Ubuntu Manpage: ncgen-hdf - From a CDL file generate a netCDF file, a C program, or a Fortran program

NAME

       ncgen-hdf - From a CDL file generate a netCDF file, a C program, or a Fortran program

SYNOPSIS

       ncgen-hdf [-b] [-c] [-f] [-n] [-o output_file] input_file

DESCRIPTION

       ncgen-hdf  generates  either a netCDF file, or C or Fortran source code to create a netCDF
       file.  The input to ncgen-hdf is a description of a netCDF file in a small language  known
       as  CDL (network Common Data form Language), described below.  If no options are specified
       in invoking ncgen-hdf, it merely checks the syntax of the input CDL file, producing  error
       messages  for  any  violations  of  CDL  syntax.   Other options can be used to create the
       corresponding netCDF file, to generate a C program that uses the  netCDF  C  interface  to
       create  the  netCDF  file,  or  to generate a Fortran program that uses the netCDF Fortran
       interface to create the same netCDF file.

       ncgen-hdf may be used with the companion program ncdump to perform some simple  operations
       on netCDF files.  For example, to rename a dimension in a netCDF file, use ncdump to get a
       CDL version of the netCDF file, edit the CDL file to change the name  of  the  dimensions,
       and use ncgen-hdf to generate the corresponding netCDF file from the edited CDL file.

OPTIONS

       -b     Create  a  (binary)  netCDF  file.  If the -o option is absent, a default file name
              will be constructed from the netCDF name (specified after the netcdf keyword in the
              input)  by  appending  the  `.nc'  extension.   If  a  file already exists with the
              specified name, it will be overwritten.

       -c     Generate C source  code  that  will  create  a  netCDF  file  matching  the  netCDF
              specification.  The C source code is written to standard output.

       -f     Generate  Fortran  source  code  that will create a netCDF file matching the netCDF
              specification.  The Fortran source code is written to standard output.

       -o outputfile
              Name for the netCDF file created.  If this option is specified, it implies the "-b"
              option.   (This option is necessary because netCDF files cannot be written directly
              to standard output, since standard output is not seekable.)

       -n     Like -b option, except creates netCDF  file  with  the  obsolete  `.cdf'  extension
              instead  of  the `.nc' extension, in the absence of an output filename specified by
              the -O option.  This option is only supported for backward compatibility.

EXAMPLES

       Check the syntax of the CDL file `foo.cdl':

              ncgen-hdf foo.cdl

       From the CDL file `foo.cdl', generate an equivalent binary netCDF file named `x.nc':

              ncgen-hdf -o x.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 named `x.nc':

              ncgen-hdf -c -o x.nc foo.cdl

USAGE

CDL Syntax Summary
Below is an example of CDL syntax, describing a netCDF file with several named dimensions
(lat, lon, and time), variables (Z, t, p, rh, lat, lon, time), variable attributes (units,
long_name, valid_range, _FillValue), and some data. CDL keywords are in boldface. (This
example is intended to illustrate the syntax; a real CDL file would have a more complete
set of attributes so that the data would be more completely self-describing.)

netcdf foo { // an 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);

// variable attributes
lat:long_name = "latitude";
lat:units = "degrees_north";
lon:long_name = "longitude";
lon:units = "degrees_east";
time:units = "seconds since 1992-1-1 00:00:00";
Z:units = "geopotential 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 characters `//' on any line.

A CDL description consists of three optional parts: dimensions, variables, and data,
beginning with the keyword dimensions:, variables:, and data, respectively. The variable
part may contain variable declarations and attribute assignments.

A netCDF dimension is used to define the shape of one or more of the multidimensional
variables contained in the netCDF file. A netCDF dimension has a name and a size. At
most one dimension in a netCDF file 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 is one-dimensional and contains coordinates of the dimension it names.
Dimensions need not have corresponding variables.

A netCDF attribute contains information about a netCDF variable or about the whole netCDF
dataset. Attributes are used to specify such properties as units, special values, maximum
and minimum valid values, scaling factors, offsets, and 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 metadata (data about data).

In CDL, an attribute is designated by a variable and attribute name, separated by `:'. It
is possible to assign global attributes not associated with any variable to the netCDF as
a whole by using `:' before the attribute name. 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 assigned to it, 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.

The names for CDL dimensions, variables, and attributes must begin with an alphabetic
character or `_', and subsequent characters may be alphanumeric or `_' or `-'.

The optional data section of a CDL specification is where netCDF variables may be
initialized. The syntax of an initialization is simple: a variable name, an equals sign,
and a comma-delimited list of constants (possibly separated by spaces, tabs and newlines)
terminated with a semicolon. For multi-dimensional 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 a type-dependent
`fill value', which can be overridden by supplying a value for a distinguished variable
attribute named `_FillValue'. The types of constants need not match the type declared for
a variable; coercions are done to convert integers to floating point, for example.

Primitive Data Types
char characters
byte 8-bit data
short 16-bit signed integers
long 32-bit signed integers
int (synonymous with long)
float IEEE single precision floating point (32 bits)
real (synonymous with float)
double IEEE double precision floating point (64 bits)

Except for the added data-type byte and the lack of unsigned, CDL supports the same
primitive data types as C. 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. In
declarations, type names may be specified in either upper or lower case.

Bytes differ from characters in that they are intended to hold a full eight bits of data,
and the zero byte has no special significance, as it does for character data. ncgen-hdf
converts byte declarations to char declarations in the output C code and to the
nonstandard BYTE declaration in output Fortran code.

Shorts can hold values between -32768 and 32767. ncgen-hdf converts short declarations to
short declarations in the output C code and to the nonstandard INTEGER*2 declaration in
output Fortran code.

Longs can hold values between -2147483648 and 2147483647. ncgen-hdf converts long
declarations to long declarations in the output C code and to INTEGER declarations in
output Fortran code. int and integer are accepted as synonyms for long in CDL
declarations. Now that there are platforms with 64-bit representations for C longs, it
may be better to use the int synonym to avoid confusion.

Floats can hold values between about -3.4+38 and 3.4+38. Their external representation is
as 32-bit IEEE normalized single-precision floating point numbers. ncgen-hdf converts
float declarations to float declarations in the output C code and to REAL declarations in
output Fortran code. real is accepted as a synonym for float in CDL declarations.

Doubles can hold values between about -1.7+308 and 1.7+308. Their external representation
is as 64-bit IEEE standard normalized double-precision floating point numbers. ncgen-hdf
converts double declarations to double declarations in the output C code and to DOUBLE
PRECISION declarations in output Fortran code.

CDL Constants
Constants assigned to attributes or variables may be of any of the basic netCDF types.
The syntax for constants is similar to C syntax, except that type suffixes must be
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)
'\377' // 377 octal = 255 decimal, non-ASCII

Character constants are enclosed in double quotes. A character array may be represented
as a string enclosed in double quotes. The usual C string escape conventions 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
Note that the netCDF character array "a" would fit in a one-element variable, since no
terminating NULL character is assumed. However, a zero byte in a character array is
interpreted as the end of the significant characters by the ncdump program, following the
C convention. Therefore, a NULL byte should not be embedded in a character string unless
at the end: use the byte data type instead for byte arrays that contain the zero byte.
NetCDF and CDL have no string type, but only fixed-length character arrays, which may be
multi-dimensional.

short integer constants are intended for representing 16-bit signed quantities. 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, except that if it begins with `0x',
it is interpreted as a hexadecimal constant. For example:
-2s // a short -2
0123s // octal
0x7ffs //hexadecimal

Long integer constants are intended for representing 32-bit signed quantities. 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,
except that if it begins with `0x', it is interpreted as a hexadecimal constant. Examples
of valid long constants include:
-2
1234567890L
0123 // octal
0x7ff // hexadecimal

Floating point constants of type float are appropriate for representing floating point
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. For example the
following are all acceptable float constants:
-2.0f
3.14159265358979f // will be truncated to less precision
1.f
.1f

Floating point constants of type double are appropriate for representing floating point
data with about sixteen 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. For
example the following are all acceptable double constants:
-2.0
3.141592653589793
1.0e-20
1.d

BUGS

       The programs generated by ncgen-hdf when using the -c or -f use initialization  statements
       to store data in variables, and will fail to produce compilable programs if you try to use
       them for large datasets, since the resulting statements may  exceed  the  line  length  or
       number of continuation statements permitted by the compiler.

       The CDL syntax makes it easy to assign what looks like an array of variable-length strings
       to a netCDF variable, but the strings will simply be concatenated into a single  array  of
       characters,  since  netCDF  cannot  represent  an  array of variable-length strings in one
       netCDF variable.

       NetCDF and CDL do not yet support a type corresponding to a 64-bit integer.