there 
> >>and i guess you are just seeing these now (??).
> >>
> >>there has been a change to allow files > 2 GB, but those files are not in 
> >>wide circulation. dump out the first 4 bytes of your file, old version has 
> >>CDF1 and new has CDF2 (where the 4th byte is numeric, not character)
> >>
> >>
> >>>I get end-of-file errors as the offsets to the variable data are larger
> >>>than the file lengths themselves.
> >>>
> >>>thanks for any helpful advice,
> >>>Scott
> >>>
> >>>java.io.EOFException
> >>>        at
> >>>javax.imageio.stream.ImageInputStreamImpl.readInt(ImageInputStreamImpl.java:235)
> >>>        at
> >>>ucar.netcdf.NetcdfStream$V1IntegerIo.readArray(NetcdfStream.java:1090)
> >>>        at ucar.netcdf.NetcdfStream$V1Io.toArray(NetcdfStream.java:757)
> >>>        at ucar.netcdf.NetcdfStream$V1Io.toArray(NetcdfStream.java:721)
> >>>        at ucar.netcdf.Variable.toArray(Variable.java:296)
> >>>        at ucar.nc2.Variable.read(Variable.java:229)
> >>>        at ucar.nc2.NetcdfStream.cacheData(NetcdfStream.java:102)
> >>>