使用ncdf4 :: ncvar_get时如何指定尺寸顺序? [英] How can I specify dimension order when using ncdf4::ncvar_get?

问题描述

在上一个问题之后(是否从netCDF中快速读取时间序列?)我已经将netCDF文件重新排列为提供快速的时间序列读取(github上的脚本脚本最终将被清理. .. ).

Following a previous question (Faster reading of time series from netCDF?) I have re-permuted my netCDF files to provide fast time-series reads (scripts on github to be cleaned up eventually ...).

简而言之，为了使读取更快，我将尺寸从lat, lon, time重新排列为time, lat, lon.现在，我现有的脚本中断了，因为它们假定对于'start'参数，尺寸遵循ncvar_get的ncdf4文档，始终为lat, lon, time:

In short, to make reads faster, I have rearranged the dimensions from lat, lon, time to time, lat, lon. Now, my existing scripts break because they assume that the dimensions will always be lat, lon, time, following the ncdf4 documentation of ncvar_get, for the 'start' argument:

订单为X-Y-Z-T(即时间维度为最后一个)

Order is X-Y-Z-T (i.e., the time dimension is last)

但是，事实并非如此.

此外，通过命令行netCDF实用程序ncdump -h和R函数ncdf4::nc_open列出的变量顺序存在相关的不一致.第一个表示维度按预期(纬度，经度，时间)顺序排列，而后者则按时间先于时间(时间，纬度，经度)看到维度.

Furthermore, there is a related inconsistency in the order of variables listed via the commandline netCDF utility ncdump -h and the R function ncdf4::nc_open. The first says that the dimensions are in the expected (lat, lon, time) order while the latter sees dimensions with time first (time, lat, lon).

作为一个最小的示例，下载文件 test.nc 并运行

For a minimal example, download the file test.nc and run

bash-$ ncdump -h .nc
bash-$ R
R> library(ncdf4)
R> print(nc_open("test.nc")

我想做的是从变量"lwdown"中获取记录5-15.

What I want to do is get records 5-15 from the variable "lwdown"

my.nc <- nc_open("test.nc")

但是这不起作用，因为R首先看到时间维度，所以我必须将脚本更改为

But this doesn't work, since R sees the time dimension first, so I must change my scripts to

ncvar_get(my.nc, "lwdown", start = c(5, 1, 1), count = c(10, 1, 1))

更新我的脚本和函数并不难，除了我希望能够从文件中读取数据而不受尺寸顺序的限制.

It wouldn't be so bad to update my scripts and functions, except that I want to be able to read data from files regardless of the dimension order.

除了可以通用化此功能以使其独立于尺寸顺序工作之外，还有其他方法吗?

Other than Is there a way to generalize this function so that it works independent of dimension order?

推荐答案

在问这个问题时，我想出了这个解决方案，尽管仍有改进的余地:

While asking the question, I figured out this solution, though there is still room for improvement:

我能得到的最接近的方法是打开文件并以这种方式查找订单:

The closest I can get is to open the file and find the order in this way:

my.nc$var$lwdown$dim[[1]]$name
[1] "time"
my.nc$var$lwdown$dim[[2]]$name
[1] "lon"
my.nc$var$lwdown$dim[[3]]$name
[1] "lat"

有点不满意，尽管它使我想到了以下解决方案:

which is a bit unsatisfying, although it led me to this solution:

如果我想从c(lat = 1, lon = 1, time = 5)开始，但ncvar_get需要任意顺序，我可以说"

If I want to start at c(lat = 1, lon = 1, time = 5), but the ncvar_get expects an arbitrary order, I can say"

start <- c(lat = 1, lon = 1, time = 5)
count <- c(lat = 1, lon = 1, time = 10)
dim.order <- sapply(my.nc$var$lwdown$dim, function(x) x$name)

ncvar_get(my.nc, "lwdown", start = start[dim.order], count = count[dim.order])

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