extract.level {cmsafops}

Extract levels from 4-dimensional NetCDF files.

Description

This function extracts one or all levels of a 4-dimensional NetCDF file. A level is defined as a dimension, which does not correspond to longitude, latitude or time. The user can choose either one specific level (given by an integer) or all levels (level = "all").

Usage

extract.level(
  var,
  infile,
  outfile,
  level = 1,
  nc34 = 4,
  overwrite = FALSE,
  verbose = FALSE,
  nc = NULL
)

Arguments

var

Name of NetCDF variable (character).

infile

Filename of input NetCDF file. This may include the directory (character).

outfile

Filename of output NetCDF file. This may include the directory (character).

level

Number of level (default = 1) or all levels (level = "all") (numeric or character).

nc34

NetCDF version of output file. If nc34 = 3 the output file will be in NetCDFv3 format (numeric). Default output is NetCDFv4.

overwrite

logical; should existing output file be overwritten?

verbose

logical; if TRUE, progress messages are shown

nc

Alternatively to infile you can specify the input as an object of class ncdf4 (as returned from ncdf4::nc_open).

Value

A NetCDF file including the selected level is written. In case of level = "all" all levels are written in separate NetCDF files and outfile names are expanded by "_level" and the level number.

See Also

Other selection and removal functions: extract.period(), sellonlatbox(), selmon(), selperiod(), selpoint(), selpoint.multi(), seltime(), selyear()

Examples

## Create an example NetCDF file with a similar structure as used by CM
## SAF. The file is created with the ncdf4 package.  Alternatively
## example data can be freely downloaded here: <https://wui.cmsaf.eu/>

library(ncdf4)

## create some (non-realistic) example data

lon <- seq(5, 15, 0.5)
lat <- seq(45, 55, 0.5)
height <- seq(0, 1000, 100)
time <- seq(as.Date("2000-01-01"), as.Date("2010-12-31"), "month")
origin <- as.Date("1983-01-01 00:00:00")
time <- as.numeric(difftime(time, origin, units = "hour"))
data <- array(250:350, dim = c(21, 21, 11, 132))

## create example NetCDF

x <- ncdim_def(name = "lon", units = "degrees_east", vals = lon)
y <- ncdim_def(name = "lat", units = "degrees_north", vals = lat)
z <- ncdim_def(name = "height", units = "m", vals = height)
t <- ncdim_def(name = "time", units = "hours since 1983-01-01 00:00:00",
 vals = time, unlim = TRUE)
var1 <- ncvar_def("SIS", "W m-2", list(x, y, z, t), -1, prec = "short")
vars <- list(var1)
ncnew <- nc_create(file.path(tempdir(),"CMSAF_example_file.nc"), vars)
ncvar_put(ncnew, var1, data)
ncatt_put(ncnew, "lon", "standard_name", "longitude", prec = "text")
ncatt_put(ncnew, "lat", "standard_name", "latitude", prec = "text")
ncatt_put(ncnew, "height", "standard_name", "height", prec = "text")
nc_close(ncnew)

## Extract the first level of the example CM SAF NetCDF file and write
## the output to a new file.
extract.level("SIS", file.path(tempdir(),"CMSAF_example_file.nc"),
 file.path(tempdir(),"CMSAF_example_file_extract.level1.nc"))
## Extract all levels of the example CM SAF NetCDF file and write the
## output to a new file.
extract.level(var = "SIS", infile = file.path(tempdir(),"CMSAF_example_file.nc"),
 outfile = file.path(tempdir(),"CMSAF_example_file_extract.level2.nc"),
 level = "all")

unlink(c(file.path(tempdir(),"CMSAF_example_file.nc"),
 file.path(tempdir(),"CMSAF_example_file_extract.level1.nc"),
 file.path(tempdir(),"CMSAF_example_file_extract.level2_level[1-9].nc"),
 file.path(tempdir(),"CMSAF_example_file_extract.level2_level10.nc"),
 file.path(tempdir(),"CMSAF_example_file_extract.level2_level11.nc")))