[R] [netcdfgroup] [ncdf4] error converting GEIA data to netCDF

[Roy Mendelssohn]

Just looked at your code, and you do call nc_sync.  I am wondering if it works if you call nc_close, reopen and then write. Perhaps the nc_sync is sufficent when you have been in define mode in the nc_create call.

-Roy

On Aug 27, 2012, at 8:31 PM, Tom Roche wrote:

> 
> summary: I can successfully ncvar_put(...) data to a file, but when I
> try to ncvar_get(...) the same data, I get
> 
>> Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset else addOffset = 0 : 
>>  argument is of length zero
> 
> How to fix or debug?
> 
> details:
> 
> R code @
> 
> https://github.com/TomRoche/GEIA_to_NetCDF
> 
> successfully (if crudely) uses R packages={ncdf4, maps, fields} to
> 
> + extract data from a GEIA-distributed datafile
> 
> https://github.com/downloads/TomRoche/GEIA_to_netCDF/N2OOC90Y.1A
> 
> + display the data (mostly successfully--the map's legend has problems
>  which I'll attack later)
> 
> https://github.com/downloads/TomRoche/GEIA_to_netCDF/output.1.png
> 
> + create a netCDF file using the data read from the GEIA file. (At
>  least, after nc_sync(netcdf.file), the file `ncdump -h`s properly.)
> 
> However, I can only *put* the data to the netCDF file:
> 
>> ncvar_put(
>> + nc=netcdf.file,
>> + varid=emis.var,
>> + vals=t(global.emis.mx),
>> + start=c(1, 1, 1),
>> + count=c(-1,-1, 1)) # -1 -> all data
> 
> When I try to *pull* the data *from* the netCDF I created,
> 
>>> target.data <- ncvar_get(
>> +   nc=netcdf.file,
>> +   varid=emis.var,
>> +   # read all the data
>> +   start=rep(1, emis.var$ndims),
>> + #  count=rep(-1, emis.var$ndims))
> 
> I get
> 
>> Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset else addOffset = 0 : 
>>  argument is of length zero
> 
> And I get the same error if I try the minor variation(s)
> 
>> target.data <- ncvar_get(
> +   nc=netcdf.file,
> + #  varid=emis.var,
> +   varid=emis.var.name,
> +   # read all the data
> +   start=rep(1, emis.var$ndims),
> +   count=c(-1, -1, 1))
> 
> But the data itself appears to be OK--at least, it virtualizes
> properly (above). So I'm thinking I must just be missing something
> simple, and hoping Someone Out There with fresh eyeballs can point to
> my error(s).
> 
> (And, in case you're wondering:
> 
> - I'm not just ncvar_put'ing the data for the exercise: I want the
>  GEIA data in netCDF format for subsequent use.
> 
> - I tried to find the GEIA data distributed in netCDF format, and
>  asked around, but have gotten no responses.
> 
> ) TIA, Tom Roche <Tom_Roche at pobox.com>
> 
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**********************
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**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address)
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