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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/software/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.
charbyteshortlongintfloatrealdouble 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 shorts and floats to distinguish them from longs
and doubles.
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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