ncgen (1) - Linux Manuals

Primitive Data Types

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.

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
 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 append an optional `l' or `L' (again, deprecated). 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. Thus one could say 10U, 100us, 100000ul, or 1000000ull, 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.

Compound Constant Expressions

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};

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 general set of rules for using braces are defined in the Specifying Datalists section below.

Scoping Rules

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;

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.

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.

2. 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.

3. For all other names, only the immediately enclosing group is searched.

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.

Specifying Enumeration Constants

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.

1.

Prefix the enumeration constant with the name of the enumeration separated by a dot: enum.econst, for example.

2.

If case one is not sufficient to disambiguate the enumeration constant, then one must specify the precise enumeration type using a group path: /g1/g2/enum.econst, for example.

Special Attributes

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', `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 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.

1.

`_Fletcher32 sets the `fletcher32' property for a variable.

2.

`_Endianness' is either `little' or `big', depending on how the variable is stored when first written.

3.

`_DeflateLevel' is an integer between 0 and 9 inclusive if compression has been specified for the variable.

4.

`_Shuffle' specifies if the the shuffle filter should be used.

5.

`_Storage' is `contiguous' or `chunked'.

6.

`_ChunkSizes' is a list of chunk sizes for each dimension of the variable

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

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.

1.

Instances of UNLIMITED dimensions (other than the first dimension) must be surrounded by {...} in order to specify the size.

2.

Compound instances must be embedded in {...}

3.

Non-scalar fields of compound instances must be embedded in {...}.

4.

Instances of vlens must be surrounded by {...} in order to specify the size.

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.

7.

No other use of braces is allowed.

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 Character Datalists

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.

1.

Assume we have a set of dimensions D1..Dn, where D1 may optionally be an Unlimited dimension. It is assumed that the sizes of the Di are all known (including unlimited dimensions).

2.

Given a sequence of string or character constants C1..Cm, our goal is to construct a single string whose length is the cross product of D1 thru Dn. Note that for purposes of this algorithm, character constants are treated as strings of size 1.

3.

Construct Dx = cross product of D1 thru D(n-1).

4.

For each constant Ci, add fill characters as needed so that its length is a multiple of Dn.

5.

Concatenate the modified C1..Cm to produce string S.

6.

Add fill characters to S to make its length be a multiple of Dn.

8.

If S is longer than the Dx * Dn, then truncate and generate a warning.

There are three other cases of note.

1.

If there is only a single, unlimited dimension, then all of the constants are concatenated and fill characers are added to the end of the resulting string to make its length be that of the unlimited dimension. If the length is larger than the unlimited dimension, then it is truncated with a warning.

2.

For the case of character typed vlen, "char(*) vlen_t" for example. we simply concatenate all the constants with no filling at all.

3.

For the case of a character typed attribute, we simply concatenate all the constants.

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"};

Consider an even more complicated case.

variables: char var(u,u2,u3);
datalist: var={{"1", "two"}}, {{"three"},{"four","xy"}};

datalist: var={{"1","t","w","o"}}, {{"t","h","r","e","e"},{"f","o","u","r","x","y"}};

datalist: var={{"1","t","w","o"," "," "}}, {{"t","h","r","e","e"," "},{"f","o","u","r","x","y"}};

datalist: var={{"1","t","w","o"," "," "},{" "," "," "," "," "," "}}, {{"t","h","r","e","e"," "},{"f","o","u","r","x","y"}};

BUGS

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

CDL Grammar

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 ;