Hello
I'm working with a large hydrological data set stored in a netCDF format.
The file stores x and y coordinates in the UTM projected coordinate system,
yet when I use image to graphically display the z variable, the image is
distorted in the sense that it does not plot the map in the correct spatial
organization.
I'm wondering if I need to define the projection of the netCDF file with
rgdal or proj4 routines first before I send it to the graphics device.
My code is as follows:
q1_2001 <- open.ncdf("H:\\SKF_DESKTOP FILES\\My
Documents\\EDEN\\EDEN\\Surfaces\\2000_q1.nc", readunlimi=FALSE) #opens ncdf
file for reading
wat.data2000q1 <- get.var.ncdf(q1_2001, verbose=FALSE ) # gets the real
information
# GENERAL EXAMINATION OF HEADER DATA in the wat.data file
day <- get.var.ncdf(q1_2001, "time") # length(day) 91 days in
quarter
UTMx <- get.var.ncdf(q1_2001, "x") # columns (eastings) #
should
return 405
UTMy <- get.var.ncdf(q1_2001, "y") # rows (northings)
#
should return 287
# plot first 91 days (3 months of the year)
for(i in 1:91) {
!is.na( image(UTMx, UTMy, z = wat.data2001q1[,,i], col=brewer.pal(8,
"YlGnBu"),
axes=T, pty="s", ylab="UTM Northing",
xlab="UTM Easting",
main = "First Quater 2001") )
}
As I indicated above the map is displayed on the graphics device. However
the orientation is distorted pulling the x axis to wide and the y axis too
tall. How can I set the graphics device to know the orientation and
scaling (if these are the correct terms) in order to display this map
correctly?
All insights will be greatly appreciated.
Thanks
Steve
Steve Friedman Ph. D.
Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
Office (305) 224 - 4282
Steve_Friedman at nps.gov
Hi Steve, If you read your netCDF files into R you end up with sp-classes which can be displayed using spplot. But you do not seem to use rgdal. If you can make a data.frame with the x, y and z coordinates this can quite easily be transformed into an sp-class: library(sp) dat = data.frame(x = UTMx, y = UTMy, z = wat.data2001q1,,i]) coordinates(dat) = ~x+y # "tell" spplot what the names of the columns with the x and y coordinates are gridded(dat) = TRUE # make clear it is a grid spplot(dat) For more details see the documentation for the sp-package, especially spplot. These kinds of questions are more suitable for the r-sig-geo mailing list and not the general r-help list. hope this helps, Paul Steve_Friedman at nps.gov schreef:> Hello > > I'm working with a large hydrological data set stored in a netCDF format. > The file stores x and y coordinates in the UTM projected coordinate system, > yet when I use image to graphically display the z variable, the image is > distorted in the sense that it does not plot the map in the correct spatial > organization. > > I'm wondering if I need to define the projection of the netCDF file with > rgdal or proj4 routines first before I send it to the graphics device. >Defining the projection is not needed> My code is as follows: > > q1_2001 <- open.ncdf("H:\\SKF_DESKTOP FILES\\My > Documents\\EDEN\\EDEN\\Surfaces\\2000_q1.nc", readunlimi=FALSE) #opens ncdf > file for reading > wat.data2000q1 <- get.var.ncdf(q1_2001, verbose=FALSE ) # gets the real > information > > # GENERAL EXAMINATION OF HEADER DATA in the wat.data file > day <- get.var.ncdf(q1_2001, "time") # length(day) 91 days in quarter > UTMx <- get.var.ncdf(q1_2001, "x") # columns (eastings) # should > return 405 > UTMy <- get.var.ncdf(q1_2001, "y") # rows (northings) # > should return 287 > > # plot first 91 days (3 months of the year) > for(i in 1:91) { > !is.na( image(UTMx, UTMy, z = wat.data2001q1[,,i], col=brewer.pal(8, > "YlGnBu"), > axes=T, pty="s", ylab="UTM Northing", xlab="UTM Easting", > main = "First Quater 2001") ) > } > > As I indicated above the map is displayed on the graphics device. However > the orientation is distorted pulling the x axis to wide and the y axis too > tall. How can I set the graphics device to know the orientation and > scaling (if these are the correct terms) in order to display this map > correctly? > > All insights will be greatly appreciated. > > Thanks > Steve > > Steve Friedman Ph. D. > Spatial Statistical Analyst > Everglades and Dry Tortugas National Park > 950 N Krome Ave (3rd Floor) > Homestead, Florida 33034 > > Office (305) 224 - 4282 > Steve_Friedman at nps.gov > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +31302535773 Fax: +31302531145 http://intamap.geo.uu.nl/~paul
Hi Steve, (I'm replying to your e-mail at the mailing list to get it included there also) I've written some stuff on graphs with sp at the R wiki: http://wiki.r-project.org/rwiki/doku.php?id=tips:spatial-data:spatial_data_visualization or have a look at the gallery containing plots with the code that created them: http://r-spatial.sourceforge.net/gallery/ cheers! Paul Steve_Friedman at nps.gov wrote:> Hello > > I'm working with a large hydrological data set stored in a netCDF format. > The file stores x and y coordinates in the UTM projected coordinate system, > yet when I use image to graphically display the z variable, the image is > distorted in the sense that it does not plot the map in the correct spatial > organization. > > I'm wondering if I need to define the projection of the netCDF file with > rgdal or proj4 routines first before I send it to the graphics device. > > My code is as follows: > > q1_2001 <- open.ncdf("H:\\SKF_DESKTOP FILES\\My > Documents\\EDEN\\EDEN\\Surfaces\\2000_q1.nc", readunlimi=FALSE) #opens ncdf > file for reading > wat.data2000q1 <- get.var.ncdf(q1_2001, verbose=FALSE ) # gets the real > information > > # GENERAL EXAMINATION OF HEADER DATA in the wat.data file > day <- get.var.ncdf(q1_2001, "time") # length(day) 91 days in quarter > UTMx <- get.var.ncdf(q1_2001, "x") # columns (eastings) # should > return 405 > UTMy <- get.var.ncdf(q1_2001, "y") # rows (northings) # > should return 287 > > # plot first 91 days (3 months of the year) > for(i in 1:91) { > !is.na( image(UTMx, UTMy, z = wat.data2001q1[,,i], col=brewer.pal(8, > "YlGnBu"), > axes=T, pty="s", ylab="UTM Northing", xlab="UTM Easting", > main = "First Quater 2001") ) > } > > As I indicated above the map is displayed on the graphics device. However > the orientation is distorted pulling the x axis to wide and the y axis too > tall. How can I set the graphics device to know the orientation and > scaling (if these are the correct terms) in order to display this map > correctly? > > All insights will be greatly appreciated. > > Thanks > Steve > > Steve Friedman Ph. D. > Spatial Statistical Analyst > Everglades and Dry Tortugas National Park > 950 N Krome Ave (3rd Floor) > Homestead, Florida 33034 > > Office (305) 224 - 4282 > Steve_Friedman at nps.gov > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +31302535773 Fax: +31302531145 http://intamap.geo.uu.nl/~paul