ncgen3 − From a CDL file generate a netCDF classic or 64 bit classicfile, a C program, or a Fortran program
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ncgen3 [-b] [-c] [-f] [-k kind_of_file] [-x] [-n] [-o netcdf_filename] input_file |
ncgen3 generates either a netCDF file, or C or Fortran source code to create a netCDF file. The input to ncgen3 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 ncgen3, it merely checks the syntax of the input CDL file, producing error messages for any violations of CDL syntax. Other options can be used to create the corresponding netCDF file, to generate a C program that uses the netCDF C interface to create the netCDF file, or to generate a Fortran program that uses the netCDF Fortran interface to create the same netCDF file.
ncgen3 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 ncgen3 to generate the corresponding netCDF file from the edited CDL file.
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-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. | ||
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-c |
Generate C source code that will create a netCDF file matching the netCDF specification. The C source code is written to standard output. | ||
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-f |
Generate Fortran source code that will create a netCDF file matching the netCDF specification. The Fortran source code is written to standard output. |
-o 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 kind_of_file
Using -k2 or -k "64-bit offset" specifies that generated file (or program) should use version 2 of format that employs 64-bit file offsets. The default is to use version 1 ("classic") format with 32-bit file offsets, although this limits the size of the netCDF file, variables, and records to the sizes supported by the classic format. (NetCDF-4 will support additional kinds of netCDF files, "netCDF-4" and "netCDF-4 classic model".) Note: -v is also accepted to mean the same thing as -k for backward compatibility, but -k is preferred, to match the corresponding ncdump option.
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-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. |
Check the syntax of the CDL file ‘foo.cdl’:
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ncgen3 foo.cdl |
From the CDL file ‘foo.cdl’, generate an equivalent binary netCDF file named ‘x.nc’:
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ncgen3 -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’:
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ncgen3 -c -o x.nc foo.cdl |
CDL Syntax
Summary
Below is an example of CDL syntax, describing a netCDF file
with several named dimensions (lat, lon, and time),
variables (Z, t, p, rh, lat, lon, time), variable attributes
(units, long_name, valid_range, _FillValue), and some data.
CDL keywords are in boldface. (This example is intended to
illustrate the syntax; a real CDL file would have a more
complete set of attributes so that the data would be more
completely self-describing.)
netcdf foo { // an example netCDF specification in CDL
dimensions:
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lat = 10, lon = 5, time = unlimited ; |
variables:
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long lat(lat), lon(lon), time(time); | |
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float Z(time,lat,lon), t(time,lat,lon); | |
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double p(time,lat,lon); | |
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long rh(time,lat,lon); | |
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// variable attributes | |
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lat:long_name = "latitude"; | |
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lat:units = "degrees_north"; | |
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lon:long_name = "longitude"; | |
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lon:units = "degrees_east"; | |
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time:units = "seconds since 1992-1-1 00:00:00"; | |
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Z:units = "geopotential meters"; | |
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Z:valid_range = 0., 5000.; | |
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p:_FillValue = -9999.; | |
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rh:_FillValue = -1; |
data:
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lat = 0, 10, 20, 30, 40, 50, 60, 70, 80, 90; | |
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lon = -140, -118, -96, -84, -52; |
}
All CDL statements are terminated by a semicolon. Spaces, tabs, and newlines can be used freely for readability. Comments may follow the characters ‘//’ on any line.
A CDL description consists of three optional parts: dimensions, variables, and data, beginning with the keyword dimensions:, variables:, and data, respectively. The variable part may contain variable declarations and attribute assignments.
A netCDF dimension is used to define the shape of one or more of the multidimensional variables contained in the netCDF file. A netCDF dimension has a name and a size. At most one dimension in a netCDF file can have the unlimited size, which means a variable using this dimension can grow to any length (like a record number in a file).
A variable represents a multidimensional array of values of the same type. A variable has a name, a data type, and a shape described by its list of dimensions. Each variable may also have associated attributes (see below) as well as data values. The name, data type, and shape of a variable are specified by its declaration in the variable section of a CDL description. A variable may have the same name as a dimension; by convention such a variable is one-dimensional and contains coordinates of the dimension it names. Dimensions need not have corresponding variables.
A netCDF attribute contains information about a netCDF variable or about the whole netCDF dataset. Attributes are used to specify such properties as units, special values, maximum and minimum valid values, scaling factors, offsets, and parameters. Attribute information is represented by single values or arrays of values. For example, "units" is an attribute represented by a character array such as "celsius". An attribute has an associated variable, a name, a data type, a length, and a value. In contrast to variables that are intended for data, attributes are intended for metadata (data about data).
In CDL, an attribute is designated by a variable and attribute name, separated by ‘:’. It is possible to assign global attributes not associated with any variable to the netCDF as a whole by using ‘:’ before the attribute name. The data type of an attribute in CDL is derived from the type of the value assigned to it. The length of an attribute is the number of data values assigned to it, or the number of characters in the character string assigned to it. Multiple values are assigned to non-character attributes by separating the values with commas. All values assigned to an attribute must be of the same type.
The names for CDL dimensions, variables, and attributes must begin with an alphabetic character or ‘_’, and subsequent characters may be alphanumeric or ‘_’ or ‘-’.
The optional data section of a CDL specification is where netCDF variables may be initialized. The syntax of an initialization is simple: a variable name, an equals sign, and a comma-delimited list of constants (possibly separated by spaces, tabs and newlines) terminated with a semicolon. For multi-dimensional arrays, the last dimension varies fastest. Thus row-order rather than column order is used for matrices. If fewer values are supplied than are needed to fill a variable, it is extended with a type-dependent ‘fill value’, which can be overridden by supplying a value for a distinguished variable attribute named ‘_FillValue’. The types of constants need not match the type declared for a variable; coercions are done to convert integers to floating point, for example. The constant ‘_’ can be used to designate the fill value for a variable.
Primitive Data Types
char characters
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byte |
8-bit data | |||
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short |
16-bit signed integers | |||
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long |
32-bit signed integers | |||
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int |
(synonymous with long) | |||
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float |
IEEE single precision floating point (32 bits) | |||
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real |
(synonymous with float) | |||
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double |
IEEE double precision floating point (64 bits) |
Except for the added data-type byte and the lack of unsigned, CDL supports the same primitive data types as C. The names for the primitive data types are reserved words in CDL, so the names of variables, dimensions, and attributes must not be type names. In declarations, type names may be specified in either upper or lower case.
Bytes differ from characters in that they are intended to hold a full eight bits of data, and the zero byte has no special significance, as it does for character data. ncgen3 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. ncgen3 converts short declarations to short declarations in the output C code and to the nonstandard INTEGER*2 declaration in output Fortran code.
Longs can hold values between -2147483648 and 2147483647. ncgen3 converts long declarations to long declarations in the output C code and to INTEGER declarations in output Fortran code. int and integer are accepted as synonyms for long in CDL declarations. Now that there are platforms with 64-bit representations for C longs, it may be better to use the int synonym to avoid confusion.
Floats can hold values between about -3.4+38 and 3.4+38. Their external representation is as 32-bit IEEE normalized single-precision floating point numbers. ncgen3 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. ncgen3 converts double declarations to double declarations in the output C code and to DOUBLE PRECISION declarations in output Fortran code.
CDL
Constants
Constants assigned to attributes or variables may be of any
of the basic netCDF types. The syntax for constants is
similar to C syntax, except that type suffixes must be
appended to shorts and floats to distinguish them from longs
and doubles.
A byte constant is represented by a single character or multiple character escape sequence enclosed in single quotes. For example,
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// ASCII ‘a’ | |||||
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// a zero byte | |||||
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// ASCII newline character | |||||
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// ASCII escape character (33 octal) | |||||
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// ASCII plus (2b hex) | |||||
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// 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
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"a" |
// ASCII ‘a’ | ||||
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"Two\nlines\n" |
// a 10-character string with two embedded newlines | ||||
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"a bell:\007" |
// a string containing an ASCII bell |
Note that the netCDF character array "a" would fit in a one-element variable, since no terminating NULL character is assumed. However, a zero byte in a character array is interpreted as the end of the significant characters by the ncdump program, following the C convention. Therefore, a NULL byte should not be embedded in a character string unless at the end: use the byte data type instead for byte arrays that contain the zero byte. NetCDF and CDL have no string type, but only fixed-length character arrays, which may be multi-dimensional.
short integer constants are intended for representing 16-bit signed quantities. The form of a short constant is an integer constant with an ‘s’ or ‘S’ appended. If a short constant begins with ‘0’, it is interpreted as octal, except that if it begins with ‘0x’, it is interpreted as a hexadecimal constant. For example:
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-2s |
// a short -2 | |||
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0123s |
// octal |
0x7ffs //hexadecimal
Long integer constants are intended for representing 32-bit signed quantities. The form of a long constant is an ordinary integer constant, although it is acceptable to append an optional ‘l’ or ‘L’. If a long constant begins with ‘0’, it is interpreted as octal, except that if it begins with ‘0x’, it is interpreted as a hexadecimal constant. Examples of valid long constants include:
-2
1234567890L
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0123 |
// octal | ||||
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0x7ff |
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// 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
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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
The programs generated by ncgen3 when using the -c or -f use initialization statements to store data in variables, and will fail to produce compilable programs if you try to use them for large datasets, since the resulting statements may exceed the line length or number of continuation statements permitted by the compiler.
The CDL syntax makes it easy to assign what looks like an array of variable-length strings to a netCDF variable, but the strings will simply be concatenated into a single array of characters, since netCDF cannot represent an array of variable-length strings in one netCDF variable.
NetCDF and CDL do not yet support a type corresponding to a 64-bit integer.