netcdf-c/ncgen/ncgen.1

.\" $Header: /upc/share/CVS/netcdf-3/ncgen/ncgen.1,v 1.10 2010/04/29 16:38:55 dmh Exp $
.TH NCGEN 1 "$Date: 2010/04/29 16:38:55 $" "Printed: \n(yr-\n(mo-\n(dy" "UNIDATA UTILITIES"
.SH NAME
ncgen \- From a CDL file generate a netCDF-3 file, a netCDF-4 file or a C program
.SH SYNOPSIS
.HP
ncgen
.nh
\%[-b]
\%[-c]
\%[-f]
\%[-k \fIfile format\fP]
\%[-l \fIoutput language\fP]
\%[-n]
\%[-o \fInetcdf_filename\fP]
\%[-x]
\%\fIinput_file\fP
.hy
.ft
.SH DESCRIPTION
\fBncgen\fP generates either a netCDF-3 (i.e. classic) binary .nc file,
a netCDF-4 (i.e. enhanced) binary .nc file
or a file in some source language that when executed will
construct the corresponding binary .nc file.
The input to \fBncgen\fP 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 \fBncgen\fP, it merely checks the
syntax of the input CDL file, producing error messages for
any violations of CDL syntax.  Other options can be used, for example,
to create the corresponding netCDF file,
or to generate a C program that uses the netCDF C
interface to create the netCDF file.
.LP
Note that this version of ncgen was originally called ncgen4.
The older ncgen program has been renamed to ncgen3.
.LP
\fBncgen\fP may be used with the companion program \fBncdump\fP to perform
some simple operations on netCDF files.  For example, to rename a dimension
in a netCDF file, use \fBncdump\fP to get a CDL version of the netCDF file,
edit the CDL file to change the name of the dimensions, and use \fBncgen\fP
to generate the corresponding netCDF file from the edited CDL file.
.SH OPTIONS
.IP "\fB-b\fP"
Create a (binary) netCDF file.  If the \fB-o\fP option is absent, a default
file name will be constructed from the netCDF name (specified after the
\fBnetcdf\fP keyword in the input) by appending the `.nc' extension.  If a
file already exists with the specified name, it will be overwritten.
.IP "\fB-c\fP"
Generate
.B C
source code that will create a netCDF file
matching the netCDF specification.  The C source code is written to
standard output; equivalent to -lc.
.IP "\fB-f\fP"
Generate
.B FORTRAN 77
source code that will create a netCDF file
matching the netCDF specification.
The source code is written to
standard output; equivalent to -lf77.
.IP "\fB-o\fP \fRnetcdf_file\fP"
Name for the binary netCDF file created.  If this option is specified, it implies
the "\fB-b\fP" option.  (This option is necessary because netCDF files
cannot be written directly to standard output, since standard output is not
seekable.)
.IP "\fB-k \fRfile_format\fP"
The -k flag specifies the format of the file to be created and, by inference,
the data model accepted by ncgen (i.e. netcdf-3 (classic) versus
netcdf-4).
The possible arguments are as follows.
.RS
.RS
.IP "'1', 'classic' => netcdf classic file format, netcdf-3 type model."
.IP "'2', '64-bit-offset', '64-bit offset' => netcdf 64 bit classic file format, netcdf-3 type model."
.IP "'3', 'hdf5', 'netCDF-4', 'enhanced' => netcdf-4 file format, netcdf-4 type model."
.IP "'4', 'hdf5-nc3', 'netCDF-4 classic model', 'enhanced-nc3' => netcdf-4 file format, netcdf-3 type model."
.RE
.RE
If no -k is specified then it defaults to -k1 (i.e. classic).
Note also that -v is accepted to mean the same thing as
-k for backward compatibility, but -k is preferred, to match
the corresponding ncdump option. 
.IP "\fB-x\fP"
Don't initialize data with fill values.  This can speed up creation of
large netCDF files greatly, but later attempts to read unwritten data
from the generated file will not be easily detectable.
.IP "\fB-l \fRoutput_language\fP"
The -l flag specifies the output language to use
when generating source code that will create or define a netCDF file
matching the netCDF specification.
The output is written to standard output.
The currently supported languages have the following flags.
.RS
.RS
.IP "c|C' => C language output."
.IP "f77|fortran77' => FORTRAN 77 language output"
; note that currently only the classic model is supported.
.IP "j|java' => (experimental) Java language output"
; targets the existing Unidata Java interface, which means that
only the classic model is supported.
.RE
.RE
.SH EXAMPLES
.LP
Check the syntax of the CDL file `\fBfoo.cdl\fP':
.RS
.HP
ncgen foo.cdl
.RE
.LP
From the CDL file `\fBfoo.cdl\fP', generate an equivalent binary netCDF file
named `\fBx.nc\fP':
.RS
.HP
ncgen -o x.nc foo.cdl
.RE
.LP
From the CDL file `\fBfoo.cdl\fP', generate a C program containing the
netCDF function invocations necessary to create an equivalent binary netCDF
file named `\fBx.nc\fP':
.RS
.HP
ncgen -c -o x.nc foo.cdl
.RE
.LP
.SH USAGE
.SS "CDL Syntax Overview"
.LP
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.)
.RS
.nf
netcdf foo {  // an example netCDF specification in CDL

\fBtypes\fP:
    \fIubyte\fP \fIenum\fP enum_t {Clear = 0, Cumulonimbus = 1, Stratus = 2};
    \fIopaque\fP(11) opaque_t;
    \fIint\fP(*) vlen_t;

\fBdimensions\fP:
	lat = 10, lon = 5, time = \fIunlimited\fP ;

\fBvariables\fP:
	\fIlong\fP    lat(lat), lon(lon), time(time);
	\fIfloat\fP   Z(time,lat,lon), t(time,lat,lon);
	\fIdouble\fP  p(time,lat,lon);
	\fIlong\fP    rh(time,lat,lon);

	\fIstring\fP  country(time,lat,lon);
	\fIubyte\fP   tag;

	// 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";

	// typed variable attributes
	\fIstring\fP Z:units = "geopotential meters";
	\fIfloat\fP Z:valid_range = 0., 5000.;
	\fIdouble\fP p:_FillValue = -9999.;
	\fIlong\fP rh:_FillValue = -1;
	\fIvlen_t\fP :globalatt = {17, 18, 19};
\fBdata\fP:
	lat   = 0, 10, 20, 30, 40, 50, 60, 70, 80, 90;
	lon   = -140, -118, -96, -84, -52;
\fBgroup\fP g {
\fBtypes\fP:
    \fIcompound\fP cmpd_t { \fIvlen_t\fP f1; \fIenum_t\fP f2;};
} // group g
\fBgroup\fP h {
\fBvariables\fP:
	/g/\fIcmpd_t\fP  compoundvar;
\fBdata\fP:
        compoundvar = { {3,4,5}, Stratus } ;
} // group h
}
.fi
.RE
.LP
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.
.LP
A CDL description consists of five optional parts:
\fItypes\fP,
\fIdimensions\fP,
\fIvariables\fP,
\fIdata\fP,
beginning with the keyword
.BR types: ,
.BR dimensions: ,
.BR variables: ,
and
.BR data ,
respectively.
The variable part may contain \fIvariable
declarations\fP and \fIattribute assignments\fP.
All sections may contain global attribute assignments.
.LP
In addition, after the \fBdata:\fP section, the user
may define a series of groups (see the example above).
Groups themselves can contain types, dimensions, variables,
data, and other (nested) groups.
.LP
The netCDF \fBtype\fP section declares the user defined types.
These may be constructed using any of the following types:
\fBenum\fP, \fBvlen\fP, \fBopaque\fP, or \fBcompound\fP.
.LP
A netCDF \fIdimension\fP 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.  A dimension
can have the \fBunlimited\fP size, which means a variable using this
dimension can grow to any length in that dimension.
.LP
A \fIvariable\fP 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
\fIattributes\fP (see below) as well as data values.  The name, data
type, and shape of a variable are specified by its declaration in the
\fIvariable\fP 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.
.LP
A netCDF \fIattribute\fP 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).
Unlike netCDF-3, attribute types can be any user defined type
as well as the usual built-in types.
.LP
In CDL, an attribute is designated by a
a type, a variable, a ':', and then an attribute name.
The type is optional and if missing, it will be inferred from the values
assigned to the attribute.
It is possible to assign \fIglobal\fP attributes
not associated with any variable to the netCDF as a whole by omitting
the variable name in the attribute declaration.
Notice that there is a potential ambiguity in a specification such as
.nf
x : a = ...
.fi
In this situation, x could be either a type for a global attribute,
or the variable name for an attribute. Since there could both be a type named
x and a variable named x, there is an ambiguity.
The rule is that in this situation, x will be interpreted as a
type if possible, and otherwise as a variable.
.LP
If not specified, the data type of an attribute in CDL
is derived from the type of the value(s) 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.
.LP
The names for CDL dimensions, variables, and attributes must begin with an
alphabetic character or `_', and subsequent characters may be alphanumeric
or `_' or `-'.
.LP
The optional \fIdata\fP 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.
The constant `_' can be used to designate the fill value for a variable.
.SS "Primitive Data Types"
.LP
.RS
.nf
\fBchar\fP	characters
\fBbyte\fP	8-bit data
\fBshort\fP	16-bit signed integers
\fBint\fP	32-bit signed integers
\fBlong\fP	(synonymous with \fBint\fP)
\fBint64\fP	64-bit signed integers
\fBfloat\fP	IEEE single precision floating point (32 bits)
\fBreal\fP	(synonymous with \fBfloat\fP)
\fBdouble\fP	IEEE double precision floating point (64 bits)
\fBubyte\fP	unsigned 8-bit data
\fBushort\fP	16-bit unsigned integers
\fBuint\fP	32-bit unsigned integers
\fBuint64\fP	64-bit unsigned integers
\fBstring\fP	arbitrary length strings
.fi
.RE
.LP
CDL supports a superset of the primitive data types of C.
The names for the primitive data types are reserved words in CDL,
so the names of variables, dimensions, and attributes must not be
primitive type names.  In declarations, type names may be specified
in either upper or lower case.
.LP
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.
\fBncgen\fP converts \fBbyte\fP declarations to \fBchar\fP
declarations in the output C code and to the nonstandard \fBBYTE\fP
declaration in output Fortran code.
.LP
Shorts can hold values between -32768 and 32767.
\fBncgen\fP converts \fBshort\fP declarations to \fBshort\fP
declarations in the output C code and to the nonstandard \fBINTEGER*2\fP
declaration in output Fortran code.
.LP
Ints can hold values between -2147483648 and 2147483647.
\fBncgen\fP converts \fBint\fP declarations to \fBint\fP
declarations in the output C code and to \fBINTEGER\fP
declarations in output Fortran code.  \fBlong\fP
is accepted as a synonym for \fBint\fP in CDL declarations, but is
deprecated since there are now platforms with 64-bit representations
for C longs.
.LP
Int64 can hold values between -9223372036854775808
and 9223372036854775807.
\fBncgen\fP converts \fBint64\fP declarations to \fBlonglong\fP
declarations in the output C code.
.\" and to \fBINTEGER\fP declarations in output Fortran code.
.LP
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.  \fBncgen\fP converts \fBfloat\fP
declarations to \fBfloat\fP declarations in the output C code and to
\fBREAL\fP declarations in output Fortran code.  \fBreal\fP is accepted
as a synonym for \fBfloat\fP in CDL declarations.
.LP
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.  \fBncgen\fP converts
\fBdouble\fP declarations to \fBdouble\fP declarations in the output C
code and to \fBDOUBLE PRECISION\fP declarations in output Fortran
code.
.LP
The unsigned counterparts of the above integer types
are mapped to the corresponding unsigned C types.
Their ranges are suitably modified to start at zero.
.LP
.SS "CDL Constants"
.LP
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.
.LP
A \fIbyte\fP constant is represented by a single character or multiple
character escape sequence enclosed in single quotes.  For example,
.RS
.nf
 '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
.fi
.RE
.LP
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
.RS
.nf
"a"		// ASCII `a'
"Two\\nlines\\n"	// a 10-character string with two embedded newlines
"a bell:\\007"	// a string containing an ASCII bell
.fi
.RE
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 \fBncdump\fP program, following the C convention.
Therefore, a NULL byte should not be embedded in a character string unless
at the end: use the \fIbyte\fP data type instead for byte arrays that
contain the zero byte.
.LP
\fIshort\fP integer constants are intended for representing 16-bit
signed quantities.  The form of a \fIshort\fP constant is an integer
constant with an `s' or `S' appended.  If a \fIshort\fP 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:
.RS
.nf
-2s	// a short -2
0123s	// octal
0x7ffs  //hexadecimal
.fi
.RE
.LP
\fIint\fP integer constants are intended for representing 32-bit signed
quantities.  The form of an \fIint\fP constant is an ordinary integer
constant, although it is acceptable to append an optional `l' or
`L' (again, deprecated).
If an \fIint\fP constant begins with `0', it is interpreted as
octal, except that if it begins with `0x', it is interpreted as a hexadecimal
constant (but see opaque constants below).
Examples of valid \fIint\fP constants include:
.RS
.nf
-2
1234567890L
0123		// octal
0x7ff		// hexadecimal
.fi
.RE
.LP
\fIint64\fP integer constants are intended for representing 64-bit
signed quantities.  The form of an \fIint64\fP constant is an integer
constant with an `ll' or `LL' appended.  If an \fIint64\fP 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:
.RS
.nf
-2ll	// an unsigned -2
0123LL	// octal
0x7ffLL  //hexadecimal
.fi
.RE
.LP
Floating point constants of type \fIfloat\fP are appropriate for representing
floating point data with about seven significant digits of precision. 
The form of a \fIfloat\fP constant is the same as a C floating point
constant with an `f' or `F' appended.  For example the following
are all acceptable \fIfloat\fP constants:
.RS
.nf
-2.0f
3.14159265358979f	// will be truncated to less precision
1.f
.1f
.fi
.RE
.LP
Floating point constants of type \fIdouble\fP are appropriate for
representing floating point data with about sixteen significant digits
of precision.  The form of a \fIdouble\fP 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 \fIdouble\fP constants:
.RS
.nf
-2.0
3.141592653589793
1.0e-20
1.d
.fi
.RE
.LP
Unsigned integer constants can be created by appending
the character 'U' or 'u' between the constant and any trailing
size specifier.  Thus one could say
10U, 100us, 100000ul, or 1000000ull, for example.
.LP
\fIString\fP constants are, like character constants,
represented using double quotes. This represents a potential
ambiguity since a multi-character string may also indicate
a dimensioned character value. Disambiguation usually occurs
by context, but care should be taken to specify the\fIstring\fP
type to ensure the proper choice.
.LP
\fIOpaque\fP constants are represented as
sequences of hexadecimal digits preceded by 0X or 0x: 0xaa34ffff,
for example.
These constants can still be used as integer constants
and will be either truncated or extended as necessary.
.SS "Compound Constant Expressions"
.LP
In order to assign values to variables (or attributes)
whose type is user-defined type, the constant notation has been
extended to include sequences of constants enclosed in curly
brackets (e.g. "{"..."}").
Such a constant is called a compound constant, and compound constants
can be nested.
.LP
Given a type "T(*) vlen_t", where T is some other arbitrary base type,
constants for this should be specified as follows.
.nf
    vlen_t var[2] = {t11,t12,...t1N}, {t21,t22,...t2m};
.fi
The values tij, are assumed to be constants of type T.
.LP
Given a type "compound cmpd_t {T1 f1; T2 f2...Tn fn}",
where the Ti are other arbitrary base types,
constants for this should be specified as follows.
.nf
    cmpd_t var[2] = {t11,t12,...t1N}, {t21,t22,...t2n};
.fi
The values tij, are assumed to be constants of type Ti.
If the fields are missing, then they will be set using any
specified or default fill value for the field's base type.
.LP
The general set of rules for using braces are defined in the
.B Specifying
.B Datalists
section below.
.LP
.SS "Scoping Rules"
.LP
With the addition of groups, the name space for defined objects
is no longer flat. References (names)
of any type, dimension, or variable may be prefixed
with the absolute path specifying a specific declaration.
Thus one might say
.nf
    variables:
        /g1/g2/t1 v1;
.fi
The type being referenced (t1) is the one within group g2, which in
turn is nested in group g1.
The similarity of this notation to Unix file paths is deliberate,
and one can consider groups as a form of directory structure.
.HP
1. When name is not prefixed, then scope rules are applied to locate the
specified declaration. Currently, there are three rules: one for dimensions,
one for types and enumeration constants, and one for all others.
.HP
2. When an unprefixed name of a dimension is used (as in a variable declaration),
ncgen first looks in the immediately enclosing group for the dimension.
If it is not found there, then it looks in the group enclosing this group.
This continues up the group hierarchy until the dimension is found,
or there are no more groups to search.
.HP
3. For all other names, only the immediately enclosing group is searched.
.LP
When an unprefixed name of a type or an enumeration constant
is used, ncgen searches the group tree using a pre-order depth-first
search. This essentially means that it will find the matching declaration
that precedes the reference textually in the cdl file and that
is "highest" in the group hierarchy.
.LP
One final note. Forward references are not allowed.
This means that specifying, for example,
/g1/g2/t1 will fail if this reference occurs before g1 and/or g2 are defined.
.SS "Special Attributes"
.LP
Special, virtual, attributes can be specified to provide
performance-related information about the file format and
about variable properties.
The file must be a netCDF-4 file for these to take effect.
.LP
These special virtual attributes are not actually part of the file,
they are merely a convenient way to set miscellaneous
properties of the data in CDL
.LP
The special attributes currently supported are as follows:
`_Format',
`_Fletcher32, 
`_ChunkSizes', 
`_Endianness', 
`_DeflateLevel', 
`_Shuffle', and
`_Storage'.
.LP
`_Format' is a global attribute specifying the netCDF format
variant. Its value must be a single string
matching one of `classic', `64-bit offset', `netCDF-4', or
`netCDF-4 classic model'.
.LP
The rest of the special attributes are all variable attributes.
Essentially all of then map to some corresponding `nc_def_var_XXX'
function as defined in the netCDF-4 API.
For the atttributes that are essentially boolean (_Fletcher32, _Shuffle,
and _NOFILL), the value true can be specified by using the strings
`true' or `1', or by using the integer 1.
The value false expects either `false', `0', or the integer 0.
The actions associated with these attributes are as follows.
.IP 1. 3
`_Fletcher32 sets the `fletcher32' property for a variable.
.IP 2. 3
`_Endianness' is either `little' or `big', depending on
how the variable is stored when first written.
.IP 3. 3
`_DeflateLevel' is an
integer between 0 and 9 inclusive if compression has been specified
for the variable.
.IP 4. 3
`_Shuffle' specifies if the the shuffle filter should be used.
.IP 5. 3
`_Storage' is `contiguous' or `chunked'.
.IP 6. 3
`_ChunkSizes' is a list of chunk sizes for each dimension of
the variable
.LP
.SS "Specifying Datalists"
.LP
Specifying datalists for variables in the `data:` section can be somewhat
complicated. There are some rules that must be followed
to ensure that datalists are parsed correctly by ncgen.
.HP
1. The top level is automatically assumed to be a list of items,
   so it should not be inside {...}.
.HP
2. Instances of UNLIMITED dimensions (other than the first dimension)
   must be surrounded by {...} in order to specify the size.
.HP
3. Instances of vlens must be surrounded by {...} in order to
   specify the size.
.HP
4. Compound instances must be embedded in {...}
.HP
5. Non-scalar fields of compound instances must be embedded in {...}.
.HP
6. Datalists associated with attributes are implicitly a vector
(i.e., a list) of values of the type of the attribute and the above
rules must apply with that in mind.
.HP
7. No other use of braces is allowed.
.LP
Note that one consequence of these rules is that
arrays of values cannot have subarrays within braces.
Thus, given, for example, int var(d1)(d2)...(dn),
a datalist for this variable must be a single list of integers,
where the number of integers is no more than D=d1*d2*...dn values;
note that the list can be less than D, in which case fill values
will be used to pad the list.
.LP
Rule 6 about attribute datalist has the following consequence.
If the type of the attribute is a compound (or vlen) type, and if
the number of entries in the list is one, then the compound instances
must be enclosed in braces.

.SH BUGS
.LP
The programs generated by \fBncgen\fP when using the \fB-c\fP flag
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.
.LP
The CDL syntax makes it easy to assign what looks like an array of
variable-length strings to a netCDF variable, but the strings may simply be
concatenated into a single array of characters.
Specific use of the \fIstring\fP type specifier may solve the problem