Robert,
Thank you very much for the tip. However, I still cannot load all the "z"
layers in only one brick. Please see the comments below:
> library(ncdf)
> library(raster)
# Reading file with ncdf package to examine its strucuture.
> n <- open.ncdf ('~/Dropbox/web/soita.clay.nc')
> n
[1] "file ~/Dropbox/web/soita.clay.nc has 5 dimensions:"
[1] "longitude Size: 720"
[1] "latitude Size: 360"
[1] "layer Size: 6"
[1] "time Size: 1"
[1] "lengthd Size: 10"
[1] "------------------------"
[1] "file ~/Dropbox/web/soita.clay.nc has 1 variables:"
[1] "double claypct[longitude,latitude,layer,time] Longname:claypct
Missval:1e+30"
# The dimension I need to make a brick of is "layer", which contains data in
six soil levels.
# Therefore, I expected to create a brick with nlayers=6, but that doesn't
happen. See below:
> b <- brick('~/Dropbox/web/soita.clay.nc',level=3)
Warning message:
In .doTime(r, nc, zvar, dim3, ncdf4) : assuming a standard calender:0
> b
class : RasterBrick
dimensions : 360, 720, 259200, 1 (nrow, ncol, ncell, nlayers)
resolution : 0.5, 0.5 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84
data source : ~/Dropbox/web/soita.clay.nc
names : X1958.01.01
Date : 1958-01-01
varname : claypct
level : 3
It looks like raster assumes that the third level in the file contains only one
layer. Is this right?
In case there's a need to inspect the input file, it is 12MB:
https://www.dropbox.com/s/hyalyip9ai8yidc/soita.clay.nc
Best,
Thiago.
________________________________
From: Robert J. Hijmans <r.hijm...@gmail.com>
Cc: R-SIG list <r-sig-geo@r-project.org>
Sent: Saturday, September 29, 2012 4:10 AM
Subject: Re: [R-sig-Geo] Create a raster brick from a netcdf using all levels
Thiago,
You can try using the (perhaps undocumented) 'level' argument
clay3 <- brick('/data/input-inland/soita.clay.nc', level=3)
With a RasterBrick you can only one level at a time (i.e. x, y and z, but not a
fourth dimension), but you can create several RasterBricks, one for each level.
Robert
ote:
Dear list,
>
> I have a netcdf file that contains 6 levels. Below is the structure of the
>file:
>
>require(ncdf)
>require(raster)
>> nctemp <- open.ncdf('/data/input-inland/soita.clay.nc')
>
>> nctemp
>[1] "file /data/input-inland/soita.clay.nc has 5 dimensions:"
>[1] "longitude Size: 720"
>[1] "latitude Size: 360"
>[1] "layer Size: 6"
>[1] "time Size: 1"
>[1] "lengthd Size: 10"
>[1] "------------------------"
>[1] "file /data/input-inland/soita.clay.nc has 1 variables:"
>[1] "double claypct[longitude,latitude,layer,time] Longname:claypct
>Missval:1e+30"
>>
>
> What I need to do is to load this netcdf to a brick raster object using all
>levels. When creating the brick file, specifying "nl=6" results in loading
>only the last level:
>
>> clay <- brick('/data/input-inland/soita.clay.nc', nl=6)
>Warning messages:
>1: In .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
> "level" set to 1 (there are 6 levels)
>2: In .doTime(r, nc, zvar, dim3, ncdf4) : assuming a standard calender:0
>> clay
>class : RasterBrick
>dimensions : 360, 720, 259200, 1 (nrow, ncol, ncell, nlayers)
>resolution : 0.5, 0.5 (x, y)
>extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
>coord. ref. : +proj=longlat +datum=WGS84
>data source : /data/input-inland/soita.clay.nc
>names : X1958.01.01
>Date : 1958-01-01
>varname : claypct
>level : 1
>
> I have also tested another approach, for example specifying "nl=1:6",
>however with no sucess at all. Does anyone know a workaround to load all leves
>of a netcdf file in a single raster brick object?
>
> Many thanks in advance,
> Thiago.
>
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>R-sig-Geo@r-project.org
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>
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