I have a shapefile of grid cells of 200km x 200km covering land areas of the world in Behrmann Equal Area Cylindrical projection. My goal is to convert the shapefile to +proj=longlat WGS84 format so I can match it to maps in commonly used projections such as wrld_simpl in maptools. However, I have not been successful and would appreciate some help with this.
rm(list = ls())
library(RCurl)
library(raster)
library(maptools)
library(rgdal)
data("wrld_simpl")
tmp <- tempfile() download.file("https://github.com/darunabas/extras/blob/master/temp_shapefile.zip?raw=true", destfile = tmp)
unzip(tmp, exdir = ".")
s <- rgdal::readOGR("temp_shapefile")
proj4string(s) = CRS("+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +ellps=WGS84 +units=m +no_defs")
p <- spTransform(s, CRS("+proj=longlat +datum=WGS84"))
I got the following error:
non finite transformation detected:
[,1] [,2] [,3] [,4]
Error in .spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args, :
failure in Polygons 1106 Polygon 1 points
In addition: Warning message:
In .spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args, :
2 projected point(s) not finite
I'm not very experienced in the geo-worls, but this might help:
library( sf )
sf <- read_sf( "./temp_shapefile.shp")
st_crs( sf ) <- "+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +ellps=WGS84 +units=m +no_defs"
sf2 <- st_transform( sf, crs = "+proj=longlat +datum=WGS84" )
Related
I'm trying to do some leaflet plots with San Francisco precinct shapefiles. It's worked before, but the precincts and their shapefiles have been updated & I can't seem to load them in a form that leaflet recognizes.
If I use st_read, the shapefile seems to load okay, but leaflet objects. If I do
sfprecincts <- readOGR(dsn=".",layer = "SF_DOE_PREC_2022_07_18_pg"), I get this warning message:
Warning messages:
1: In OGRSpatialRef(dsn, layer, morphFromESRI = morphFromESRI, dumpSRS = dumpSRS, :
Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=#null +wktext +no_defs
2: In OGRSpatialRef(dsn, layer, morphFromESRI = morphFromESRI, dumpSRS = dumpSRS, :
Discarded datum WGS_1984 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=#null +wktext +no_defs
3: In showSRID(wkt2, "PROJ") :
Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=#null +wktext +no_defs +type=crs
4: In showSRID(wkt2, "PROJ") :
Discarded datum World Geodetic System 1984 in Proj4 definition
I am struggling to open a NetCDF file and convert it into a raster using R. The
data is supposed to be on a regular grid of 25 km by 25 km. It contains sea
ice concentration in the Arctic.
library(terra)
#> terra 1.5.21
library(ncdf4)
file <- "~/Downloads/data_sat_Phil_changt_grid/SIC_SMMR_month_2015.nc"
I am getting a warning about the extent not found.
r <- rast(file)
#> Error in R_nc4_open: No such file or directory
#> Warning: [rast] GDAL did not find an extent. Cells not equally spaced?
We can see that there is a problem with the coordinates/extent.
r
#> class : SpatRaster
#> dimensions : 448, 304, 12 (nrow, ncol, nlyr)
#> resolution : 0.003289474, 0.002232143 (x, y)
#> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84
#> source : SIC_SMMR_month_2015.nc:sic
#> varname : sic
#> names : sic_1, sic_2, sic_3, sic_4, sic_5, sic_6, ...
I can open the nc file with nc_open() and I see that the coordinates are present.
nc <- nc_open(file)
names(nc$var)
#> [1] "lat" "lon" "sic"
lat <- ncvar_get(nc, "lat")
lon <- ncvar_get(nc, "lon")
dim(lat)
#> [1] 304 448
dim(lon)
#> [1] 304 448
dim(r)
#> [1] 448 304 12
Is it possible to assemble this data (the SIC values and the coordinates) to create a SpatRaster?
The nc file can be downloaded here: https://easyupload.io/pfth0s
Created on 2022-05-20 by the reprex package (v2.0.1)
The data are gridded, but the file does not specify the coordinates, nor the coordinate reference system. The file specifies the lon/lat values associated with the cells, but does not help us much, as these are clearly not on a regular grid. That is easy to see from plot(r)
NAflag(r) = -9999
plot(r,1)
And also from
p = cbind(as.vector(lon), as.vector(lat))
plot(p, cex=.1, xlab="lon", ylab="lat")
So what you need to find out, is which coordinate reference system (crs) is used, clearly some kind of polar crs. And what the extent of the data set is.
From the website you point to, I take it we can use:
crs(r) = "+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +k=1 +x_0=0 +y_0=0 +a=6378273 +b=6356889.449 +units=m +no_defs"
ext(r) = c(-3850000, 3750000, -5350000, 5850000)
r
#class : SpatRaster
#dimensions : 448, 304, 12 (nrow, ncol, nlyr)
#resolution : 25000, 25000 (x, y)
#extent : -3850000, 3750000, -5350000, 5850000 (xmin, xmax, ymin, ymax)
#coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +a=6378273 +b=6356889.449 +units=m +no_defs
#source : SIC_SMMR_month_2015.nc:sic
#varname : sic
#names : sic_1, sic_2, sic_3, sic_4, sic_5, sic_6, ...
The results look good:
g = geodata::gadm("Greenland", level=0, path=".")
gg = project(g, crs(r))
plot(r,1)
lines(gg)
But this is of course not a good way to do such things; the ncdf file should have contained all the metadata required.
Below is the rasterLayer RASTER_slope in a plot (4 NAs are shown in white):
Here is the metadata of RASTER_slope
class : RasterLayer
dimensions : 4, 4, 16 (nrow, ncol, ncell)
resolution : 500, 500 (x, y)
extent : 2227000, 2229000, 1316500, 1318500 (xmin, xmax, ymin, ymax)
crs : +proj=lcc +lat_0=12 +lon_0=-102 +lat_1=17.5 +lat_2=29.5 +x_0=2500000 +y_0=0 +datum=WGS84 +units=m +no_defs
source : memory
names : values
values : -143.2145, 214.1981 (min, max)
Then I used mapview to get a dynamic visualization of RASTER_slope:
> mapview(RASTER_slope)
Warning messages:
1: In showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=#null +wktext +no_defs +type=crs
2: In showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
Discarded datum World Geodetic System 1984 in Proj4 definition
3: In showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=#null +wktext +no_defs +type=crs
4: In showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
Discarded datum World Geodetic System 1984 in Proj4 definition
The resulting mapview object looks like this:
The mapview object is displaying only 2 pixels with NA.
Probably I am wrong but I have the feeling that the key here is to pass a crs to RASTER_slope in a WKT format but I do not know how to do that.
Any help will be appreciated.
Following #dww, the key is in adding method="ngb" when calling mapview, no need to re project the rasterLayer, though. Here the code and output
mapview(RASTER_slope, method="ngb", na.color="transparent")
I am trying to plot data in R using mapView for the grid in the Pacific that crosses the longitude 180deg. The native crs is "+proj=merc +lon_0=150 +lat_ts=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0".
The example of equivalent data is:
test.coords<-as.data.frame(cbind(c(runif(15,-180,-130),runif(5,160,180)),runif(20,40,60)))
test.sp <- SpatialPointsDataFrame(coords = cbind(test.coords$V1,test.coords$V2), data = test.coords,
proj4string = CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"))
test.sp <- spTransform(test.sp,
"+proj=merc +lon_0=150 +lat_ts=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0")
plot(test.sp)
mapview(test.sp)
When using plot function, the points are centered, while using mapView they get split between two sides of the map (linked image). Can the view using mapView be centered on a different longitude?
Using native crs for this map does not help. I get an error.
mapview(plot, native.crs=TRUE)
Warning message:
sf layer is not long-lat data
Thank you
mapView image Pacific
Ok, so this is a semi-optimal solution to your question for several reasons:
this will only work for point data
it may not scale well for large point collections
projecting to another CRS may not work anymore (though that is not really related, as the issue at hand is about visualising)
For sets of lines or polygons, we would need another approach, but I am currently not aware of a sp/sf native solution to round-tripping coordinates of an object.
library(sp)
library(sf)
#> Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
library(mapview)
test.coords<-as.data.frame(cbind(c(runif(15,-180,-130),runif(5,160,180)),runif(20,40,60)))
test.sp <- SpatialPointsDataFrame(coords = cbind(test.coords$V1,test.coords$V2), data = test.coords,
proj4string = CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"))
test_sf = st_as_sf(test.sp)
shift = function(x) {
geom = st_geometry(x)
st_geometry(x) = st_sfc(
lapply(seq_along(geom), function(i) {
geom[[i]][1] = ifelse(geom[[i]][1] < 0, geom[[i]][1] + 360, geom[[i]][1])
return(geom[[i]])
})
, crs = st_crs(geom)
)
return(x)
}
mapview(shift(test_sf)) +
mapview(test_sf, col.regions = "orange")
Created on 2019-12-11 by the reprex package (v0.3.0)
I chose to use sf rather than sp for this because mapview uses sf internally and was hoping to find a general approach to this problem which could potentially be integrated.
Here is a workaround for polygons - it produces some warnings, but overall does the job.
# transform grid to standard latitude and longitude
# original grid in crs "+proj=merc +lon_0=150 +lat_ts=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"
grid<-spTransform(grid,"+init=epsg:4326")
summary(coordinates(grid))
# V1 V2
# Min. :-179.8 Min. :37.17
# 1st Qu.:-168.8 1st Qu.:51.70
# Median :-154.3 Median :55.02
# Mean :-118.0 Mean :54.65
# 3rd Qu.:-131.4 3rd Qu.:58.31
# Max. : 179.8 Max. :65.56
out <- lapply(1:length(grid), function(i) grid[i, ])
for (i in 1:length(grid)) {
cds <- slot(slot(slot(out[[i]], "polygons")[[1]], "Polygons")[[1]], "coords")
cds_polygon <- Polygons(list(Polygon(cds)), ID="out.x")
out.x <- SpatialPolygons(list(cds_polygon))
proj4string(out.x) <- CRS("+init=epsg:4326")
if (cds[1,1]>0) { # depending to which side one want to move polygons that are on both sides of International Date Line
out.y <- elide(out.x, shift=c(-360,0))
} else {
out.y<-out.x}
if(i==1){grid.shifted<-out.y} else {
grid.shifted<-raster::union(grid.shifted,out.y)
}
}
# add data in the original grid
grid.shifted <- SpatialPolygonsDataFrame(grid.shifted, grid#data, match.ID = F)
mapview(grid.shifted)
I have a problem to use the over function.
CRS.new=CRS("+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0")
proj4string(ANFR_IDF)=CRS.new
proj4string(parti)=CRS.new
test=over(pc100m,parti)
> Erreur : identicalCRS(x, y) is not TRUE
crs(parti)
> CRS arguments:
+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
crs(ANFR_IDF)
> CRS arguments:
+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
test=over(parti,pc100m)
>Erreur : identicalCRS(x, y) is not TRUE
I don't understand what is hapenning. Any idea?
Many thanks!
I had a similar issue in my program when I used the same projection string.
I added "+init=epsg:4326" component at the beginning of the projection string and noticed some transformation operations (package concaveman in my case) remove this component, so identicalCRS function returned FALSE.
Try to include "+init" component in your projection string.