在带有ncdf4的R中，打开netcdf文件，修改并保存到磁盘

Question

我正在尝试修改并保存R中的netcdf文件。我可以修改这些值，但似乎不能让文件保存和保留修改后的值。下面是我正在做的事情：

使用ncdf4包打开文件

library(ncdf4)
nc=nc_open('RMinit_newvalues2017.nc', write=T)

重新分配缺失值-该文件有2000个变量，大约一半需要修改它们的缺失值，我可以成功地做到这一点：

for (i in 1:10){
   print(nc$var[[i]]$name) # use to match aaR/aaS
   test=grep("_Nums", nc$var[[i]]$name) # search for Nums, skip to next
   if (length(test) ==1){
     next
   }
   test2=grep("_ResN", nc$var[[i]]$name) # search for RN
    if (length(test2) == 1) {
      print(nc$var[[i]]$missval) # print orginal value
      print(xR$RN[which(xR$Variables==nc$var[[i]]$name)]) # print new value
      nc$var[[i]]$missval=xR$RN[which(xR$Variables==nc$var[[i]]$name)] # assign new value
      print(nc$var[[i]]$missval) # print assigned value

    } else if (length(test2) != 1) {
       print(nc$var[[i]]$missval)
       print(xS$SN[which(xS$Variables==nc$var[[i]]$name)])
       nc$var[[i]]$missval=xS$SN[which(xS$Variables==nc$var[[i]]$name)]
       print(nc$var[[i]]$missval)

    }
}

下面是带注释的输出，显示它正在更改'_ResN‘和’_StructN‘的值：

[1] "Anchovies10_Nums" (nothing done here, next)
[1] "Anchovies10_ResN" (first replacement)
[1] 987.7794 (original value)
[1] 200.1975 (replacement value, printed after assignment)
[1] "Anchovies10_StructN" (repeat pattern...)
[1] 372.7469
[1] 75.54621
[1] "Anchovies1_Nums"
[1] "Anchovies1_ResN"
[1] 130.3665
[1] 15.67022
[1] "Anchovies1_StructN"
[1] 49.19491
[1] 5.913289
[1] "Anchovies2_Nums"
[1] "Anchovies2_ResN"
[1] 228.1891
[1] 34.30677
[1] "Anchovies2_StructN"
[1] 86.10911
[1] 12.94595
[1] "Anchovies3_Nums"

最后，我同步并关闭nc文件，这应该会将其保存到磁盘。但这里什么都没发生。没有错误，一切看起来都很好，除了文件没有保存。我错过了什么？

nc_sync(nc)
nc_close(nc)

编辑:在循环中切换命令后，我能够获得要保存的文件。与使用nc$var[[i]]$missval=...赋值相比，使用ncatt_put似乎可以解决这个问题。我还意识到我一开始就编辑了错误的值，因为我需要更改_Fillvalue，而不是missval。这现在起作用了：

for (i in 1:dim(a)[1]){
test=grep("_Nums", nc$var[[i]]$name) # search for Nums, skip to next
if (length(test) ==1){
  next
}
test2=grep("_ResN", nc$var[[i]]$name) # search for RN
if (length(test2) == 1) {
  ncatt_put(nc,a[i,1],"_FillValue", xR$RN[which(xR$Variables==nc$var[[i]]$name)])
} else if (length(test2) != 1) {
  ncatt_put(nc,a[i,1],"_FillValue", xS$SN[which(xS$Variables==nc$var[[i]]$name)])  
}
nc_sync(nc)
}
nc_sync(nc)
nc_close(nc)

Answer 1

将我的解决方案发布为一个FYI，也许是为了帮助别人……

我暂时解决了我的问题。仍然不确定为什么第一次尝试没有更新文件。我需要使用ncdf4::ncatt_put编辑_FillValue的属性，使用ncdf4::ncvar_put添加数据。然后，在循环中执行nc_sync会有所帮助。

for (i in 1:length(b)){
  vv=as.numeric(b[i]) # index of ResN and StructN in entire list of nc file 'a'
  testSN=grep("_StructN", a[vv,1]) # use to select SN values
  testRN=grep("_ResN", a[vv,1]) # use to select RN values

  if (length(testRN) ==1){
    ncatt_put(nc,a[vv,1],"_FillValue", xR$RN[which(xR$Variables==a[vv,1])])
    ncvar_put(nc,a[vv,1], rep(xR$RN[which(xR$Variables==a[vv,1])],150)) # replicate 5x30
  } else if (length(testSN) ==1){
    ncatt_put(nc,a[vv,1],"_FillValue", xS$SN[which(xS$Variables==a[vv,1])])
    ncvar_put(nc,a[vv,1], rep(xS$SN[which(xS$Variables==a[vv,1])],150))
  }
  nc_sync(nc)
}
nc_sync(nc)
nc_close(nc)