在 R 中创建多维 NetCDF

Question

我正在尝试使用 R 包 ncdf 创建多维 NetCDF 文件。我正在对一组 1500 个点进行气候日常观测，每个点的观测数约为 18250。 问题是NetCDF文件的结构（create.ncdf）占用4Gb，每个点使文件大小增加3Gb以上（put.var.ncdf em>)

这是我正在使用的代码：

# Make a few dimensions we can use
dimX <- dim.def.ncdf( "Long", "degrees", Longvector )
dimY <- dim.def.ncdf( "LAT", "degrees", Latvector )
dimT <- dim.def.ncdf( "Time", "days", 1:18250, unlim=FALSE )

# Make varables of various dimensionality, for illustration purposes
mv <- -9999 # missing value to use
var1d <- var.def.ncdf( "var1d", "units", dimX, mv,prec="double" )
var2d <- var.def.ncdf( "var2d", "units", list(dimX,dimY), mv,prec="double" )
var3d <- var.def.ncdf( "var3d", "units", list(dimX,dimY,dimT), mv,prec="double" )

# Create the test file
nc <- create.ncdf( "writevals.nc", list(var1d,var2d,var3d) )
# !!Creates a nc file with + 4 Gb

# Adding the complete time series for one point (the first point in the list of the dataset)
put.var.ncdf( nc, var3d,dataset[[1]], start=c(Longvector[1],Latvector[1],1),         count=c(1,1,-1))

Longvector 和 Latvector 是从每个点的 Long 和 Lat 矩阵中获取的向量。数据集是一个列表格式，对于每个点我都有一个数值列表。

dataset[[1]]=c(0,0,0,9.7,0,7.5,3.6,2.9,0,0.5,....) 

是我遗漏了什么还是应该尝试其他软件包？？

Answer 1

您的不可重现代码中存在一些错误，据我估计，该文件为 219Mb（1500 * 18250 * 8 字节）。

library(ncdf)

提供前两个维度的向量和数据集以匹配至少一个切片

Longvector = seq(-180, 180, length = 50)
Latvector = seq(-90, 90, length = 30)
dataset <- list(1:18250)

dimX <- dim.def.ncdf("Long", "degrees", Longvector)
dimY <- dim.def.ncdf("LAT", "degrees", Latvector)
dimT <- dim.def.ncdf("Time", "days", 1:18250, unlim = FALSE)

mv <- -9999 
var1d <- var.def.ncdf( "var1d", "units", dimX, mv,prec="double")
var2d <- var.def.ncdf( "var2d", "units", list(dimX,dimY), mv,prec="double")
var3d <- var.def.ncdf( "var3d", "units", list(dimX,dimY,dimT), mv,prec="double")

nc <- create.ncdf( "writevals.nc", list(var1d,var2d,var3d))

count是维度的索引，不是轴位置值，所以我们把start改成1，使用第3维度的count（长度）（不是-1）。

put.var.ncdf(nc, var3d, dataset[[1]], start = c(1, 1, 1),  count = c(1, 1, length(dataset[[1]])))

close.ncdf(nc)

查询文件大小。

file.info("writevals.nc")$size/1e6
[1] 219.0866

Answer 2

这是 mdsumner 答案的更新版本，它适用于 R (ncdf4) 的 NetCDF4 包。

# Open library
library(ncdf4)

# Get x and y vectors (dimensions)
Longvector = seq(-180, 180, length = 50)
Latvector = seq(-90, 90, length = 30)
# Define data
dataset = list(1:18250)

# Define the dimensions
dimX = ncdim_def("Long", "degrees", Longvector)
dimY = ncdim_def("Lat", "degrees", Latvector)
dimT = ncdim_def("Time", "days", 1:18250)

# Define missing value
mv = -9999

# Define the data
var1d = ncvar_def( "var1d", "units", dimX, mv, prec="double")
var2d = ncvar_def( "var2d", "units", list(dimX,dimY), mv, prec="double")
var3d = ncvar_def( "var3d", "units", list(dimX,dimY,dimT), mv, prec="double")

# Create the NetCDF file
# If you want a NetCDF4 file, explicitly add force_v4=T
nc = nc_create("writevals.nc", list(var1d, var2d, var3d))

# Write data to the NetCDF file
ncvar_put(nc, var3d, dataset[[1]], start=c(1, 1, 1),
    count=c(1, 1, length(dataset[[1]])))

# Close your new file to finish writing
nc_close(nc)