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