ncdf4 (version 1.23)

ncvar_put: Write data to a netCDF file

Description

Writes data to an existing netCDF file. The variable to be written to must already exist on disk (i.e., you must call either nc_create or nc_open before calling this function).

Usage

ncvar_put( nc, varid, vals, start=NA, count=NA, verbose=FALSE, na_replace="fast" )

Arguments

nc

An object of class ncdf4 (as returned by either function nc_open or nc_create), indicating what file to write to.

varid

What variable to write the data to. Can be a string with the name of the variable or an object of class ncvar4, as returned by ncvar_def or nc_open.

vals

The values to be written.

start

A vector of indices indicating where to start writing the passed values (starting at 1). The length of this vector must equal the number of dimensions the variable has. Order is X-Y-Z-T (i.e., the time dimension is last). If not specified, writing starts at the beginning of the file (1,1,1,...).

count

A vector of integers indicating the count of values to write along each dimension (order is X-Y-Z-T). The length of this vector must equal the number of dimensions the variable has. If not specified and the variable does NOT have an unlimited dimension, the entire variable is written. If the variable has an unlimited dimension, this argument must be specified. As a special case, the value "-1" indicates that all entries along that dimension should be written.

verbose

If true, prints information while executing.

na_replace

This is either the string "fast" or the string "safe". When the 'vals' array is written out, NA's have to be replaced by the missing value specified when the variable was created. If na_replace is "fast", then this is done in-place without copying the 'vals' data array. This results in the passed 'vals' array being modified such that NA's are replaced with the missing value. This is fast but not standard in R and may be unexpected. If na_replace is "safe" then the vals array is copied before the NA replacement, so that the vals array is not modified. This is more expected and standard R, but can be slow and might cause memory issues if a very large 'vals' array is passed in. Default value is "fast".

Author

David W. Pierce

Details

This routine writes data values to a variable in a netCDF file. The file should have either been created with nc_create, or opened with nc_open called with parameter write=TRUE.

Note that the data type (i.e., precision) of the values written to the file is determined when the variable is created; in particular, it does not matter what type you pass to this function to be written. In other words, if the variable was created with type 'integer', passing double precision values to this routine will still result in integer values being written to disk.

Values of "NA" are supported; they are converted to the netCDF variable's missing value attribute before being written. See ncvar_change_missval for more information.

Data in a netCDF file is conceived as being a multi-dimensional array. The number and length of dimensions is determined when the variable is created. The 'start' and 'count' indices that this routine takes indicate where the writing starts along each dimension, and the count of values along each dimension to write.

References

http://dwpierce.com/software

See Also

ncdim_def, nc_create, nc_open, ncvar_get.

Examples

if (FALSE) {
#--------------------------------
# Make a few dimensions we can use
#--------------------------------
nx <- 3
ny <- 4
nt <- 5
xvals <- (1:nx)*100.
dimX <- ncdim_def( "X", "meters", xvals )
dimY <- ncdim_def( "Y", "meters", (1:ny)*100. )
dimT <- ncdim_def( "Time", "seconds", (1:nt)/100., unlim=TRUE )

#-------------------------------------------------------------------
# Make varables of various dimensionality, for illustration purposes
#-------------------------------------------------------------------
mv <- 1.e30		# missing value to use
var1d <- ncvar_def( "var1d", "units", dimX, mv )
var2d <- ncvar_def( "var2d", "units", list(dimX,dimY), mv )
var3d <- ncvar_def( "var3d", "units", list(dimX,dimY,dimT), mv )

#---------------------
# Create the test file
#---------------------
nc <- nc_create( "writevals.nc", list(var1d,var2d,var3d) )

#----------------------------
# Write some data to the file
#----------------------------
data1d <- runif(nx)
ncvar_put( nc, var1d, data1d )	# no start or count: write all values
ncvar_put( nc, var1d, 27.5, start=3, count=1 ) # Write a value to the third slot

data2d <- runif(nx*ny)
ncvar_put( nc, var2d, data2d )	# no start or count: write all values

#--------------------------------
# Write a 1-d slice to the 2d var
#--------------------------------
ncvar_put( nc, var2d, data1d, start=c(1,2), count=c(nx,1) )	

#--------------------------------------------------------------
# Note how "-1" in the count means "the whole dimension length", 
# which equals nx in this case
#--------------------------------------------------------------
ncvar_put( nc, var2d, data1d, start=c(1,3), count=c(-1,1) )	

#-------------------------------------------------------------------------------
# The 3-d variable has an unlimited dimension.  We will loop over the timesteps,
# writing one 2-d slice per timestep.
#-------------------------------------------------------------------------------
for( i in 1:nt) 
	ncvar_put( nc, var3d, data2d, start=c(1,1,i), count=c(-1,-1,1) )

nc_close(nc)

#----------------------------------------------------------------------
# Illustrate creating a character type variable
#----------------------------------------------------------------------
cnames   <- c("red", "orange", "green", "yellow", "puce", "colorwithverylongname" )
nstrings <- length(cnames)

#--------------------------------------------------------------
# Make dimensions. Setting "dimnchar" to have a length of 12
# means that the maximum color name
# length can be 12.  Longer names will be truncated to this.
# We don't need dimvars for this example.
#--------------------------------------------------------------
dimnchar   <- ncdim_def("nchar",   "", 1:12, create_dimvar=FALSE )
dimcolorno <- ncdim_def("colorno", "", 1:nstrings, create_dimvar=FALSE )

#------------------------------------------------------------------------
# NOTE in the following call that units is set to the empty string (""),
# which suppresses creation of a units attribute, and the missing value
# is entirely omitted, which suppresses creation of the missing value att
#------------------------------------------------------------------------
varcolors  <- ncvar_def("colors", "", list(dimnchar, dimcolorno), " ",
			prec="char" )

ncid <- nc_create( "colornames.nc", list(varcolors) )

ncvar_put( ncid, "colors", cnames, verbose=TRUE )

nc_close( ncid )

#---------
# Clean up
#---------
file.remove( "colornames.nc" )
file.remove( "writevals.nc" )
}