ncatted (1) - Linux Manuals

ncatted: netCDF Attribute Editor

NAME

ncatted - netCDF Attribute Editor

SYNTAX

ncatted [-a att_dsc] [-a ...] [--bfr sz][-D dbg_lvl] [-h] [--hdr_pad sz] [-l path] [-O] [-p path] [-R] [-r] [--ram_all] input-file [ output-file]

DESCRIPTION

ncatted edits attributes in a netCDF file. If you are editing attributes then you are spending too much time in the world of metadata, and ncatted was written to get you back out as quickly and painlessly as possible. ncatted can append, create, delete, modify, and overwrite attributes (all explained below). Furthermore, ncatted allows each editing operation to be applied to every variable in a file, thus saving you time when you want to change attribute conventions throughout a file. ncatted interprets character attributes as strings.

Because repeated use of ncatted can considerably increase the size of the history global attribute, the -h switch is provided to override automatically appending the command to the history global attribute in the output-file.

When ncatted is used to change the _FillValue attribute, it changes the associated missing data self-consistently. If the internal floating point representation of a missing value, e.g., 1.0e36, differs between two machines then netCDF files produced on those machines will have incompatible missing values. This allows ncatted to change the missing values in files from different machines to a single value so that the files may then be concatenated together, e.g., by ncrcat, without losing any information.

The key to mastering ncatted is understanding the meaning of the structure describing the attribute modification, att_dsc. Each att_dsc contains five elements, which makes using ncatted somewhat complicated, but powerful. The att_dsc argument structure contains five arguments in the following order:

att_dsc = att_nm, var_nm, mode, att_type, att_val

att_nm

Attribute name. Example: units

var_nm

Variable name. Example: pressure

mode

Edit mode abbreviation. Example: a. See below for complete listing of valid values of mode.

att_type

Attribute type abbreviation. Example: c. See below for complete listing of valid values of att_type.

att_val

Attribute value. Example: pascal. There should be no empty space between these five consecutive arguments. The description of these arguments follows in their order of appearance.

The value of att_nm is the name of the attribute you want to edit. This meaning of this should be clear to all users of the ncatted operator.

The value of var_nm is the name of the variable containing the attribute (named att_nm) that you want to edit. There are two very important and useful exceptions to this rule. The value of var_nm can also be used to direct ncatted to edit global attributes, or to repeat the editing operation for every variable in a file. A value of var_nm of global" indicates that att_nm refers to a global attribute, rather than a particular variable's attribute. This is the method ncatted supports for editing global attributes. If var_nm is left blank, on the other hand, then ncatted attempts to perform the editing operation on every variable in the file. This option may be convenient to use if you decide to change the conventions you use for describing the data.

The value of mode is a single character abbreviation ( a, c, d, m, or o) standing for one of five editing modes:

a

Append. Append value att_val to current var_nm attribute att_nm value att_val, if any. If var_nm does not have an attribute att_nm, there is no effect.

c

Create. Create variable var_nm attribute att_nm with att_val if att_nm does not yet exist. If var_nm already has an attribute att_nm, there is no effect.

d

Delete. Delete current var_nm attribute att_nm. If var_nm does not have an attribute att_nm, there is no effect. When Delete mode is selected, the att_type and att_val arguments are superfluous and may be left blank.

m

Modify. Change value of current var_nm attribute att_nm to value att_val. If var_nm does not have an attribute att_nm, there is no effect.

o

Overwrite. Write attribute att_nm with value att_val to variable var_nm, overwriting existing attribute att_nm, if any. This is the default mode.

The value of att_type is a single character abbreviation ( f, d, l, s, c, or b) standing for one of the six primitive netCDF data types:

f

Float. Value(s) specified in att_val will be stored as netCDF intrinsic type NC_FLOAT.

d

Double. Value(s) specified in att_val will be stored as netCDF intrinsic type NC_DOUBLE.

l

Long. Value(s) specified in att_val will be stored as netCDF intrinsic type NC_LONG.

s

Short. Value(s) specified in att_val will be stored as netCDF intrinsic type NC_SHORT.

c

Char. Value(s) specified in att_val will be stored as netCDF intrinsic type NC_CHAR.

b

Byte. Value(s) specified in att_val will be stored as netCDF intrinsic type NC_BYTE. The specification of att_type is optional in Delete mode.

The value of att_val is what you want to change attribute att_nm to contain. The specification of att_val is optional in Delete mode. Attribute values for all types besides NC_CHAR must have an attribute length of at least one. Thus att_val may be a single value or one-dimensional array of elements of type att_type. If the att_val is not set or is set to empty space, and the att_type is NC_CHAR, e.g., -a units,T,o,c, or -a units,T,o,c,, then the corresponding attribute is set to have zero length. When specifying an array of values, it is safest to enclose att_val in double or single quotes, e.g., -a levels,T,o,s,1,2,3,4 or -a levels,T,o,s,'1,2,3,4'. The quotes are strictly unnecessary around att_val except when att_val contains characters which would confuse the calling shell, such as spaces, commas, and wildcard characters.

NCO processing of NC_CHAR attributes is a bit like Perl in that it attempts to do what you want by default (but this sometimes causes unexpected results if you want unusual data storage). If the att_type is NC_CHAR then the argument is interpreted as a string and it may contain C-language escape sequences, which NCO will interpret before writing anything to disk. NCO translates valid escape sequences and stores the appropriate ASCII code instead. Since two byte escape sequences represent one byte ASCII codes, e.g., ASCII 10 (decimal), the stored string attribute is one byte shorter than the input string length for each embedded escape sequence. These sequences in particular allow convenient editing of formatted text attributes. See ncks netCDF Kitchen Sink, for more examples of string formatting (with the ncks -s option) with special characters.

Analogous to printf, other special characters are also allowed by ncatted if they are "protected" by a backslash. NCO simply strips away the leading backslash from these characters before editing the attribute. No other characters require protection by a backslash. Backslashes which precede any other character will not be filtered and will be included in the attribute.

Note that the NUL character which terminates C language strings is assumed and need not be explicitly specified. If NUL is input, it will not be translated (because it would terminate the string in an additional location). Because of these context-sensitive rules, if wish to use an attribute of type NC_CHAR to store data, rather than text strings, you should use ncatted with care.

EXAMPLES

Append the string "Data version 2.0.\n" to the global attribute history:

ncatted -O -a history,global,a,c,"Data version 2.0\n" in.nc

Note the use of embedded C language printf()-style escape sequences.

Change the value of the long_name attribute for variable T from whatever it currently is to "temperature":

ncatted -O -a long_name,T,o,c,temperature in.nc

Delete all existing units attributes:

ncatted -O -a units,,d,, in.nc

The value of var_nm was left blank in order to select all variables in the file. The values of att_type and att_val were left blank because they are superfluous in Delete mode.

Modify all existing units attributes to "meter second-1"

ncatted -O -a units,,m,c,"meter second-1" in.nc

Overwrite the quanta attribute of variable energy to an array of four integers.

ncatted -O -a quanta,energy,o,s,"010,101,111,121" in.nc

See the manual for more complex examples, including how to input C-language escape sequences and other special characters like backslashes and question marks.

AUTHOR

NCO manual pages written by Charlie Zender and originally formatted by Brian Mays.

REPORTING BUGS

Report bugs to <http://sf.net/bugs/?group_id=3331>.

COPYRIGHT

Copyright © 1995-2012 Charlie Zender
This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

HOMEPAGE

The NCO homepage at <http://nco.sf.net> contains more information.