If you look at the file with ncview and analyse the header with ncdump -
h you will find that en extent is missing.
The standard tool ncview shows also a "flipped version"
Try to use gdal more directly like this snippet
library(raster)
library(gdalUtils)
library(mapview)
# necessary because of nc file see configuration options
http://www.gdal.org/frmt_netcdf.html
Sys.setenv(GDAL_NETCDF_BOTTOMUP="NO")
extentNC <- extent(0, 360,-60, 60)
proj4str <- '+proj=longlat +datum=WGS84 +no_defs'
ncfilename <- "PERSIANN-CDR_v01r01_20090101_c20140523.nc"
dataset<- "precipitation"
band <-1
x<-gdal_translate(paste0("NETCDF:",ncfilename,":",dataset),
paste0(ncfilename,".tif"),
b=band,
of="GTiff",
output_Raster=TRUE,
verbose=TRUE,
overwrite=TRUE)
# due to GDAL_NETCDF_BOTTOMUP="NO" we have to flip the raster
x <- flip(x, direction='y')
extent(x) <- extentNC
projection(x) <- proj4str
mapview(x)
plot(x)
cheers Chris
Am 03.02.2016 um 16:20 schrieb MAURICIO ZAMBRANO BIGIARINI:
On 3 February 2016 at 11:34, Michael Sumner <mdsum...@gmail.com> wrote:
On Thu, 4 Feb 2016 at 01:26 MAURICIO ZAMBRANO BIGIARINI
<mauricio.zambr...@ufrontera.cl> wrote:
Dear spatial community,
While reading some netCDFfiles with the raster package , I got a
"rotated" file, where the columns where read as rows and vice versa:
------------- START ----------------
x <- raster("PERSIANN-CDR_v01r01_20090101_c20140523.nc")
Loading required namespace: ncdf4
plot(x)
x
class : RasterLayer
dimensions : 1440, 480, 691200 (nrow, ncol, ncell)
resolution : 0.25, 0.25 (x, y)
extent : -60, 60, 0, 360 (xmin, xmax, ymin, ymax)
coord. ref. : NA
data source : /home/hzambran/PERSIANN-CDR_v01r01_20090101_c20140523.nc
names : NOAA.Climate.Data.Record.of.PERSIANN.CDR.daily.precipitation
z-value : 2009-01-01
zvar : precipitation
------------- END ----------------
Transpose might be sufficient?
tx <- t(x)
plot(tx)
tx
Thanks Michale,
In fact, that is what I'm doing for reading the files, and the spatial
extent is correct and the precipitation values also seems to be right.
However, my question was more "conceptual", in the sense that the
provider says that the original file is NOT rotated, while the only
way I have to get the correct files is rotating the original file
with the 't' command you mentioned.
In addition, while reading the file with the latest version of GRASS
GIS (7.0.3), and I got the following error message:
"
(Tue Feb 2 19:41:29 2016)
r.in.gdal input=/home/hzambran/PERSIANN-CDR_v01r01_20090101_c20140523.nc
output=PERSIANN_CDR_v01r01_20090101_c20140523 -e
Warning 1: dimension #2 (lat) is not a Longitude/X
dimension.
Warning 1: dimension #1 (lon) is not a Latitude/Y dimension.
ERROR: Input raster map is flipped or rotated - cannot import. You may
use 'gdalwarp' to transform the map to North-up.
"
So, I'm quite sure that the original file IS rotated, but I didn't
have more technical arguments to give to the data provider to
demonstrate that the file is rotated, because they insist that the
rotation is because R is not reading the file in the proper way....
mzb
=====================================
"In the end, it's not the years in your life that count.
It's the life in your years". (Abraham Lincoln)
=====================================
Linux user #454569 -- Linux Mint user
60W-60E and 0-360N, while the correct extent should be: 60S, 60N, 0E,
360E.
The file can be downloaded from:
ftp://data.ncdc.noaa.gov/cdr/persiann/files/2009/PERSIANN-CDR_v01r01_20090101_c20140523.nc
After contacting the providers of the file, they mentioned that when
reading the file I have to provide the dimension information, i.e.,
480 rows and 1440 columns, while the raster package detects the other
way around.
I would highly appreciate if you could tell me:
1) is the previous situation a bug of my netCDF driver (netCDF 4.1.3,
GDAL 1.11.2, released 2015/02/10) or a problem of the dimensions
actually recorded in the netCDF file ?
2) is there any way to overwrite the dimensions detected by netcdf4
when reading the file with the 'raster' command ?
My sessionInfo():
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] raster_2.5-2 sp_1.2-1
loaded via a namespace (and not attached):
[1] tools_3.2.3 Rcpp_0.12.3 ncdf4_1.15 grid_3.2.3
[5] lattice_0.20-33
Thanks in advance and kind regards
Mauricio Zambrano-Bigiarini, PhD
=====================================
Dept. of Civil Engineering
Faculty of Engineering and Sciences
Universidad de La Frontera
PO Box 54-D, Temuco, Chile
http://ingenieriacivil.ufro.cl/
=====================================
mailto : mauricio.zambr...@ufrontera.cl
work-phone : +56 45 259 2812
=====================================
"In the end, it's not the years in your life that count.
It's the life in your years". (Abraham Lincoln)
=====================================
Linux user #454569 -- Linux Mint user
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--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia
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