R help - Sep 2011 - Editing the variables attributes section in the netCDF header of netCDF files created using the package ncdf.

Hi,

I am using the package ncdf to create netCDF files and I want to mimic the the
header of an exiting netCDF file created outside of R. Below is what the
existing header looks like (part of it that is different):

netcdf ccd1984_05_08 {
dimensions:
        lat = 1974 ;
        lon = 1894 ;
        time = UNLIMITED ; // (1 currently)
variables:
        int time(time) ;
                time:long_name = "time" ;
                time:units = "days since 1984-05-01 0:0:0" ;
                time:day_begins = "06:15" ;
        double lat(lat) ;
                lat:long_name = "latitude" ;
                lat:standard_name = "latitude" ;
                lat:units = "degrees_north" ;
                lat:axis = "Y" ;
        double lon(lon) ;
                lon:long_name = "longitude" ;
                lon:standard_name = "longitude" ;
                lon:units = "degrees_east" ;
                lon:axis = "X" ;
        byte ccd(time, lat, lon) ;
                ccd:Unit_duration = 7.5f ;
                ccd:units = "Unit_duration mins" ;
                ccd:long_name = "Cold Cloud Duration" ;
                ccd:short_name = "ccd" ;
                ccd:_FillValue = -1b ;

And here is my attempt when using the ncdf package:

netcdf ccd1983_04_08_r {
dimensions:
        lon = 1894 ;
        lat = 1974 ;
        time = UNLIMITED ; // (1 currently)
variables:
        double lon(lon) ;
                lon:units = "" ;
        double lat(lat) ;
                lat:units = "" ;
        double time(time) ;
                time:units = "days since 1900-01-01" ;
        byte ccd(time, lat, lon) ;
                ccd:units = "" ;
                ccd:missing_value = -99b ;
                ccd:long_name = "Cold Cloud Duration" ;

I am unable to replicate the variables attributes that exist in the first
example in the second example. Is there anyway to transfer across the header
information or edit the ncdf package to do this?

Thanks in advance,
Ross (PhD Student)

On Wed, Sep 7, 2011 at 2:25 PM, Ross Maidment <
R.I.Maidment@pgr.reading.ac.uk> wrote:
> Hi,
>
> I am using the package ncdf to create netCDF files and I want to mimic the
> the header of an exiting netCDF file created outside of R. Below is what
the
> existing header looks like (part of it that is different):
>
> netcdf ccd1984_05_08 {
> dimensions:
>        lat = 1974 ;
> [...listings omitted...]
> I am unable to replicate the variables attributes that exist in the first
> example in the second example. Is there anyway to transfer across the
header
> information or edit the ncdf package to do this?
>
Hi Ross,

to specify the units attribute in the output file, you just set the units
parameter correctly when calling dim.def.ncdf. Since your ncdf-created file
has blank units attributes, I can only assume your R code is doing something
like this:

dim_lon <- dim.def.ncdf( 'lon', "", lonvals )

when it should be doing something more like this:

dim_lon <- dim.def.ncdf( 'lon', "degrees_east", lonvals ),
etc.

Easiest way to "copy" a dimension is R code like this:

file2copy = 'old_file.nc'
ncid_old = open.ncdf( file2copy )
dim2copy = "lon"
old_dim = ncid_old$dim[[ dim2copy ]]
new_dim = dim.def.ncdf( old_dim$name, old_dim$units, old_dim$vals,
unlim=old_dim$unlim, longname=old_dim$longname )

For attributes other than units, you can use the att.put.ncdf() call. You
make this call AFTER you have created the output file:

...
ncid_out = create.ncdf( 'new_output_file.nc',
list(output_vars1,...,output_varN))

att.put.ncdf( ncid_out, 'lat', 'axis', 'Y' )
att.put.ncdf( ncid_out, 'ccd', 'Unit_duration', 7.5 )

etc.

--Dave

>
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>


-- 
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography
(858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce@ucsd.edu

	[[alternative HTML version deleted]]

Hi Dave, 

Many thanks for you prompt and useful reply. It worked a treat! 

Another question which you might be able to answer is, is it possible to set
the order of the variables attributes in which they appear? For example, I
would like to set the order of Example 2 to Example 1:

Example 1:
double lon(lon) ;
                lon:long_name = "longitude" ;
                lon:standard_name = "longitude" ;
                lon:units = "degrees_east" ;
                lon:axis = "X" ;

Example 2:
double lon(lon) ;
                lon:units = "degrees_east" ;
                lon:long_name = "longitude" ;
                lon:standard_name = "longitude" ;
                lon:axis = "X" ;

Many thanks,
Ross

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On Fri, Sep 9, 2011 at 3:18 PM, RMaidment
<r.i.maidment at pgr.reading.ac.uk> wrote:
> Another question which you might be able to answer is, is it possible to
set
> the order of the variables attributes in which they appear? [...]
Hi Ross,

The ncdf package makes the units and longname attributes
automatically, so those will always be the first and second
attributes, and the ones you add using att.put.ncdf will follow later
in the order of your att.put.ncdf calls. So no, there is no way of
arranging them all in arbitrary order.

I would personally consider any software that cares about the order of
the attributes to be non-compliant with netCDF standards, but perhaps
there is some software out there that does care about the order
anyway.

Regards,

--Dave

-- 
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography
(858) 534-8276 (voice) ?/ ?(858) 534-8561 (fax) ? ?dpierce at ucsd.edu