The variable from a netcdf file comes out flipped

netcdf, r

Solution

Just as a complement to @mdsumner far better solution, here is a way to do that using library `ncdf` only.

library(ncdf)
f <- open.ncdf("LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040101.nc")
A <- get.var.ncdf(nf,"soil_moisture_c")

All you need is to find your dimensions in order to have a coherent x and y-axis. If you look at your netCDF objects dimensions, here what you see:

str(f$dim)
List of 2
 $ Longitude:List of 8
  ..$ name         : chr "Longitude"
  ..$ len          : int 1440
  ..$ unlim        : logi FALSE
  ..$ id           : int 1
  ..$ dimvarid     : num 2
  ..$ units        : chr "degrees_east"
  ..$ vals         : num [1:1440(1d)] -180 -180 -179 -179 -179 ...
  ..$ create_dimvar: logi TRUE
  ..- attr(*, "class")= chr "dim.ncdf"
 $ Latitude :List of 8
  ..$ name         : chr "Latitude"
  ..$ len          : int 720
  ..$ unlim        : logi FALSE
  ..$ id           : int 2
  ..$ dimvarid     : num 1
  ..$ units        : chr "degrees_north"
  ..$ vals         : num [1:720(1d)] 89.9 89.6 89.4 89.1 88.9 ...
  ..$ create_dimvar: logi TRUE
  ..- attr(*, "class")= chr "dim.ncdf"

Hence your dimensions are:

 f$dim$Longitude$vals -> Longitude
 f$dim$Latitude$vals -> Latitude

Now your `Latitude` goes from 90 to -90 instead of the opposite, which `image` prefers, so:

 Latitude <- rev(Latitude)
 A <- A[nrow(A):1,]

Finally, as you noticed, the x and y of your object A are flipped so you need to transpose it, and your NA values are represented for some reasons by value `-32767`:

A[A==-32767] <- NA
A <- t(A)

And finally the plot:

image(Longitude, Latitude, A)
library(maptools)
data(wrld_simpl)
plot(wrld_simpl, add = TRUE)

Edit: To do that on your 31 files, let's call your vector of file names `ncfiles` and `yourpath` the directory where you stored them (for simplicity i'm going to assume your variable is always called `soil_moisture_c` and your NAs are always `-32767`):

ncfiles
 [1] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040101.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040102.nc"
 [3] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040103.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040104.nc"
 [5] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040105.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040106.nc"
 [7] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040107.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040108.nc"
 [9] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040109.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040110.nc"
[11] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040111.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040112.nc"
[13] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040113.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040114.nc"
[15] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040115.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040116.nc"
[17] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040117.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040118.nc"
[19] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040119.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040120.nc"
[21] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040121.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040122.nc"
[23] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040123.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040124.nc"
[25] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040125.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040126.nc"
[27] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040127.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040128.nc"
[29] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040129.nc" "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040130.nc"
[31] "LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T173800Z_20040131.nc"

yourpath
 [1] "C:\\Users"

library(ncdf)
library(maptools)
data(wrld_simpl)
for(i in 1:length(ncfiles)){
    f <- open.ncdf(paste(yourpath,ncfiles[i], sep="\\"))
    A <- get.var.ncdf(f,"soil_moisture_c")
    f$dim$Longitude$vals -> Longitude
    f$dim$Latitude$vals -> Latitude
    Latitude <- rev(Latitude)
    A <- A[nrow(A):1,]
    A[A==-32767] <- NA
    A <- t(A)
    close.ncdf(f) # this is the important part
    png(paste(gsub("\\.nc","",ncfiles[i]), "\\.png", sep="")) # or any other device such as pdf, jpg...
    image(Longitude, Latitude, A)
    plot(wrld_simpl, add = TRUE)
    dev.off()
    }

Problem

I have downloaded a nc file from ``` f=open.ncdf("file.nc") [1] "file Lfile.nc has 2 dimensions:" [1] "Longitude Size: 1440" [1] "Latitude Size: 720" [1] "------------------------" [1] "file filr.nc has 8 variables:" [1] "short ts[Latitude,Longitude] Longname:Skin Temperature (2mm) Missval:NA" ``` I then wanted to work with the variable soil_moisture_c ``` A = get.var.ncdf(nc=f,varid="soil_moisture_c",verbose=TRUE) ``` I then plot A with `image(A)`. I got the map shown below,I even transposed it `image(t(a))` but that was changed to other direction,and not how it should be. Anyway,in order to know what is wrong,I used the netcdf viewer Panoply and the map was correctly plotted as you can see below.

Original source