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ncgen

NAME

ncgen - From a CDL file generate a netCDF-3 file, a netCDF-4 file or a C program

SYNOPSIS

ncgen [-b] [-c] [-f] [-k file format] [-l output language] [-n] [-o netcdf_filename] [-x] input_file

DESCRIPTION

ncgen 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 ncgen 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, 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.

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.

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; equivalent to -lc.

-f

Generate 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.

-o netcdf_file

Name for the binary 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.)

-k file_format

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.

'1', 'classic' => netcdf classic file format, netcdf-3 type model.

'2', '64-bit-offset', '64-bit offset' => netcdf 64 bit classic file format, netcdf-3 type model.

'3', 'hdf5', 'netCDF-4', 'enhanced' => netcdf-4 file format, netcdf-4 type model.

'4', 'hdf5-nc3', 'netCDF-4 classic model', 'enhanced-nc3' => netcdf-4 file format, netcdf-3 type model.

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.

-x

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.

-l output_language

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.

c|C' => C language output.

f77|fortran77' => FORTRAN 77 language output

; note that currently only the classic model is supported.

j|java' => (experimental) Java language output

; targets the existing Unidata Java interface, which means that only the classic model is supported.

EXAMPLES

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 `x.nc':

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

USAGE

CDL Syntax Overview

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}, 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. The variable part 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 type 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, 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. The constant `_' can be used to designate the fill value for a variable.

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 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 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.

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.

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.

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.

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};
 

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.

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;
 

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.

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.

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.

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

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.

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.

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. `_Fletcher32 sets the `fletcher32' property for a variable. `_Endianness' is either `little' or `big', depending on how the variable is stored when first written. `_DeflateLevel' is an integer between 0 and 9 inclusive if compression has been specified for the variable. `_Shuffle' is 1 if use of the shuffle filter is specified for the variable. `_Storage' is `contiguous' or `chunked'. `_ChunkSizes' is a list of chunk sizes for each dimension of the variable

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.

1. The top level is automatically assumed to be a list of items,
   so it should not be inside {...}.

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

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

4. Compound instances must be embedded in {...}

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

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.

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. 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.

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.

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