raster pkg: overwriting the dimensions detected by netcdf4 (PERSIANN-CDR)

On 3 February 2016 at 11:34, Michael Sumner <mdsumner at gmail.com> wrote:

On Thu, 4 Feb 2016 at 01:26 MAURICIO ZAMBRANO BIGIARINI
<mauricio.zambrano at 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.

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.zambrano at 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

--
La informaci?n contenida en este correo electr?nico y cualquier anexo o
respuesta relacionada, puede contener datos e informaci?n confidencial y no
puede ser usada o difundida por personas distintas a su(s) destinatario(s).
Si usted no es el destinatario de esta comunicaci?n, le informamos que
cualquier divulgaci?n, distribuci?n o copia de esta informaci?n constituye
un delito conforme a la ley chilena. Si lo ha recibido por error, por favor
borre el mensaje y todos sus anexos y notifique al remitente.