One of the primary reasons for using the netCDF interface for
applications that deal with arrays is to
take advantage of higher-level netCDF utilities and generic applications
for netCDF data. Currently two netCDF utilities are available as part
of the netCDF software distribution: ncgen
and ncdump
.
Users have contributed other netCDF utilities, and various visualization
and analysis packages are available that access netCDF data. For an
up-to-date list of freely-available and commercial software
that can access or manipulate netCDF data, see the
NetCDF Software list
(`http://www.unidata.ucar.edu/packages/netcdf/software.html').
This chapter describes the ncgen
and ncdump
utilities.
These two tools convert between binary netCDF files and a text
representation of netCDF files. The output of ncdump
and the
input to ncgen
is a text description of a netCDF file in a tiny
language known as CDL (network Common data form Description Language).
Below is an example of CDL, describing a netCDF file with several named
dimensions (lat
, lon
, time
), variables
(z
, t
, p
, rh
, lat
, lon
,
time
), variable attributes (units
, _FillValue
,
valid_range
), and some data.
netcdf foo { // example netCDF specification in CDL dimensions: lat = 10, lon = 5, time = unlimited ; variables: long lat(lat), lon(lon), time(time); float z(time,lat,lon), t(time,lat,lon); double p(time,lat,lon); long rh(time,lat,lon); lat:units = "degrees_north"; lon:units = "degrees_east"; time:units = "seconds"; z:units = "meters"; z:valid_range = 0., 5000.; p:_FillValue = -9999.; rh:_FillValue = -1; data: lat = 0, 10, 20, 30, 40, 50, 60, 70, 80, 90; lon = -140, -118, -96, -84, -52; }
All CDL statements are terminated by a semicolon. Spaces, tabs, and
newlines can be used freely for readability. Comments may follow the
double slash characters //
on any line.
A CDL description consists of three optional parts: dimensions, variables, and data. The variable part may contain variable declarations and attribute assignments.
A dimension is used to define the shape of one or more of the multidimensional variables described by the CDL description. A dimension has a name and a size. At most one dimension in a CDL description can have the unlimited size, which means a variable using this dimension can grow to any length (like a record number in a file).
A variable represents a multidimensional array of values of the same type. A variable has a name, a data type, and a shape described by its list of dimensions. Each variable may also have associated attributes (see below) as well as data values. The name, data type, and shape of a variable are specified by its declaration in the variable section of a CDL description. A variable may have the same name as a dimension; by convention such a variable contains coordinates of the dimension it names.
An attribute contains information about a variable or about the whole
netCDF dataset. Attributes may be used to specify such properties as
units, special values, maximum and minimum valid values, and packing
parameters. Attribute information is represented
by single values or arrays of values. For example, units
is an
attribute represented by a character array such as celsius
. An
attribute has an associated variable, a name, a data type, a length, and
a value. In contrast to variables that are intended for data,
attributes are intended for ancillary data (data about data).
In CDL, an attribute is designated by a variable and attribute name, separated by a colon (`:'). It is possible to assign global attributes to the netCDF file as a whole by omitting the variable name and beginning the attribute name with a colon (`:'). The data type of an attribute in CDL is derived from the type of the value assigned to it. The length of an attribute is the number of data values or the number of characters in the character string assigned to it. Multiple values are assigned to non-character attributes by separating the values with commas (`,'). All values assigned to an attribute must be of the same type.
CDL names for variables, attributes, and dimensions may be any combination of alphabetic or numeric characters as well as `_' and `-' characters, but names beginning with `_' are reserved for use by the library. Case is significant in CDL names. The netCDF library does not enforce any restrictions on netCDF names, so it is possible (though unwise) to define variables with names that are not valid CDL names. The names for the primitive data types are reserved words in CDL, so the names of variables, dimensions, and attributes must not be type names.
The optional data section of a CDL description is where netCDF variables may be initialized. The syntax of an initialization is simple:
variable = value_1, value_2, ...;
The comma-delimited list of constants may be separated by spaces, tabs, and newlines. For multidimensional arrays, the last dimension varies fastest. Thus, row-order rather than column order is used for matrices. If fewer values are supplied than are needed to fill a variable, it is extended with the fill value. The types of constants need not match the type declared for a variable; coercions are done to convert integers to floating point, for example. All meaningful type conversions are supported.
A special notation for fill values is supported: the `_' character designates a fill value for variables.
char
byte
short
long
int
float
real
double
Except for the added data-type byte
and the lack of the type
qualifier unsigned
, CDL supports the same primitive data types as
C. In declarations, type names may be specified in either upper or
lower case.
The byte
type differs from the char
type in that it is
intended for
eight-bit data, and the zero byte has no special significance, as it
may for character data. The ncgen
utility converts byte
declarations
to char
declarations in the output C code and to
BYTE
, INTEGER*1
, or similar platform-specific declaration in
output FORTRAN code.
The short
type holds values between -32768 and 32767. The ncgen
utility converts
short
declarations to short
declarations in the output
C code and to INTEGER*2
declaration in output
FORTRAN code.
The long
type can hold values between -2147483648 and 2147483647.
The ncgen
utility converts long
declarations to nclong
declarations in the output C code and to INTEGER
declarations in
output FORTRAN code. In CDL declarations int
and integer
are accepted as synonyms for long
.
The float
type can hold values between about -3.4+38 and 3.4+38,
with external representation as 32-bit IEEE normalized
single-precision floating-point numbers. The ncgen
utility converts
float
declarations to float
declarations in the output C
code and to REAL
declarations in output FORTRAN code.
In CDL declarations real
is accepted as a synonym for float
.
The double
type can hold values between about -1.7+308 and 1.7+308,
with external representation as 64-bit IEEE standard
normalized double-precision, floating-point numbers. The ncgen
utility
converts double
declarations to double
declarations in the
output C code and to DOUBLE PRECISION
declarations in output
FORTRAN code.
This section describes the CDL notation for constants.
Attributes are initialized in the variables
section of a CDL description
by providing a list of constants that determines the attribute's type
and length. (In the C and FORTRAN procedural interfaces to the netCDF
library, the type and length of an attribute must be explicitly provided
when it is defined.) CDL defines a
syntax for constant values that permits distinguishing among different
netCDF types.
The syntax for CDL constants is similar to C syntax, except that type
suffixes are appended to short
s and float
s to distinguish
them from long
s and double
s.
A byte
constant is represented by a single character or multiple
character escape sequence enclosed in single quotes. For example:
'a' // ASCII a '\0' // a zero byte '\n' // ASCII newline character '\33' // ASCII escape character (33 octal) '\x2b' // ASCII plus (2b hex) '\376' // 377 octal = -127 (or 254) decimal
Character constants are enclosed in double quotes. A character array may be represented as a string enclosed in double quotes. Multiple strings are concatenated into a single array of characters, permitting long character arrays to appear on multiple lines. To support multiple variable-length string values, a conventional delimiter such as `,' may be used, but interpretation of any such convention for a string delimiter must be implemented in software above the netCDF library layer. The usual escape conventions for C strings are honored. For example:
"a" // ASCII `a' "Two\nlines\n" // a 10-character string with two embedded newlines "a bell:\007" // a string containing an ASCII bell "ab","cde" // the same as "abcde"
The form of a short
constant is an integer constant with an
`s' or `S' appended. If a short
constant begins with
`0', it is interpreted as octal. When it begins with
`0x', it is interpreted as a hexadecimal constant. For example:
2s // a short 2 0123s // octal 0x7ffs // hexadecimal
The form of a long
constant is an ordinary integer constant,
although it is acceptable to append an optional `l' or `L'.
If a long
constant begins with `0', it is interpreted as
octal. When it begins with `0x', it is interpreted as a
hexadecimal constant. Examples of valid long
constants include:
-2 1234567890L 0123 // octal 0x7ff // hexadecimal
The float
type is appropriate for representing
data with about seven significant digits of precision.
The form of a float
constant is the same as a C floating-point constant
with an `f' or `F' appended. A decimal point is required in a CDL
float
to distinguish it from an integer. For example,
the following are all acceptable float
constants:
-2.0f 3.14159265358979f // will be truncated to less precision 1.f .1f
The double
type is appropriate for representing floating-point
data with about 16 significant digits of precision. The form of a
double
constant is the same as a C floating-point constant. An
optional `d' or `D' may be appended. A decimal point is
required in a CDL double
to distinguish it from an
integer
. For example, the following are all acceptable double
constants:
-2.0 3.141592653589793 1.0e-20 1.d
The ncgen
tool generates a netCDF file or a C or FORTRAN
program that creates a netCDF file. If no options are
specified in invoking ncgen
, the program merely checks the
syntax of the CDL input, producing error messages for any violations
of CDL syntax.
UNIX syntax for invoking ncgen
:
ncgen [-b] [-o netcdf-file] [-c] [-f] [-n] [input-file]
where:
netcdf
keyword in the input) by appending the
`.nc' extension. Warning: if a file already exists with
the specified name it will be overwritten.
Check the syntax of the CDL file `foo.cdl':
ncgen foo.cdl
From the CDL file `foo.cdl', generate an equivalent binary netCDF file named `bar.nc':
ncgen -o bar.nc foo.cdl
From the CDL file `foo.cdl', generate a C program containing the netCDF function invocations necessary to create an equivalent binary netCDF file:
ncgen -c foo.cdl > foo.c
The ncdump
tool generates the CDL text representation of a netCDF
file on standard output, optionally excluding some or all of the
variable data in the output. The output from ncdump
is intended
to be acceptable as input to ncgen
. Thus ncdump
and
ncgen
can be used as inverses to transform data representation
between binary and text representations.
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
defines a default format used for each type of netCDF
variable data, but this can be overridden if a C_format
attribute is
defined for a netCDF variable. In this case, ncdump
will use the
C_format
attribute to format values for that variable. For example,
if floating-point data for the netCDF variable Z
is known to be
accurate to only three significant digits, it might be appropriate to
use this variable attribute:
Z:C_format = "%.3g"
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 unless the variable is of byte type.
UNIX syntax for invoking ncdump
:
ncdump [ -c | -h] [-v var1,...] [-b lang] [-f lang] [-l len] [ -p fdig[,ddig]] [ -n name] [input-file]
where:
C_format
attribute, if any, for a variable. 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 precisions are specified, the two values must appear
separated by a comma (no blanks) as a single argument to the command.
ncdump
constructs this name from the last component of the file name 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 inadvertently 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.
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
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