netcdf文件中的变量出现翻转

Question

我已经从中下载了一个nc文件

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"

然后我想使用变量soil_moisture_c

A = get.var.ncdf(nc=f,varid="soil_moisture_c",verbose=TRUE)

然后我绘制用image(A).我得到了下面显示的地图,我甚image(t(a))至改变了它,但是它改变了其他方向,而不是它应该如何.无论如何,为了知道出了什么问题,我使用netcdf查看器Panoply并正确绘制了地图,如下所示.

Answer 1

原因是您使用的NetCDF界面非常低级,您所做的就是读取变量而不显示任何维度信息.网格的方向实际上是任意的,并且需要在特定的上下文中理解坐标信息.

library(raster) ## requires ncdf package for this file  
d <- raster("LPRM-AMSR_E_L3_D_SOILM3_V002-20120520T185959Z_20040114.nc", varname = "soil_moisture_c")

(我使用了不同的文件,但它应该工作相同).

事实证明,即使是光栅也没有正常工作,但它确实很容易纠正:

d <-  flip(t(d), direction = "x")

转换数据并翻转"x"(经度),使地理配准保持原始上下文.

用maptools中的地图绘制它来检查:

plot(d)

library(maptools)
data(wrld_simpl)
plot(wrld_simpl, add = TRUE)

通过从文件中读取维度信息,还有许多其他方法可以实现这一点,但这至少是为您完成大部分艰苦工作的捷径.

Answer 2

作为@mdsumner更好的解决方案的补充,这里只是使用库的方法ncdf.

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

您所需要的只是找到您的尺寸,以便具有连贯的x和y轴.如果你看一下你的netCDF对象尺寸,你看到的是:

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"

因此,您的尺寸是:

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

现在你Latitude从90到90而不是相反,这image更喜欢,所以:

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

最后,正如您所注意到的,对象A的x和y被翻转,因此您需要对其进行转置,并且由于某些原因,您的NA值由值表示-32767:

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

最后的情节:

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

编辑:要对31个文件执行此操作,让我们调用您的文件名向量ncfiles和yourpath存储它们的目录(为简单起见,我将假设您的变量始终被调用,soil_moisture_c并且您的NA始终是-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()
    }