netcdf-c/ncdump/ncdump.1

.\" $Header: /upc/share/CVS/netcdf-3/ncdump/ncdump.1,v 1.10 2009/07/28 14:48:36 russ Exp $
.TH NCDUMP 1 "2012-03-08" "Release 4.2" "UNIDATA UTILITIES"
.SH NAME
ncdump \- Convert netCDF file to text form (CDL)
.SH SYNOPSIS
.ft B
.HP
ncdump
.nh
\%[-c]
\%[-h]
\%[-v \fIvar1,...\fP]
\%[-g \fIgrp1,...\fP]
\%[-b \fIlang\fP]
\%[-f \fIlang\fP]
\%[-l \fIlen\fP]
\%[-n \fIname\fP]
\%[-p \fIf_digits[,d_digits]\fP]
\%[-x]
\%[-s]
\%[-t]
\%\fIfile\fP
.br
.ft B
.HP
ncdump
.nh
\%-k
\%\fIfile\fP
.hy
.ft
.SH DESCRIPTION
\fBncdump\fP 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 \fBncgen\fP.  \fBncgen\fP is a companion program that can
generate a binary netCDF file from a CDL file.  Hence \fBncgen\fP and
\fBncdump\fP can be used as inverses to transform the data representation
between binary and text representations.  See \fBncgen\fP for a description
of CDL and netCDF representations.
.LP
As of NetCDF version 4.1, and if DAP support was enabled when \fBncdump\fP
was built, the file name may specify a DAP URL. This allows \fBncdump\fP
to print out data sources from DAP servers.  When used with
the \fB-h\fP option, \fBncdump\fP can be used to show the translation
from the DAP DDS data model to the NetCDF data model.
.LP
\fBncdump\fP 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, \fBncdump\fP 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
.RS
.HP
Z:C_format = "%.3g"
.RE
.LP
\fBncdump\fP 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.
.LP
\fBncdump\fP 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.
.LP
\fBncdump\fP may also be used to determine what kind of netCDF file is used
(which variant of the netCDF file format) with the -k option.
.SH OPTIONS
.IP "\fB-c\fP"
Show the values of \fIcoordinate\fP 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.
.IP "\fB-h\fP"
Show only the \fIheader\fP 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 \fB-c\fP option except
that the values of coordinate variables are not included.  (At most one of
\fB-c\fP or \fB-h\fP options may be present.)
.IP "\fB-v\fP \fIvar1,...,varn\fP"
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.  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
path name, such as `/GroupA/GroupA2/var'.  Use of a relative path name
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 \fB-c\fP or \fB-h\fP
options, is to include data values for \fIall\fP variables in the output.
.IP "\fB-g\fP \fIgrp1,...,grpn\fP"
For netCDF-4 files, the output will include data values only for the
specified groups.  One or more groups must be specified by name in the
comma-delimited list following this option. The list must be a single
argument to the command. The named groups must be valid netCDF groups
in the input-file.  A group in a netCDF-4 file may be specified with
an absolute or relative path name.  Use of a relative path name
specifies all matching group names in the file.  The default, without
this option and in the absence of the \fB-c\fP or \fB-h\fP options, is
to include data values for \fIall\fP groups in the output.
.IP "\fB-b\fP \fIlang\fP"
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 \fIlang\fP begins with `C' or `c', then C language
conventions will be used (zero-based indices, last dimension varying
fastest).  If \fIlang\fP 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.
.IP "\fB-f\fP \fIlang\fP"
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 \fIlang\fP
begins with `C' or `c', then C language conventions will be used (zero-based
indices, last dimension varying fastest).  If \fIlang\fP 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.
.IP "\fB-l\fP \fIlen\fP"
Changes the default maximum line length (80) used in formatting lists of
non-character data values.
.IP "\fB-n\fP \fIname\fP"
CDL requires a name for a netCDF data set, for use by \fBncgen -b\fP in
generating a default netCDF file name.  By default, \fIncdump\fP constructs
this name from the last component of the path name of the input netCDF file
by stripping off any extension it has.  Use the \fB-n\fP option to specify a
different name.  Although the output file name used by \fBncgen -b\fP can be
specified, it may be wise to have \fIncdump\fP change the default name to
avoid inadvertently overwriting a valuable netCDF file when using
\fBncdump\fP, editing the resulting CDL file, and using \fBncgen -b\fP to
generate a new netCDF file from the edited CDL file.
.IP "\fB-p\fP \fIfloat_digits[,double_digits]\fP"
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
\fIfloat_digits\fP significant digits.  If \fIdouble_digits\fP is also
specified, double-precision values will be displayed with that many
significant digits.  In the absence of any
\fB-p\fP 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-precision 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 \fB-p 9,17\fP (according to Theorem 15 of the
paper listed under REFERENCES).
.IP "\fB-k\fP"
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.
.IP "\fB-x\fP"
Output XML (NcML) instead of CDL.  The NcML does not include data values.
The NcML output option currently only works for netCDF classic model data.
.IP "\fB-s\fP"
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.
.IP "\fB-t\fP"
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', a variable
identified in a "bounds" attribute of such a time variable, or a numeric
attribute of a time variable.  If this option is
specified, time data values are displayed as human-readable date-time
strings rather than numerical values, interpreted in terms of a 
`calendar' variable attribute, if specified.  For numeric attributes
of time variables, the human-readable time value is displayed after the
actual value, in an associated CDL comment.  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', and `julian'.
.SH EXAMPLES
.LP
Look at the structure of the data in the netCDF file `\fBfoo.nc\fP':
.RS
.HP
ncdump -c foo.nc
.RE
.LP
Produce an annotated CDL version of the structure and data in the
netCDF file `\fBfoo.nc\fP', using C-style indexing for the annotations:
.RS
.HP
ncdump -b c foo.nc > foo.cdl
.RE
.LP
Output data for only the variables `uwind' and `vwind' from the netCDF file
`\fBfoo.nc\fP', and show the floating-point data with only three significant
digits of precision:
.RS
.HP
ncdump -v uwind,vwind -p 3 foo.nc
.RE
.LP
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':
.RS
.HP
ncdump -v omega -f fortran -n omega foo.nc > Z.cdl
.RE
.SH REFERENCES
 \fIWhat
Every Computer Scientist should Know About Floating-Point Arithmetic\fP, D.
Goldberg, \fBACM Computing Surveys, Vol. 23, No. 1\fP, March 1991, pp. 5-48.
.BR
Climate and Forecast Metadata Conventions, http://www.cfconventions.org.
.SH "SEE ALSO"
.LP
.BR ncgen (1),
.BR netcdf (3)
.SH BUGS
.LP
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.