R-sig-Geo Digest, Vol 189, Issue 3

The problem might be in the PROJ version; PROJ has seen a lot of
development the last few years. I'm on

Linking to GEOS 3.7.0, GDAL 2.4.0, PROJ 5.2.0

Since you are on ubuntu, it should be pretty easy to get that too; see
sf github pages for installing from ppa:ubuntugis-unstable:
https://github.com/r-spatial/sf

On 5/4/19 5:19 PM, Maurizio Marchi wrote:

Dear Prof.
Many thanks for your quick reply. Anyway I still have some differences
with your output, as well as some errors in the R console. Actually,
practically speaking, in my .png plot (attached) the origin of the axes
is still in Germany and the left and right borders of the image are
still rectilinear.

*Here my R output using your code with the sessionInfo() at the end. I
hope it helps*

R version 3.6.0 (2019-04-26) -- "Planting of a Tree" Copyright (C) 2019
The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu
(64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You
are welcome to redistribute it under certain conditions. Type
'license()' or 'licence()' for distribution details. Natural language
support but running in an English locale R is a collaborative project
with many contributors. Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications. Type
'demo()' for some demos, 'help()' for on-line help, or 'help.start()'
for an HTML browser interface to help. Type 'q()' to quit R. > f =
'tas_rcp85_land-rcm_eur_12km_01_mon_198012-208011.nc
<http://tas_rcp85_land-rcm_eur_12km_01_mon_198012-208011.nc>' >
library(stars) Loading required package: abind Loading required package:
sf Linking to GEOS 3.6.2, GDAL 2.2.3, PROJ 4.9.3 > r = read_ncdf(f,
ncsub = cbind(start = c(1, 1, 1, 1), count = c(418, 406, 3, 1)),
eps=1e-3) > rx = read_stars(f, proxy = TRUE) # only for the crs! Warning
messages: 1: In CPL_read_gdal(as.character(x), as.character(options),
as.character(driver), : GDAL Message 1: The dataset has several
variables that could be identified as vector fields, but not all share
the same primary dimension. Consequently they will be ignored. 2: In
CPL_read_gdal(as.character(x), as.character(options),
as.character(driver), : GDAL Message 1: dimension #1 (time) is not a
Time dimension. 3: In CPL_read_gdal(as.character(x),
as.character(options), as.character(driver), : GDAL Message 1: dimension
#0 (ensemble_member) is not a Time dimension. > st_crs(r) = st_crs(rx) >
r0 = stars:::st_transform_proj.stars(r, 4326) > plot(r0[,,,1], border =
NA, axes = TRUE, reset = FALSE) Warning messages: 1: In
classInt::classIntervals(na.omit(values), min(nbreaks - 1, n.unq), : N
is large, and some styles will run very slowly; sampling imposed 2: In
st_is_longlat(x) : bounding box has potentially an invalid value range
for longlat data 3: In st_is_longlat(x) : bounding box has potentially
an invalid value range for longlat data 4: In st_is_longlat(x) :
bounding box has potentially an invalid value range for longlat data 5:
In st_is_longlat(x) : bounding box has potentially an invalid value
range for longlat data 6: In st_is_longlat(x) : bounding box has
potentially an invalid value range for longlat data >
library(rnaturalearth) > plot(ne_coastline(returnclass = "sf"), add =
TRUE, col = 'orange') Warning message: In
plot.sf(ne_coastline(returnclass = "sf"), add = TRUE, col = "orange") :
ignoring all but the first attribute > sessionInfo() R version 3.6.0
(2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under:
Ubuntu 18.04.2 LTS Matrix products: default BLAS:
/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK:
/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 locale: [1]
LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8
LC_COLLATE=en_GB.UTF-8 LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages:
[1] stats graphics grDevices utils datasets methods base other attached
packages: [1] rnaturalearth_0.1.0 stars_0.3-1 sf_0.7-4 abind_1.4-5
loaded via a namespace (and not attached): [1] Rcpp_1.0.1 magrittr_1.5
units_0.6-3 tidyselect_0.2.5 lattice_0.20-38 R6_2.4.0 rlang_0.3.4 [8]
rnaturalearthdata_0.2.0 dplyr_0.8.0.1 tools_3.6.0 parallel_3.6.0
grid_3.6.0 KernSmooth_2.23-15 ncmeta_0.0.4 [15] e1071_1.7-1 DBI_1.0.0
class_7.3-15 assertthat_0.2.1 tibble_2.1.1 RNetCDF_1.9-1 crayon_1.3.4
[22] tidyr_0.8.3 purrr_0.3.2 PCICt_0.5-4.1 glue_1.3.1 sp_1.3-1
compiler_3.6.0 pillar_1.3.1 [29] classInt_0.3-3 pkgconfig_2.0.2


--
Maurizio Marchi,
PhD Forest Science - Ecological Mathematics
Skype ID: maurizioxyz
linux user 552742
#EUFGIS national Focal point for Italy
#Annals of Silvicultural Research Associated Editor
https://scholar.google.it/citations?hl=en&user=_2X6fu8AAAAJ
<https://scholar.google.it/citations?hl=en&user=_2X6fu8AAAAJ*>




Il giorno sab 4 mag 2019 alle ore 12:10 <r-sig-geo-request at r-project.org
<mailto:r-sig-geo-request at r-project.org>> ha scritto:

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    Message: 1
    Date: Fri, 3 May 2019 16:58:01 +0200
    From: Edzer Pebesma <edzer.pebesma at uni-muenster.de
    <mailto:edzer.pebesma at uni-muenster.de>>
    To: r-sig-geo at r-project.org <mailto:r-sig-geo at r-project.org>
    Subject: Re: [R-sig-Geo] Strange spatial reference system netCDF
    Message-ID: <82193e8b-8fcc-3308-7874-a22ae6985c01 at uni-muenster.de
    <mailto:82193e8b-8fcc-3308-7874-a22ae6985c01 at uni-muenster.de>>
    Content-Type: text/plain; charset="utf-8"

    Dear Maurizio,

    an attempt to do something along this line is:

    f = "tas_rcp85_land-rcm_eur_12km_01_mon_198012-208011.nc
    <http://tas_rcp85_land-rcm_eur_12km_01_mon_198012-208011.nc>"
    library(stars)
    r = read_ncdf(f, ncsub = cbind(start = c(1, 1, 1, 1), count = c(418,
    406, 3, 1)), eps=1e-3)
    rx = read_stars(f, proxy = TRUE) # only for the crs!
    st_crs(r) = st_crs(rx)
    r0 = stars:::st_transform_proj.stars(r, 4326)
    png("x.png")
    plot(r0[,,,1], border = NA, axes = TRUE, reset = FALSE)
    library(rnaturalearth)
    plot(ne_coastline(returnclass = "sf"), add = TRUE, col = 'orange')

    Note that the output object time stamps respect the 360-day calendar
    (using pkg PCICt).

    You'll find some discussion, and the output image, here:
    https://github.com/r-spatial/stars/issues/175

    Feel free to post follow-up questions here, or to github.

    On 5/2/19 6:49 PM, Maurizio Marchi wrote:

    > Dear list,
    > I'm working with large netCDF files from the UK Climate

    Projections portal (

    > https://www.metoffice.gov.uk/research/collaboration/ukcp). More in

    detail

    > I'm reading with the ncdf4 library this
    >

    <

http://data.ceda.ac.uk/badc/ukcp18/data/land-rcm/eur/12km/rcp85/01/tas/mon/latest/

    > file. Once loaded O can easily handle it but it is a strange

reference

    > system as follow:
    > rotated_latitude_longitude[]
    >             grid_mapping_name: rotated_latitude_longitude
    >             longitude_of_prime_meridian: 0
    >             earth_radius: *6371229*
    >             grid_north_pole_latitude: 39.25
    >             grid_north_pole_longitude: 198
    >             north_pole_grid_longitude: 0
    > If I load the .nc file in QGIS I see that the SR is "+proj=longlat
    > +a=6371229 +b=6371229 +no_defs" where the values associated to *a*

and

    > *b* variables
    > are the earth radius. Even if QGIS can read it, the raw file isn't
    > projected properly (it seems tha QGIS is not able to handle such
    > projection).
    > Finally, using the ncdf4+raster libraries, I can easily generate e

    raster

    > image but then I'm not able to understand I could I re project

    this raster

    > in WGS84 reference system.
    > Any helps?
    > Cheers
    >
    > --
    > Maurizio Marchi,
    > PhD Forest Science - Ecological Mathematics
    > Skype ID: maurizioxyz
    > linux user 552742
    > #EUFGIS national Focal point for Italy
    > #Annals of Silvicultural Research Associated Editor
    > https://scholar.google.it/citations?hl=en&user=_2X6fu8AAAAJ
    > <https://scholar.google.it/citations?hl=en&user=_2X6fu8AAAAJ*>
    >
    >       [[alternative HTML version deleted]]
    >
    > _______________________________________________
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    --
    Edzer Pebesma
    Institute for Geoinformatics
    Heisenbergstrasse 2, 48151 Muenster, Germany
    Phone: +49 251 8333081

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--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081