[R-sig-Geo] Problem with raster package and nc4 file
Michael Sumner
mdsumner at gmail.com
Sat Jun 6 01:52:42 CEST 2015
Just another short comment below
On Sat, 6 Jun 2015 at 09:37 Andrea Timmermann <timmermann at gmx.at> wrote:
> Hi!
> Thanks a lot !!! I could get the raster now.
> This is what I got:
> > r
> class : RasterLayer
> band : 1 (of 365 bands)
> dimensions : 4823, 5268, 25407564 (nrow, ncol, ncell)
>
> resolution : 1000, 1000 (x, y)
> extent : -2015000, 3253000, -3037000, 1786000 (xmin, xmax, ymin,
> ymax)
> coord. ref. : +proj=lcc +lon_0=-100 +lat_0=42.5 +x_0=0 +y_0=0 +lon_0=0
> +lat_1=25 +lat_2=60
> data source : C:\Users\Andi\Desktop\1980\tmin_1980.nc4
> names : daily.minimum.temperature
> z-value : 1980-01-01
> zvar : tmin
>
>
> and
>
> > print(ncic)
> [1] "File tmin_1980.nc4 (NC_FORMAT_NETCDF4_CLASSIC):"
> [1] ""
> [1] " 6 variables (excluding dimension variables):"
> [1] " short lambert_conformal_conic[] "
> [1] " grid_mapping_name: lambert_conformal_conic"
> [1] " longitude_of_central_meridian: -100"
> [1] " latitude_of_projection_origin: 42.5"
> [1] " false_easting: 0"
> [1] " false_northing: 0"
> [1] " standard_parallel: 25" " standard_parallel: 60"
> [1] " longitude_of_prime_meridian: 0"
> [1] " float lat[x,y] "
> [1] " units: degrees_north"
> [1] " long_name: latitude coordinate"
> [1] " standard_name: latitude"
> [1] " float lon[x,y] "
> [1] " units: degrees_east"
> [1] " long_name: longitude coordinate"
> [1] " standard_name: longitude"
> [1] " float time_bnds[nv,time] "
> [1] " float tmin[x,y,time] "
> [1] " long_name: daily minimum temperature"
> [1] " units: degrees C"
> [1] " missing_value: -9999"
> [1] " _FillValue: -9999"
> [1] " valid_range: -50" " valid_range: 50"
> [1] " coordinates: lat lon"
> [1] " grid_mapping: lambert_conformal_conic"
> [1] " cell_methods: area: mean time: minimum"
> [1] " short yearday[time] "
> [1] " long_name: yearday"
> [1] " valid_range: 1" " valid_range: 365"
> [1] ""
> [1] " 4 dimensions:"
> [1] " y Size:4823"
> [1] " units: m"
> [1] " long_name: y coordinate of projection"
> [1] " standard_name: projection_y_coordinate"
> [1] " x Size:5268"
> [1] " units: m"
> [1] " long_name: x coordinate of projection"
> [1] " standard_name: projection_x_coordinate"
> [1] " time Size:365 *** is unlimited ***"
> [1] " long_name: time"
> [1] " calendar: standard"
> [1] " units: days since 1980-01-01 00:00:00 UTC"
> [1] " bounds: time_bnds"
> [1] " nv Size:2"
> [1] ""
> [1] " 8 global attributes:"
> [1] " start_year: 1980"
> [1] " source: Daymet Software Version 2.0"
> [1] " Version_software: Daymet Software Version 2.0"
> [1] " Version_data: Daymet Data Version 2.1"
> [1] " Conventions: CF-1.4"
> [1] " citation: Please see http://daymet.ornl.gov/ for current
> Daymet data citation information"
> [1] " references: Please see http://daymet.ornl.gov/ for current
> information on Daymet references"
> [1] " institution: Oak Ridge National Laboratory Distributed Active
> Archive Center (ORNL DAAC)"
>
> The file can be downloaded from: http://daymet.ornl.gov/mosaics.html (The
> files with the daylength data are much smaller.)
> When I open the lat layer I see that the differences between consecutive
> cells are different depending on the location on the file, so I think that
> the sizes are not uniform.
> I am not sure how I can fix that.
>
There's nothing to fix, this is a regular grid in metres and is sensibly
specified by an extent in the projected coordinates - you don't need to
work with every cell's coordinate explicitly, and you can always generate
them on the fly as required - in whatever coordinate system you want. But I
don't think you need that at all.
Storing every coordinate in lon/lat arrays in that file is just an
unnecessary waste really, this is one of those "modelling/GIS" crossover
areas where things just don't quite mesh in a sensible way.
Cheers, Mike.
>
> Thanks a lot.
> Andi
> *Gesendet:* Freitag, 05. Juni 2015 um 23:53 Uhr
> *Von:* "Michael Sumner" <mdsumner at gmail.com>
> *An:* "Andrea Timmermann" <timmermann at gmx.at>, r-sig-geo at r-project.org
> *Betreff:* Re: [R-sig-Geo] Problem with raster package and nc4 file
>
> On Sat, 6 Jun 2015 at 08:04 Andrea Timmermann <timmermann at gmx.at> wrote:
>
>> Hi,
>>
>> I have daymet data in nc4 format and could open it with the ncdf4
>> package. I also have the coordinates of some polygons representing
>> ecological areas.
>> Both, the polygon vertices and the nc4 file have the same projection
>> (LCC) and units (degrees).
>
>
>
> Do you have grid data in LCC but stored with longitude/latitude
> coordinates? This is unfortunate, but you can restore the LCC grid
> probably. I would try
>
> r <- raster("tmin_1980.nc4")
>
> and then print it out and tell us the result (or post the errors if it
> fails):
>
> r
>
> Do you have the details of the LCC projection? At a bare minimum you need
> the centre longitude and centre latitude, and the two standard parallels,
> and the datum/ellipsoid. Can you open the file with ncdf4 and print out
> this?
>
> ncic <- nc_open("tmin_1980.nc4")
> print(ncic)
>
> You are not supposed to mix use of the ncdf4 package functions with those
> of raster, raster is designed to do all the work - but it does expect
> sensibly specified regular grids. If your data really are regular in LCC I
> would recommend sorting that out. Can you share the file, or a link to an
> analogous one?
>
> Once you have it sorted out in raster, you can read your shapefile in and
> do this
>
> meanpolydata <- extract(r, poly, fun = mean)
>
> Cheers, Mike.
>
>
>> What I would like to do is to get the average temperature for each
>> ecological area. So I wanted to use the polygons as a mask for the
>> temperature raster and then get the average temperature for each polygon.
>>
>> I wanted to create a raster object (using the raster function in the
>> raster package):
>>
>> ncic <- nc_open("tmin_1980.nc4")
>> raster(ncic, 'tmin')
>>
>> But I get this error:
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function ‘raster’ for signature
>> ‘"ncdf4"’
>>
>> Does anyone know how to fix this? Is there another way to get the data
>> that I need?
>>
>> I am a bit confused by the fact that the temperature data consists of one
>> matrix with latitude data, one with longitude data and one with the
>> temperature values. And by the fact that the spacing between the latitude
>> and longitude matrices is not uniform. Is the raster package accounting
>> somehow for this?
>>
>> Thanks a lot. Andi.
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
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