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

[Roy Mendelssohn]

Hi Tom:

Sorry for top-posting.  My bad etiquette for the day.  The order that you do things when you create nercdf files matters a lot.  Here is a section from the help for ncdf4:

> If you want to WRITE data to a new netCDF file, the procedure is to first define the dimensions your data array has, then define the variable, then create the file. So, first call ncdim_def to define the dimensions that your data exists along (for example, latitude, longitude, and time). Then call ncvar_def to define a variable that uses those dimensions, and will hold your data. Then callnc_create to create the netCDF file. Finally, call ncvar_put to write your data to the newly created netCDF file, and nc_closewhen you are done.


And here is the relevant section from your code:

> netcdf.file <- nc_create(
>   filename=netcdf.fn,
> #  vars=list(emis.var),
> #  verbose=TRUE)
>   vars=list(emis.var))
> 
> # Write data to data variable: gotta have file first.
> # Gotta convert 2d global.emis.mx[lat,lon] to 3d global.emis.arr[time,lat,lon]
> # Do this before adding _FillValue to prevent:
> # > Error in R_nc4_put_vara_double: NetCDF: Not a valid data type or _FillValue type mismatch
> ## global.emis.arr <- global.emis.mx
> ## dim(global.emis.arr) <- c(1, dim(global.emis.mx))
> ## global.emis.arr[1,,] <- global.emis.mx
> 
> # Note
> # * global.emis.mx[lat,lon]
> # * datavar needs [lon, lat, time] (with time *last*)
> 
> ncvar_put(
>   nc=netcdf.file,
>   varid=emis.var,
> #  vals=global.emis.arr,
>   vals=t(global.emis.mx),
> #  start=rep.int(1, length(dim(global.emis.arr))),
>   start=c(1, 1, 1),
> #  count=dim(global.emis.arr))
>   count=c(-1,-1, 1)) # -1 -> all data

You can't write until all dimensions have been defined, and all variables defined.

HTH,

-Roy



On Aug 28, 2012, at 4:29 AM, Tom Roche wrote:

> 
> Tom Roche Mon, 27 Aug 2012 23:31:23 -0400
>>> summary: I can successfully ncvar_put(...) data to a file, but when
>>> I try to ncvar_get(...) the same data
> 
> in the one and only datavar
> 
>>> I get
> 
>>>> Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset else addOffset = 0 : 
>>>>  argument is of length zero
> 
> David W. Pierce Mon, 27 Aug 2012 21:35:35 -0700
>> If you want to create a file and write to it, and then read back in from that same file, close it first and then reopen it.
> 
> So nc_sync is not enough--good to know. But ...
> 
> Unfortunately I do that (nc_close then nc_open) in the latest code @
> 
> https://github.com/TomRoche/GEIA_to_NetCDF
> 
> (direct link to relevant file=
> 
> https://github.com/TomRoche/GEIA_to_netCDF/blob/master/GEIA.to.netCDF.r
> 
> ) but no fix--same error. Any other suggestions?
> 
> your assistance is appreciated, 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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