[R-sig-Geo] Rasterbrick to netCDF
ppanday
ppanday at clarku.edu
Thu Jan 31 22:51:00 CET 2013
Robert,
The ncdf4 through David Pierce's site seems incompatible with R version 2.15.2.
( package ‘C:/Data/Downloads/ncdf4_1.4.zip’ is not available (for R version 2.15.2).
Is there an alternate way to get it for R 32 bit windows? Or is it easier to switch my code to ncdf package?
Prajjwal
________________________________
From: Robert Hijmans [via R-sig-geo] [ml-node+s2731867n7582444h84 at n2.nabble.com]
Sent: Thursday, January 31, 2013 4:04 PM
To: Panday, Prajjwal
Subject: Re: Rasterbrick to netCDF
Prajjwal, you can install ncdf4 on windows (not from CRAN, but from here
http://cirrus.ucsd.edu/~pierce/ncdf/ ) but it may be easier to use the ncdf
library instead. Robert
On Thu, Jan 31, 2013 at 11:21 AM, ppanday <[hidden email]<UrlBlockedError.aspx>> wrote:
> Robert
>
> Yes, the ncdf4 packages works fine. However, it seems it runs in the unix
> environment currently. Thank you for your response.
>
> Sincerely,
> Prajjwal
> ________________________________
> From: Robert Hijmans [via R-sig-geo] [
> [hidden email]<UrlBlockedError.aspx>]
> Sent: Wednesday, January 30, 2013 7:57 PM
> To: Panday, Prajjwal
> Subject: Re: Rasterbrick to netCDF
>
> Prajjwal,
> As Thiago shows you can do such things directly via the ncdf(4) package;
> raster does not provide too many options beyond setting variable names
> (arguments varname, varunit, longname, xname, yname, zname, zunit), see
> ?writeRaster. It would be nice to expand that and allow for more flexible
> ncdf file writing from Raster objects.
> Robert
>
>
> On Thu, Jan 24, 2013 at 6:37 PM, Thiago V. dos Santos <
> [hidden email]<UrlBlockedError.aspx>> wrote:
>
> > Hi Prajjwal,
> >
> > I think the best approach in your case is to create a new, updated netcd
> > file instead of adding a dimension to an existing file. By using the
> ncdf4
> > package to create the file, you have lots of options to customize names
> and
> > descriptions of variables and dimensions.
> >
> > At the end of this message you can see the code that I use to create a
> > netcdf file with global coverage at 0.5 degree resolution based obviously
> > on a netcdf with the same features. The resulting netcdf will contain one
> > level "slice" and 12 time "slices". One detail about netcdf files is that
> > the coordinates of point refers to the center of the point and not to the
> > edge. That's why I start longitude at -179.75 instead of -180 and
> longitude
> > at 89.75 instead of 90.
> >
> > If the resulting file looks like longitude and latitude are inverted, you
> > must transpose the data when converting raster to matrix:
> > data <- t(as.matrix(r))
> >
> >
> > I hope it helps,
> >
> > Thiago.
> >
> > #--------------------------------------------------------begin of
> > code-----------------------------------------------------
> >
> > # Load required packages
> > library(raster)
> > library(ncdf4)
> >
> > # Load your data
> > r <- raster('old_file.nc')
> >
> > # Here's the trick: convert your data to a matrix
> > data <- as.matrix(r)
> >
> > # Now that we have the data we need, make output file in the correct
> format
> >
> > # Create dimensions lon, lat, level and time
> > dim_lon <- ncdim_def('longitude', 'degrees_east',
> > seq(-179.75,179.75,by=0.5))
> > dim_lat <- ncdim_def('latitude', 'degrees_north',
> > seq(89.75,-89.75,by=-0.5))
> > dim_lev <- ncdim_def('level', 'level/index', 1)
> > dim_time <- ncdim_def('time', "years since 1990-01-01", 1:12, unlim=T)
> >
> > # Create a new variable "precipitation", create netcdf file, put updated
> > contents on it and close file
> > # Note that variable "data" is the actual contents of the original netcdf
> > file
> > var_out <- ncvar_def('precipitation', 'mm/day',
> > list(dim_lon,dim_lat,dim_lev,dim_time), 9.e20)
> > ncid_out <- nc_create('updated_netcdf.nc', var_out)
> > ncvar_put(ncid_out, var_out, data, start=c(1, 1, 1, 1), count=c(720, 360,
> > 1, 12))
> > nc_close(ncid_out)
> > #--------------------------------------------------------end of
> > code-----------------------------------------------------
> >
> >
> > ----- Original Message -----
> > From: ppanday <[hidden email]<UrlBlockedError.aspx>>
> > To: [hidden email]<UrlBlockedError.aspx>
> > Cc:
> > Sent: Thursday, January 24, 2013 3:54 PM
> > Subject: [R-sig-Geo] Rasterbrick to netCDF
> >
> > Hello
> >
> > I have an output from R-script in the form of a rasterbrick with 3
> > dimensions (time, latitude, longitude). I want to be able to write it to
> a
> > netCDF format, add another dimension (time, level, latitude, longitude),
> > and
> > be able to edit dimension attributes.
> > Below you will see the properties when I write my rasterbrick to a netCDF
> > format using writeRaster.
> > I would like to change 'value' dimension to time, and edit time:units as
> > well.
> > Alternatively, is there a way I can copy dimensions and attributes from
> > another netCDF template and put my rasterbrick in that empty netCDF file?
> > Any help is greatly appreciated.
> >
> > Sincerely,
> > Prajjwal
> >
> >
> > dimensions:
> > longitude = 720 ;
> > latitude = 360 ;
> > value = UNLIMITED ; // (12 currently)
> > variables:
> > double longitude(longitude) ;
> > longitude:units = "degrees_east" ;
> > longitude:long_name = "longitude" ;
> > double latitude(latitude) ;
> > latitude:units = "degrees_north" ;
> > latitude:long_name = "latitude" ;
> > int value(value) ;
> > value:units = "unknown" ;
> > value:long_name = "value" ;
> > float prec(value, latitude, longitude) ;
> > prec:_FillValue = -3.4e+38 ;
> > prec:missing_value = -3.4e+38 ;
> > prec:long_name = "prec" ;
> > prec:projection = "+proj=longlat +datum=WGS84 +ellps=WGS84
> > +towgs84=0,0,0"
> > ;
> > prec:projection_format = "PROJ.4" ;
> > prec:min = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. ;
> > prec:max = 663.033325195312, 553.867553710938, 595.225219726562,
> > 577.460388183594, 688.026123046875, 1178.05859375, 1098.39819335938,
> > 1269.41442871094, 1184.70092773438, 1013.62524414062, 755.313537597656,
> > 633.667541503906 ;
> >
> > // global attributes:
> > :Conventions = "CF-1.4" ;
> > :created_by = "R, packages ncdf and raster (version 2.0-31)" ;
> > :date = "2013-01-24 15:58:09" ;
> >
> >
> >
> >
> >
> >
> >
> > --
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