Note that this version of ncgen was originally called ncgen4. The older ncgen program has been renamed to ncgen3.
ncgen 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 to generate the corresponding netCDF file from the edited CDL file.
Note: The old version format numbers '1', '2', '3', '4', equivalent to the format names 'nc3', 'nc6', 'nc4', or 'nc7' respectively, are also still accepted but deprecated, due to easy confusion between format numbers and format names. Various old format name aliases are also accepted but deprecated, e.g. 'hdf5', 'enhanced-nc3', etc. Also, note that -v is accepted to mean the same thing as -k for backward compatibility.
Note that there is an ambiguity between the netCDF-4 case and the CDF-5 case is only an unsigned type is seen in the input.
The rules are as follows, in order of application.
Check the syntax of the CDL file `foo.cdl':
From the CDL file `foo.cdl', generate an equivalent binary netCDF file named `x.nc':
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':
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
types:
ubyte enum enum_t {Clear = 0, Cumulonimbus = 1, Stratus = 2};
opaque(11) opaque_t;
int(*) vlen_t;
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);
string country(time,lat,lon);
ubyte 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
string Z:units = "geopotential meters";
float Z:valid_range = 0., 5000.;
double p:_FillValue = -9999.;
long rh:_FillValue = -1;
vlen_t :globalatt = {17, 18, 19};
data:
lat = 0, 10, 20, 30, 40, 50, 60, 70, 80, 90;
lon = -140, -118, -96, -84, -52;
group: g {
types:
compound cmpd_t { vlen_t f1; enum_t f2;};
} // group g
group: h {
variables:
/g/cmpd_t compoundvar;
data:
compoundvar = { {3,4,5}, enum_t.Stratus } ;
} // group h
}
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 five optional parts: types, dimensions, variables, data, beginning with the keyword `types:', `dimensions:', `variables:', and `data:', respectively. Note several things: (1) the keyword includes the trailing colon, so there must not be any space before the colon character, and (2) the keywords are required to be lower case.
The variables: section may contain variable declarations and attribute assignments. All sections may contain global attribute assignments.
In addition, after the data: 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.
The netCDF types: section declares the user defined types. These may be constructed using any of the following types: enum, vlen, opaque, or compound.
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. A dimension can have the unlimited size, which means a variable using this dimension can grow to any length in that dimension.
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). Unlike netCDF-3, attribute types can be any user defined type as well as the usual built-in types.
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 global 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
x : a = ...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.
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.
The names for CDL dimensions, variables, attributes, types, and groups may contain any non-control utf-8 character except the forward slash character (`/'). However, certain characters must escaped if they are used in a name, where the escape character is the backward slash `\'. In particular, if the leading character off the name is a digit (0-9), then it must be preceded by the escape character. In addition, the characters ` !"#$%&()*,:;<=>?[]^`'{}|~\' must be escaped if they occur anywhere in a name. Note also that attribute names that begin with an underscore (`_') are reserved for the use of Unidata and should not be used in user defined attributes.
Note also that the words `variable', `dimension', `data', `group', and `types' are legal CDL names, but be careful that there is a space between them and any following colon character when used as a variable name. This is mostly an issue with attribute declarations. For example, consider this.
netcdf ... {
...
variables:
int dimensions;
dimensions: attribute=0 ; // this will cause an error
dimensions : attribute=0 ; // this is ok.
...
}
char characters byte 8-bit data short 16-bit signed integers int 32-bit signed integers long (synonymous with int) int64 64-bit signed integers float IEEE single precision floating point (32 bits) real (synonymous with float) double IEEE double precision floating point (64 bits) ubyte unsigned 8-bit data ushort 16-bit unsigned integers uint 32-bit unsigned integers uint64 64-bit unsigned integers string arbitrary length strings
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.
Bytes are intended to hold a full eight bits of data, and the zero byte has no special significance, as it mays for character data. ncgen 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 converts short declarations to short declarations in the output C code and to the nonstandard INTEGER*2 declaration in output Fortran code.
Ints can hold values between -2147483648 and 2147483647. ncgen converts int declarations to int declarations in the output C code and to INTEGER declarations in output Fortran code. long is accepted as a synonym for int in CDL declarations, but is deprecated since there are now platforms with 64-bit representations for C longs.
Int64 can hold values between -9223372036854775808 and 9223372036854775807. ncgen converts int64 declarations to longlong declarations in the output C code.
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 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 converts double declarations to double declarations in the output C code and to DOUBLE PRECISION declarations in output Fortran code.
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.
The technical interpretation of the char type is that it is an unsigned 8-bit value. The encoding of the 256 possible values is unspecified by default. A variable of char type may be marked with an "_Encoding" attribute to indicate the character set to be used: US-ASCII, ISO-8859-1, etc. Note that specifying the encoding of UTF-8 is equivalent to specifying US-ASCII This is because multi-byte UTF-8 characters cannot be stored in an 8-bit character. The only legal single byte UTF-8 values are by definition the 7-bit US-ASCII encoding with the top bit set to zero.
Strings are assumed by default to be encoded using UTF-8. Note that this means that multi-byte UTF-8 encodings may be present in the string, so it is possible that the number of distinct UTF-8 characters in a string is smaller than the number of 8-bit bytes used to store the string.
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 an integer constant with a `b' (or `B') appended. In the old netCDF-2 API, byte constants could also be represented using single characters or standard C character escape sequences such as `a' or `. This is still supported for backward compatibility, but deprecated to make the distinction clear between the numeric byte type and the textual char type. Example byte constants include:
0b // a zero byte -1b // -1 as an 8-bit byte 255b // also -1 as a signed 8-bit byte
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
int integer constants are intended for representing 32-bit signed quantities. The form of an int constant is an ordinary integer constant, although it is acceptable to optionally append a single `l' or `L' (again, deprecated). Be careful, though, the L suffix is interpreted as a 32 bit integer, and never as a 64 bit integer. This can be confusing since the C long type can ambigously be either 32 bit or 64 bit.
If an int 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 int constants include:
-2 1234567890L 0123 // octal 0x7ff // hexadecimal
int64 integer constants are intended for representing 64-bit signed quantities. The form of an int64 constant is an integer constant with an `ll' or `LL' appended. If an int64 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:
-2ll // an unsigned -2 0123LL // octal 0x7ffLL //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
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
Unsigned integer constants can be created by appending the character 'U' or 'u' between the constant and any trailing size specifier, or immediately at the end of the size specifier. Thus one could say 10U, 100su, 100000ul, or 1000000llu, for example.
Single character constants may be enclosed in single quotes. If a sequence of one or more characters is enclosed in double quotes, then its interpretation must be inferred from the context. If the dataset is created using the netCDF classic model, then all such constants are interpreted as a character array, so each character in the constant is interpreted as if it were a single character. If the dataset is netCDF extended, then the constant may be interpreted as for the classic model or as a true string (see below) depending on the type of the attribute or variable into which the string is contained.
The interpretation of char constants is that those that are in the printable ASCII range (' '..'~') are assumed to be encoded as the 1-byte subset ofUTF-8, which is equivalent to US-ASCII. In all cases, the usual C string escape conventions are honored for values from 0 thru 127. Values greater than 127 are allowed, but their encoding is undefined. For netCDF extended, the use of the char type is deprecated in favor of the string type.
Some character constant examples are as follows.
'a' // ASCII `a' "a" // equivalent to 'a' "Two\nlines\n" // a 10-character string with two embedded newlines "a bell:\007" // a string containing an ASCII bell
String 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 thestring type to ensure the proper choice. String constants are assumed to always be UTF-8 encoded. This specifically means that the string constant may actually contain multi-byte UTF-8 characters. The special constant `NIL` can be used to represent a nil string, which is not the same as a zero length string.
Opaque 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.
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.
Given a type "T(*) vlen_t", where T is some other arbitrary base type, constants for this should be specified as follows.
vlen_t var[2] = {t11,t12,...t1N}, {t21,t22,...t2m};
The values tij, are assumed to be constants of type T.
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.
cmpd_t var[2] = {t11,t12,...t1N}, {t21,t22,...t2n};
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.
The general set of rules for using braces are defined in the Specifying Datalists section below.
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
variables:
/g1/g2/t1 v1;
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.
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.
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.
References to Enumeration constants (in data lists) can be ambiguous since the same enumeration constant name can be defined in more than one enumeration. If a cdl file specified an ambiguous constant, then ncgen will signal an error. Such constants can be disambiguated in two ways.
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.
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
The special attributes currently supported are as follows: `_Format', `_Fletcher32, `_ChunkSizes', `_Endianness', `_DeflateLevel', `_Shuffle', and `_Storage'.
`_Format' is a global attribute specifying the netCDF format variant. Its value must be a single string matching one of `classic', `64-bit offset', `64-bit data', `netCDF-4', or `netCDF-4 classic model'.
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 attributes 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.
Note that attributes such as "add_offset" or "scale_factor" have no special meaning to ncgen. These attributes are currently conventions, handled above the library layer by other utility packages, for example NCO.
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.
First, the top level is automatically assumed to be a list of items, so it should not be inside {...}. That means that if the variable is a scalar, there will be a single top-level element and if the variable is an array, there will be N top-level elements. For each element of the top level list, the following rules should be applied.
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.
Note that one consequence of these rules is that arrays of values cannot have subarrays within braces. Consider, for example, int var(d1)(d2)...(dn), where none of d2...dn are unlimited. 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.
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.
Specifying datalists for variables of type char also has some complications. consider, for example
dimensions: u=UNLIMITED; d1=1; d2=2; d3=3;
d4=4; d5=5; u2=UNLIMITED;
variables: char var(d4,d5);
datalist: var="1", "two", "three";
We have twenty elements of var to fill (d5 X d4) and we have three strings of length 1, 3, 5. How do we assign the characters in the strings to the twenty elements?
This is challenging because it is desirable to mimic the original ncgen (ncgen3). The core algorithm is notionally as follows.
There are three other cases of note.
In netcdf-4, dimensions other than the first can be unlimited. Of course by the rules above, the interior unlimited instances must be delimited by {...}. For example.
variables: char var(u,u2);
datalist: var={"1", "two"}, {"three"};
In this case u will have the effective length of two.
Within each instance of u2, the rules above will apply, leading
to this.
datalist: var={"1","t","w","o"}, {"t","h","r","e","e"};
The effective size of u2 will be the max of the two instance lengths
(five in this case)
and the shorter will be padded to produce this.
datalist: var={"1","t","w","o","\0"}, {"t","h","r","e","e"};
Consider an even more complicated case.
variables: char var(u,u2,u3);
datalist: var={{"1", "two"}}, {{"three"},{"four","xy"}};
In this case u again will have the effective length of two.
The u2 dimensions will have a size = max(1,2) = 2;
Within each instance of u2, the rules above will apply, leading to this.
datalist: var={{"1","t","w","o"}}, {{"t","h","r","e","e"},{"f","o","u","r","x","y"}};
The effective size of u3 will be the max of the two instance lengths
(six in this case) and the shorter ones will be padded to produce this.
datalist: var={{"1","t","w","o"," "," "}}, {{"t","h","r","e","e"," "},{"f","o","u","r","x","y"}};
Note however that the first instance of u2 is less than the max length
of u2, so we need to add a filler for another instance of u2, producing this.
datalist: var={{"1","t","w","o"," "," "},{" "," "," "," "," "," "}}, {{"t","h","r","e","e"," "},{"f","o","u","r","x","y"}};
The programs generated by ncgen when using the -c 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.
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 string type specifier may solve the problem
The file ncgen.y is the definitive grammar for CDL, but a stripped down version is included here for completeness.
ncdesc: NETCDF
datasetid
rootgroup
;
datasetid: DATASETID
rootgroup: '{'
groupbody
subgrouplist
'}';
groupbody:
attrdecllist
typesection
dimsection
vasection
datasection
;
subgrouplist:
/*empty*/
| subgrouplist namedgroup
;
namedgroup: GROUP ident '{'
groupbody
subgrouplist
'}'
attrdecllist
;
typesection: /* empty */
| TYPES
| TYPES typedecls
;
typedecls:
type_or_attr_decl
| typedecls type_or_attr_decl
;
typename: ident ;
type_or_attr_decl:
typedecl
| attrdecl ';'
;
typedecl:
enumdecl optsemicolon
| compounddecl optsemicolon
| vlendecl optsemicolon
| opaquedecl optsemicolon
;
optsemicolon:
/*empty*/
| ';'
;
enumdecl: primtype ENUM typename ;
enumidlist: enumid
| enumidlist ',' enumid
;
enumid: ident '=' constint ;
opaquedecl: OPAQUE '(' INT_CONST ')' typename ;
vlendecl: typeref '(' '*' ')' typename ;
compounddecl: COMPOUND typename '{' fields '}' ;
fields: field ';'
| fields field ';'
;
field: typeref fieldlist ;
primtype: CHAR_K
| BYTE_K
| SHORT_K
| INT_K
| FLOAT_K
| DOUBLE_K
| UBYTE_K
| USHORT_K
| UINT_K
| INT64_K
| UINT64_K
;
dimsection: /* empty */
| DIMENSIONS
| DIMENSIONS dimdecls
;
dimdecls: dim_or_attr_decl ';'
| dimdecls dim_or_attr_decl ';'
;
dim_or_attr_decl: dimdeclist | attrdecl ;
dimdeclist: dimdecl
| dimdeclist ',' dimdecl
;
dimdecl:
dimd '=' UINT_CONST
| dimd '=' INT_CONST
| dimd '=' DOUBLE_CONST
| dimd '=' NC_UNLIMITED_K
;
dimd: ident ;
vasection: /* empty */
| VARIABLES
| VARIABLES vadecls
;
vadecls: vadecl_or_attr ';'
| vadecls vadecl_or_attr ';'
;
vadecl_or_attr: vardecl | attrdecl ;
vardecl: typeref varlist ;
varlist: varspec
| varlist ',' varspec
;
varspec: ident dimspec ;
dimspec: /* empty */
| '(' dimlist ')'
;
dimlist: dimref
| dimlist ',' dimref
;
dimref: path ;
fieldlist:
fieldspec
| fieldlist ',' fieldspec
;
fieldspec: ident fielddimspec ;
fielddimspec: /* empty */
| '(' fielddimlist ')'
;
fielddimlist:
fielddim
| fielddimlist ',' fielddim
;
fielddim:
UINT_CONST
| INT_CONST
;
/* Use this when referencing defined objects */
varref: type_var_ref ;
typeref: type_var_ref ;
type_var_ref:
path
| primtype
;
/* Use this for all attribute decls */
/* Watch out; this is left recursive */
attrdecllist: /*empty*/ | attrdecl ';' attrdecllist ;
attrdecl:
':' ident '=' datalist
| typeref type_var_ref ':' ident '=' datalist
| type_var_ref ':' ident '=' datalist
| type_var_ref ':' _FILLVALUE '=' datalist
| typeref type_var_ref ':' _FILLVALUE '=' datalist
| type_var_ref ':' _STORAGE '=' conststring
| type_var_ref ':' _CHUNKSIZES '=' intlist
| type_var_ref ':' _FLETCHER32 '=' constbool
| type_var_ref ':' _DEFLATELEVEL '=' constint
| type_var_ref ':' _SHUFFLE '=' constbool
| type_var_ref ':' _ENDIANNESS '=' conststring
| type_var_ref ':' _NOFILL '=' constbool
| ':' _FORMAT '=' conststring
;
path:
ident
| PATH
;
datasection: /* empty */
| DATA
| DATA datadecls
;
datadecls:
datadecl ';'
| datadecls datadecl ';'
;
datadecl: varref '=' datalist ;
datalist:
datalist0
| datalist1
;
datalist0:
/*empty*/
;
/* Must have at least 1 element */
datalist1:
dataitem
| datalist ',' dataitem
;
dataitem:
constdata
| '{' datalist '}'
;
constdata:
simpleconstant
| OPAQUESTRING
| FILLMARKER
| NIL
| econstref
| function
;
econstref: path ;
function: ident '(' arglist ')' ;
arglist:
simpleconstant
| arglist ',' simpleconstant
;
simpleconstant:
CHAR_CONST /* never used apparently*/
| BYTE_CONST
| SHORT_CONST
| INT_CONST
| INT64_CONST
| UBYTE_CONST
| USHORT_CONST
| UINT_CONST
| UINT64_CONST
| FLOAT_CONST
| DOUBLE_CONST
| TERMSTRING
;
intlist:
constint
| intlist ',' constint
;
constint:
INT_CONST
| UINT_CONST
| INT64_CONST
| UINT64_CONST
;
conststring: TERMSTRING ;
constbool:
conststring
| constint
;
/* Push all idents thru here for tracking */
ident: IDENT ;