Error plotting data from netcdf file “increasing x

问题:

I want to plot sea surface temperature data from a regular grid but can't find the proper way to do it. My data comes in nc format and can be downloaded from http://www.nodc.noaa.gov/SatelliteData/pathfinder4km/

I use this R code to access data but the problem appears when trying to plot

library("ncdf")
download.file("ftp://ftp.nodc.noaa.gov/pub/data.nodc/pathfinder/Version5.2/2003/20030715000715-NODC-L3C_GHRSST-SSTskin-AVHRR_Pathfinder-PFV5.2_NOAA17_G_2003196_night-v02.0-fv02.0.nc", destfile="sst.nc")
data=open.ncdf("sst.nc")
x <- get.var.ncdf(data,"lon")
y <- get.var.ncdf(data,"lat")
sst=get.var.ncdf(data,"sea_surface_temperature")

filled.contour(x,y,sst, color = terrain.colors, asp = 1)

And then get this error message

Error en filled.contour(x, y, sst, color = terrain.colors, asp = 1) : increasing 'x' and 'y' values expected

I think the problem comes from y coordinate, latitude runs from 90 to -90. I've seen some questions on stackoverflow in creating a new grid with akima package but it should not be necessary in this case.

Here you can find a summary of data file

http://ubuntuone.com/1mIdYVqoePn24gKQbtXy7K

Thanks in advance for your help

SOLVED

Thanks to Paul Hiemstra

The point was not read lat-lon values from data set but to know the i,j coordinates of data points in the matrix and then select the geographic area I want to plot. Following are the commands that work for me:

library("ncdf")
download.file("ftp://ftp.nodc.noaa.gov/pub/data.nodc/pathfinder/Version5.2/2003/20030715000715-NODC-L3C_GHRSST-SSTskin-AVHRR_Pathfinder-PFV5.2_NOAA17_G_2003196_night-v02.0-fv02.0.nc", destfile="sst.nc")
data=open.ncdf("sst.nc")
sst=get.var.ncdf(data,"sea_surface_temperature")
x = seq(1, 8640, length.out = nrow(sst))         # Matrix dimension 8640x4320
y = seq(1, 4320, length.out = ncol(sst))

sst1 <- sst[c(1000:1500),c(1000:1500)]           # Subsetting a region
x = seq(1, 500, length.out = nrow(sst1))
y = seq(1, 500, length.out = ncol(sst1))

png(filename="sst.png",width=800,height=600,bg="white")
filled.contour(x,y,sst1, color = terrain.colors, asp = 1)
dev.off()

Now I have to figure out how to label the plot with longtiude and latitude at x-y coordinates.

回答1:

The problem is probably the following. Your x and y variables are of the same size of sst, i.e. they provide maps of x and y coordinates. What the filled_contour function needs is not these maps, but more simply the x and y coordinates associated with the rows and columns in sst with increasing x values.

回答2:

Although my question was solved with the help of Paul Hiemstra I've still investigated on plotting my netcdf data and found another thread in Stackoverflow that has also helped me. It uses image instead of filled.contour.

You can find the thread at The variable from a netcdf file comes out flipped

Now, this is the code I am using to plot SST data:

library("ncdf")
download.file("ftp://ftp.nodc.noaa.gov/pub/data.nodc/pathfinder/Version5.2/2000/20000107010122-NODC-L3C_GHRSST-SSTskin-AVHRR_Pathfinder-PFV5.2_NOAA14_G_2000007_night-v02.0-fv01.0.nc", destfile="sst.nc")
data=open.ncdf("sst.nc")


sst=get.var.ncdf(data,"sea_surface_temperature")
lon=get.var.ncdf(data,"lon")
lat=get.var.ncdf(data,"lat")

data$dim$lon$vals -> lon
data$dim$lat$vals -> lat
lat <- rev(lat)
sst <- sst[,ncol(sst):1]
png(filename="sst2.png",width=1215,height=607,bg="white")
image(lon, lat, sst, zlim=c(270,320), col = heat.colors(37))
library("sp", lib.loc="/usr/lib/R/site-library")
library("maptools", lib.loc="/usr/lib/R/site-library")
data(wrld_simpl)
plot(wrld_simpl, add = TRUE)
dev.off()

that leads to this image: