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[netCDFJava #LUX-868625]: From ncML to netCDF file using netCDF-Java: FillValue is not handled properly

Hi Daniel,

I've answered this question on GitHub. See 
https://github.com/Unidata/thredds/issues/1036.

Cheers,
Christian

> Full Name: Daniel Risquez
> Package Version: 4.6.11
> Operating System: Linux version 3.1.10-1.29-desktop (SUSE)
> Hardware:
> Description of problem: I am generating an empty netCDF file using the ncML 
> description as input. However, I cannot define a FillValue for these 
> variables.
> 
> This issue could be related to "Ncml mishandling signedness" #923.
> 
> I follow these steps:
> 
> The following ncML code is the input description. It only defines 2 variables 
> (short and unsigned short), and tries to set their FillValue attribute to 
> "1". Note: the same problem is applicable to other data types as double, 
> float, int, etc).
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <ncml:netcdf 
> xmlns:ncml="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";>
> <ncml:variable name="my_short" shape="" type="short">
> <ncml:attribute name="_FillValue" type="short" value="1"/>
> </ncml:variable>
> <ncml:variable name="my_ushort" shape="" type="short">
> <ncml:attribute name="_Unsigned" value="true" />
> <ncml:attribute name="_FillValue" type="short" value="1" isUnsigned="true" />
> </ncml:variable>
> </ncml:netcdf>
> 
> I generate the netCDF file using this command:
> 
> java -Xmx1g -classpath netcdfAll-4.6.11.jar ucar.nc2.write.Nccopy --input 
> test_FillValue.ncml --output test_FillValue.nc --format netcdf4
> 
> (Note: I am using the latest netCDF-Java library, 4.6.11 from 4/Dec/2017; and 
> Java 1.8.0).
> 
> I dump the netCDF file with the usual command (netCDF-C version 4.3.2):
> 
> ncdump -s test_FillValue.nc
> 
> and the output is:
> 
> netcdf test_FillValue {
> variables:
> short my_short ;
> my_short:_FillValue = 1s ;
> my_short:_Endianness = "little" ;
> ushort my_ushort ;
> my_ushort:_Unsigned = "true" ;
> my_ushort:_Endianness = "little" ;
> // global attributes:
> :_Format = "netCDF-4" ;
> data:
> my_short = -32767 ;
> my_ushort = 32769 ;
> }
> 
> The data value for the "short" data type equals NC_FILL_SHORT=-32767, ok, its 
> default value (NC_FILL_SHORT). However, I defined it equal to "1"!).
> In addition, the value for the "ushort" is 32769. It is not "1" (what I 
> defined as FillValue), neither 65535 (default FillValue, NC_FILL_USHORT).
> https://www.unidata.ucar.edu/software/netcdf/docs/netcdf_8h_source.html
> 
> Summarizing:
> * FillValue attributes cannot be defined for any data type using the 
> netCDF-Java library and ncML as an input (no problem with other attributes, 
> or attributes starting by underscore like "_example"). Is this a bug?
> * When the FillValue is defined, automatically all data should be populated 
> with that value (and therefore it requires some processing time). Am I 
> correct?
> * Default FillValue attributes for unsigned data types do not match their 
> default values.
> 
> Note: this requested was initially posted here:
> https://github.com/Unidata/thredds/issues/1036

Ticket Details
===================
Ticket ID: LUX-868625
Department: Support netCDF Java
Priority: Normal
Status: Closed
===================
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