[ncl-talk] variable metadata getting overwritten when variable is written to a NetCDF4 file

[David Brown]

Well yes that would definitely be a bug, But that is not what I was
seeing with your script (I ran it only on my Mac with my 6.3.1
development version).

Here is the output of your test script on my system:

 ncl file_var_metadata_clobber.ncl
 Copyright (C) 1995-2015 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.3.1
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.

netcdf file_var_metadata_clobber {
variables:
float testvar ;
testvar:long_name = "long_name" ;
testvar:units = "units" ;
}

netcdf file_var_metadata_clobber {
variables:
float testvar ;
testvar:long_name = "long_name" ;
testvar:units = "units" ;
testvar:_FillValue = -99.f ;
}

The copy & paste seems to have removed the indentation, but otherwise
this seems like the expected output to me.

Is the script giving different results somewhere else?
 -dave



On Mon, Nov 2, 2015 at 7:28 PM, Keith Lindsay <klindsay at ucar.edu> wrote:
> Dave,
>
> Thanks for your description of the subtleties of _FillValue and the
> value-only assignment. Please note though that not only is the _FillValue
> attribute getting added, the variable's pre-existing attributes are getting
> lost. Do you consider this latter aspect a bug or feature? It is this that I
> am more concerned about. Also, this removal of the pre-existing attributes
> happens with NetCDF4 (for ncl version 6.3.0, but not 6.2.1) and not with
> NetCDF3.
>
> Keith
>
> On Mon, Nov 2, 2015 at 5:13 PM, David Brown <dbrown at ucar.edu> wrote:
>>
>> Hi Keith,
>> I think that what you are seeing is actually documented (although
>> poorly apparently) behavior. At least, if, as I am assuming from your
>> test script, the only attribute that gets passed through the
>> value-only assignment is the _FillValue. The NCL Reference Manual says
>> this about value-only assignment:
>>
>> "No dimension names, coordinate variables or attributes other than
>> _FillValue are assigned. "
>>
>> In fact the _FillValue is a special attribute that even values (as
>> opposed to variables) in NCL carry around. And it is propagated even
>> through value-only assignment. That is because it is considered an
>> essential component of the value.
>>
>> If in fact you are seeing other attributes get propagated let us know.
>> Your test script only showed the _FillValue propagation as far as I
>> could tell.
>>  -dave
>>
>>
>>
>>
>>
>>
>> On Mon, Nov 2, 2015 at 9:03 AM, Keith Lindsay <klindsay at ucar.edu> wrote:
>> > Hi,
>> > Thanks Dennis. For other users that run into this behavior, a workaround
>> > to
>> > avoid it is to ensure that the variable on the rhs of the problematic
>> > assignment does not have the _FillValue attribute. I.e.
>> >       if (isatt(tmpvar, "_FillValue")) then
>> >         delete(tmpvar at _FillValue)
>> >       end if
>> > Keith
>> >
>> >
>> > On Mon, Nov 2, 2015 at 8:44 AM, Dennis Shea <shea at ucar.edu> wrote:
>> >>
>> >> A JIRA ticket [  NCL-2302 ] has been opened.  THX
>> >>
>> >> On Mon, Nov 2, 2015 at 8:06 AM, Keith Lindsay <klindsay at ucar.edu>
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > I have come across an instance where I'm writing a variable to a file
>> >> > and
>> >> > the variable metadata in the file is getting overwritten, even though
>> >> > I'm
>> >> > using (/ ... /) on the right-hand side of the write to file
>> >> > statement.
>> >> > That
>> >> > is, the statement
>> >> > f->$varname$ = (/ tmpvar /)
>> >> > is overwriting the metadata for the file variable $varname$ in the
>> >> > file
>> >> > pointed to by f. The attached script demonstrates the problem. This
>> >> > seems
>> >> > like an ncl bug to me.
>> >> >
>> >> > Details of my script that seem to matter are:
>> >> > 1) the file is NetCDF4
>> >> > 2) the file variable whose metadata is getting overwritten has been
>> >> > defined
>> >> > in the file but not written to yet
>> >> > 3) the file variable whose metadata is getting overwritten does not
>> >> > have
>> >> > the
>> >> > _FillValue attribute
>> >> > 4) the variable on rhs of write to file statement has _FillValue
>> >> > attribute
>> >> >
>> >> > The problem happens with ncl 6.3.0 on yellowstone. It does not happen
>> >> > with
>> >> > ncl 6.2.1, though with 6.2.1 the _FillValue gets added to the file
>> >> > variable's metadata, which is unexpected to me.
>> >> >
>> >> > Keith
>> >> >
>> >> > _______________________________________________
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>> >
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