NAME
ncdump - Convert netCDF file to text form (CDL)
SYNOPSIS
ncdump [-c] [-h] [-v var1,...] [-b lang] [-f lang] [-l len] [-n name]
[-p f_digits[,d_digits]] [-k] [-x] [-s] [-t] file
DESCRIPTION
ncdump generates a text representation of a specified netCDF file on
standard output. The text representation is in a form called CDL
(‘‘network Common Data form Language’’) that can be viewed, edited, or
serve as input to ncgen. ncgen is a companion program that can
generate a binary netCDF file from a CDL file. Hence ncgen and ncdump
can be used as inverses to transform the data representation between
binary and text representations. See ncgen for a description of CDL
and netCDF representations.
As of NetCDF version 4.1, and if DAP support was enabled when ncdump
was built, the file name may specify a DAP URL. This allows ncdump to
print out data sources from DAP servers. When used with the -h option,
ncdump can be used to show the translation from the DAP DDS data model
to the NetCDF data model.
ncdump defines a default display format used for each type of netCDF
data, but this can be changed if a ‘C_format’ attribute is defined for
a netCDF variable. In this case, ncdump will use the ‘C_format’
attribute to format each value. For example, if floating-point data
for the netCDF variable ‘Z’ is known to be accurate to only three
significant digits, it would be appropriate to use the variable
attribute
Z:C_format = "%.3g"
ncdump may also be used as a simple browser for netCDF data files, to
display the dimension names and sizes; variable names, types, and
shapes; attribute names and values; and optionally, the values of data
for all variables or selected variables in a netCDF file.
ncdump uses ‘_’ to represent data values that are equal to the
‘_FillValue’ attribute for a variable, intended to represent data that
has not yet been written. If a variable has no ‘_FillValue’ attribute,
the default fill value for the variable type is used if the variable is
not of byte type.
ncdump may also be used to determine what kind of netCDF file is used
(which variant of the netCDF file format) with the -k option.
OPTIONS
-c Show the values of coordinate variables (variables that are also
dimensions) as well as the declarations of all dimensions,
variables, and attribute values. Data values of non-coordinate
variables are not included in the output. This is the most
suitable option to use for a brief look at the structure and
contents of a netCDF file.
-h Show only the header information in the output, that is the
declarations of dimensions, variables, and attributes but no
data values for any variables. The output is identical to using
the -c option except that the values of coordinate variables are
not included. (At most one of -c or -h options may be present.)
-v var1,...,varn
The output will include data values for the specified variables,
in addition to the declarations of all dimensions, variables,
and attributes. One or more variables must be specified by name
in the comma-delimited list following this option. The list
must be a single argument to the command, hence cannot contain
blanks or other white space characters unless escaped. The
named variables must be valid netCDF variables in the input-
file. A variable within a group in a netCDF-4 file may be
specified with an absolute pathname, such as
‘/GroupA/GroupA2/var’. Use of a relative pathname such as ‘var’
or ‘grp/var’ specifies all matching variable names in the file.
The default, without this option and in the absence of the -c or
-h options, is to include data values for all variables in the
output.
-b lang
A brief annotation in the form of a CDL comment (text beginning
with the characters ‘‘//’’) will be included in the data section
of the output for each ‘row’ of data, to help identify data
values for multidimensional variables. If lang begins with ‘C’
or ‘c’, then C language conventions will be used (zero-based
indices, last dimension varying fastest). If lang begins with
‘F’ or ‘f’, then Fortran language conventions will be used (one-
based indices, first dimension varying fastest). In either
case, the data will be presented in the same order; only the
annotations will differ. This option is useful for browsing
through large volumes of multidimensional data.
-f lang
Full annotations in the form of trailing CDL comments (text
beginning with the characters ‘‘//’’) for every data value
(except individual characters in character arrays) will be
included in the data section. If lang begins with ‘C’ or ‘c’,
then C language conventions will be used (zero-based indices,
last dimension varying fastest). If lang begins with ‘F’ or
‘f’, then Fortran language conventions will be used (one-based
indices, first dimension varying fastest). In either case, the
data will be presented in the same order; only the annotations
will differ. This option may be useful for piping data into
other filters, since each data value appears on a separate line,
fully identified.
-l len Changes the default maximum line length (80) used in formatting
lists of non-character data values.
-n name
CDL requires a name for a netCDF data set, for use by ncgen -b
in generating a default netCDF file name. By default, ncdump
constructs this name from the last component of the pathname of
the input netCDF file by stripping off any extension it has.
Use the -n option to specify a different name. Although the
output file name used by ncgen -b can be specified, it may be
wise to have ncdump change the default name to avoid
inadvertantly overwriting a valuable netCDF file when using
ncdump, editing the resulting CDL file, and using ncgen -b to
generate a new netCDF file from the edited CDL file.
-p float_digits[,double_digits]
Specifies default precision (number of significant digits) to
use in displaying floating-point or double precision data values
for attributes and variables. If specified, this value
overrides the value of the ‘C_format’ attribute for any variable
that has such an attribute. Floating-point data will be
displayed with float_digits significant digits. If
double_digits is also specified, double-precision values will be
displayed with that many significant digits. In the absence of
any -p specifications, floating-point and double-precision data
are displayed with 7 and 15 significant digits respectively.
CDL files can be made smaller if less precision is required. If
both floating-point and double-presision precisions are
specified, the two values must appear separated by a comma (no
blanks) as a single argument to the command. If you really want
every last bit of precision from the netCDF file represented in
the CDL file for all possible floating-point values, you will
have to specify this with -p 9,17 (according to Theorem 15 of
the paper listed under REFERENCES).
-k Show what kind of netCDF file the pathname references, one of
‘classic’, ‘64-bit offset’,‘netCDF-4’, or ‘netCDF-4 classic
model’. Before version 3.6, there was only one kind of netCDF
file, designated as ‘classic’ (also know as format variant 1).
Large file support introduced another variant of the format,
designated as ‘64-bit offset’ (known as format variant 2).
NetCDF-4, uses a third variant of the format, ‘netCDF-4’ (format
variant 3). Another format variant, designated ‘netCDF-4
classic model’ (format variant 4), is restricted to features
supported by the netCDF-3 data model but represented using the
HDF5 format, so that an unmodified netCDF-3 program can read or
write the file just by relinking with the netCDF-4 library. The
string output by using the ‘-k’ option may be provided as the
value of the ‘-k’ option to ncgen(1) to specify exactly what
kind of netCDF file to generate, when you want to override the
default inferred from the CDL.
-x Output XML (NcML) instead of CDL. The NcML does not include
data values. The NcML output option doesn’t yet display
netCDF-4 data correctly.
-s Output special virtual attributes that provide performance-
related information about the file format and variable
properties for netCDF-4 data. These special virtual attributes
are not actually part of the data, they are merely a convenient
way to display miscellaneous properties of the data in CDL (and
eventually NcML). They include ‘_ChunkSizes’, ‘_DeflateLevel’,
‘_Endianness’, ‘_Fletcher32’, ‘_Format’, ‘_NoFill’, ‘_Shuffle’,
and ‘_Storage’. ‘_ChunkSizes’ is a list of chunk sizes for each
dimension of the variable. ‘_DeflateLevel’ is an integer
between 0 and 9 inclusive if compression has been specified for
the variable. ‘_Endianness’ is either ‘little’ or ‘big’,
depending on how the variable was stored when first written.
‘_Fletcher32’ is ‘true’ if the checksum property was set for the
variable. ‘_Format’ is a global attribute specifying the netCDF
format variant, one of ‘classic’, ‘64-bit offset’, ‘netCDF-4’,
or ‘netCDF-4 classic model’. ‘_NoFill’ is ‘true’ if the
persistent NoFill property was set for the variable when it was
defined. ‘_Shuffle’ is ‘true’ if use of the shuffle filter was
specified for the variable. ‘_Storage’ is ‘contiguous’ or
‘chunked’, depending on how the variable’s data is stored.
-t Controls display of time data, if stored in a variable that uses
a udunits compliant time representation such as ‘days since
1970-01-01’ or ‘seconds since 2009-03-15 12:01:17’. If this
option is specified, time values are displayed as human-readable
date-time strings rather than numerical values, interpreted in
terms of a ‘calendar’ variable attribute, if specified.
Calendar attribute values interpreted with this option include
the CF Conventions values ‘gregorian’ or ‘standard’,
‘proleptic_gregorian’, ‘noleap’ or ‘365_day’, ‘all_leap’ or
‘366_day’, ‘360_day’, or ‘julian’.
EXAMPLES
Look at the structure of the data in the netCDF file ‘foo.nc’:
ncdump -c foo.nc
Produce an annotated CDL version of the structure and data in the
netCDF file ‘foo.nc’, using C-style indexing for the annotations:
ncdump -b c foo.nc > foo.cdl
Output data for only the variables ‘uwind’ and ‘vwind’ from the netCDF
file ‘foo.nc’, and show the floating-point data with only three
significant digits of precision:
ncdump -v uwind,vwind -p 3 foo.nc
Produce a fully-annotated (one data value per line) listing of the data
for the variable ‘omega’, using Fortran conventions for indices, and
changing the netCDF dataset name in the resulting CDL file to ‘omega’:
ncdump -v omega -f fortran -n omega foo.nc > Z.cdl
REFERENCES
What Every Computer Scientist should Know About Floating-Point
Arithmetic, D. Goldberg, ACM Computing Surveys, Vol. 23, No. 1, March
1991, pp. 5-48. Climate and Forecast Metadata Conventions,
http://www.cfconventions.org.
SEE ALSO
ncgen(1), netcdf(3)
BUGS
Character arrays that contain a null-byte are treated like C strings,
so no characters after the null byte appear in the output.
Multidimensional character string arrays are not handled well, since
the CDL syntax for breaking a long character string into several
shorter lines is weak.
There should be a way to specify that the data should be displayed in
‘record’ order, that is with the all the values for ‘record’ variables
together that have the same value of the record dimension.