NetCDF User's Guide for C
ncdump reads a netCDF dataset and prints a textual representation of the information in the dataset
ncgen reads a textual representation of a netCDF dataset and generates the corresponding binary netCDF file or a C or FORTRAN program to create the netCDF dataset
ncmeta prints selected metadata from one or more netCDF datasets
ncrob performs various operations (copy, sum, mean, max, min, ...) with data read from and printed or written to text files and/or selected parts of netCDF variables or attributes.
http://www.unidata.ucar.edu/packages/netcdf/fan_utils.html.
Users have contributed other netCDF utilities, and various visualization and analysis packages are available that access netCDF data. For an up-to-date list of freely-available and commercial software that can access or manipulate netCDF data, see the NetCDF Software list, http://www.unidata.ucar.edu/packages/netcdf/software.html.
This chapter describes the ncgen and ncdump utilities. These two tools convert between binary netCDF datasets and a text representation of netCDF datasets. The output of ncdump and the input to ncgen is a text description of a netCDF dataset in a tiny language known as CDL (network Common data form Description Language).
lat, lon, time), variables (z, t, p, rh, lat, lon, time), variable attributes (units, _FillValue, valid_range), and some data.
netcdf foo { // example netCDF specification in CDL
dimensions:
lat = 10, lon = 5, time = unlimited;
variables:
int lat(lat), lon(lon), time(time);
float z(time,lat,lon), t(time,lat,lon);
double p(time,lat,lon);
int rh(time,lat,lon);
lat:units = "degrees_north";
lon:units = "degrees_east";
time:units = "seconds";
z:units = "meters";
z:valid_range = 0., 5000.;
p:_FillValue = -9999.;
rh:_FillValue = -1;
data:
lat = 0, 10, 20, 30, 40, 50, 60, 70, 80, 90;
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 double slash characters // on any line. A CDL description consists of three optional parts: dimensions, variables, and data. The variable part may contain variable declarations and attribute assignments.
A dimension is used to define the shape of one or more of the multidimensional variables described by the CDL description. A dimension has a name and a length. At most one dimension in a CDL description can have the unlimited length, 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 contains coordinates of the dimension it names.
An attribute contains information about a variable or about the whole netCDF dataset. Attributes may be used to specify such properties as units, special values, maximum and minimum valid values, and packing 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 ancillary data (data about data).
In CDL, an attribute is designated by a variable and attribute name, separated by a colon (':'). It is possible to assign global attributes to the netCDF dataset as a whole by omitting the variable name and beginning the attribute name with a colon (':'). 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 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.
CDL names for variables, attributes, and dimensions may be any combination of alphabetic or numeric characters as well as '_' and '-' characters, but names beginning with '_' are reserved for use by the library. Case is significant in CDL names. The netCDF library does not enforce any restrictions on netCDF names, so it is possible (though unwise) to define variables with names that are not valid CDL names. 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.
The optional data section of a CDL description is where netCDF variables may be initialized. The syntax of an initialization is simple:
variable = value_1, value_2, ...;
The comma-delimited list of constants may be separated by spaces, tabs, and newlines. For multidimensional 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 the fill value. The types of constants need not match the type declared for a variable; coercions are done to convert integers to floating point, for example. All meaningful type conversions are supported.
A special notation for fill values is supported: the _ character designates a fill value for variables.
char | Characters. |
byte | Eight-bit integers. |
short | 16-bit signed integers. |
int | 32-bit signed integers. |
long | (Deprecated, currently synonymous with int) |
float | IEEE single-precision floating point (32 bits). |
real | (Synonymous with float). |
double | IEEE double-precision floating point (64 bits). |
Except for the added data-type byte and the lack of the type qualifier unsigned, CDL supports the same primitive data types as C. In declarations, type names may be specified in either upper or lower case.
The byte type differs from the char type in that it is intended for eight-bit data, and the zero byte has no special significance, as it may for character data. The ncgen utility converts byte declarations to char declarations in the output C code and to BYTE, INTEGER*1, or similar platform-specific declaration in output FORTRAN code.
The short type holds values between -32768 and 32767. The ncgen utility converts short declarations to short declarations in the output C code and to INTEGER*2 declaration in output FORTRAN code.
The int type can hold values between -2147483648 and 2147483647. The ncgen utility converts int declarations to int declarations in the output C code and to INTEGER declarations in output FORTRAN code. In CDL declarations integer and long are accepted as synonyms for int.
The float type can hold values between about -3.4+38 and 3.4+38, with external representation as 32-bit IEEE normalized single-precision floating-point numbers. The ncgen utility converts float declarations to float declarations in the output C code and to REAL declarations in output FORTRAN code. In CDL declarations real is accepted as a synonym for float.
The double type can hold values between about -1.7+308 and 1.7+308, with external representation as 64-bit IEEE standard normalized double-precision, floating-point numbers. The ncgen utility converts double declarations to double declarations in the output C code and to DOUBLE PRECISION declarations in output FORTRAN code.
Attributes are initialized in the variables section of a CDL description by providing a list of constants that determines the attribute's type and length. (In the C and FORTRAN procedural interfaces to the netCDF library, the type and length of an attribute must be explicitly provided when it is defined.) CDL defines a syntax for constant values that permits distinguishing among different netCDF types. The syntax for CDL constants is similar to C syntax, except that type suffixes are appended to shorts and floats to distinguish them from ints 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) '\376' // 377 octal = -127 (or 254) decimal
,' may be used, but interpretation of any such convention for a string delimiter must be implemented in software above the netCDF library layer. The usual escape conventions for C strings 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 "ab","cde" // the same as "abcde"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. When it begins with '0x', it is interpreted as a hexadecimal constant. For example:
2s // a short 2 0123s // octal 0x7ffs // hexadecimalThe form of an
int constant is an ordinary integer constant. If an int constant begins with '0', it is interpreted as octal. When it begins with '0x', it is interpreted as a hexadecimal constant. Examples of valid int constants include:
-2 0123 // octal 0x7ff // hexadecimal 1234567890L // deprecated, uses old long suffixThe
float type is appropriate for representing 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. A decimal point is required in a CDL float to distinguish it from an integer. For example, the following are all acceptable float constants:
-2.0f 3.14159265358979f // will be truncated to less precision 1.f .1fThe
double type is appropriate for representing floating-point data with about 16 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. A decimal point is required in a CDL double to distinguish it from an integer. For example, the following are all acceptable double constants:
-2.0 3.141592653589793 1.0e-20 1.d
ncgenncgen tool generates a netCDF file or a C or FORTRAN program that creates a netCDF dataset. If no options are specified in invoking ncgen, the program merely checks the syntax of the CDL input, producing error messages for any violations of CDL syntax.
UNIX syntax for invoking ncgen:
ncgen [-b] [-o netcdf-file] [-c] [-f] [-n] [input-file]where:
foo.cdl:
ncgen foo.cdlFrom the CDL file
foo.cdl, generate an equivalent binary netCDF file named bar.nc:
ncgen -o bar.nc foo.cdlFrom the CDL file
foo.cdl, generate a C program containing netCDF function invocations that will create an equivalent binary netCDF dataset:
ncgen -c foo.cdl > foo.c
ncdumpncdump tool generates the CDL text representation of a netCDF dataset on standard output, optionally excluding some or all of the variable data in the output. The output from ncdump is intended to be acceptable as input to ncgen. Thus ncdump and ncgen can be used as inverses to transform data representation between binary and text representations.
ncdump may also be used as a simple browser for netCDF datasets, to display the dimension names and lengths; variable names, types, and shapes; attribute names and values; and optionally, the values of data for all variables or selected variables in a netCDF dataset.
ncdump defines a default format used for each type of netCDF variable data, but this can be overridden if a C_format attribute is defined for a netCDF variable. In this case, ncdump will use the C_format attribute to format values for that variable. For example, if floating-point data for the netCDF variable Z is known to be accurate to only three significant digits, it might be appropriate to use this variable attribute:
Z:C_format = "%.3g"
ncdump uses '_' to represent data values that are equal to the _FillValue attribute for a variable, intended to represent data that has not yet been written. If a variable has no _FillValue attribute, the default fill value for the variable type is used unless the variable is of byte type.
UNIX syntax for invoking ncdump:
ncdump [ -c | -h] [-v var1,...] [-b lang] [-f lang] [-l len] [ -p fdig[,ddig]] [ -n name] [input-file]where:
| -c | Show the values of coordinate variables (variables that are also dimensions) as well as the declarations of all dimensions, variables, and attribute values. Data values of non-coordinate variables are not included in the output. This is often the most suitable option to use for a brief look at the structure and contents of a netCDF dataset. |
-h | Show only the header information in the output, that is, output only the declarations for the netCDF dimensions, variables, and attributes of the input file, but no data values for any variables. The output is identical to using the '-c' option except that the values of coordinate variables are not included. (At most one of '-c' or '-h' options may be present.) |
-v var1,... | The output will include data values for the specified variables, in addition to the declarations of all dimensions, variables, and attributes. One or more variables must be specified by name in the comma-delimited list following this option. The list must be a single argument to the command, hence cannot contain blanks or other white space characters. The named variables must be valid netCDF variables in the input-file. The default, without this option and in the absence of the '-c' or '-h' options, is to include data values for all variables in the output. |
-b lang | A brief annotation in the form of a CDL comment (text beginning with the characters '//') will be included in the data section of the output for each 'row' of data, to help identify data values for multidimensional variables. If lang begins with 'C' or 'c', then C language conventions will be used (zero-based indices, last dimension varying fastest). If lang begins with 'F' or 'f', then FORTRAN language conventions will be used (one-based indices, first dimension varying fastest). In either case, the data will be presented in the same order; only the annotations will differ. This option may be useful for browsing through large volumes of multidimensional data. |
-f lang | Full annotations in the form of trailing CDL comments (text beginning with the characters '//') for every data value (except individual characters in character arrays) will be included in the data section. If lang begins with 'C' or 'c', then C language conventions will be used (zero-based indices, last dimension varying fastest). If lang begins with 'F' or 'f', then FORTRAN language conventions will be used (one-based indices, first dimension varying fastest). In either case, the data will be presented in the same order; only the annotations will differ. This option may be useful for piping data into other filters, since each data value appears on a separate line, fully identified. (At most one of '-b' or '-f' options may be present.) |
-l len | Changes the default maximum line length (80) used in formatting lists of non-character data values. |
-p float_digits[,double_digits] | |
Specifies default precision (number of significant digits) to use in displaying floating-point or double precision data values for attributes and variables. If specified, this value overrides the value of the C_format attribute, if any, for a variable. Floating-point data will be displayed with float_digits significant digits. If double_digits is also specified, double-precision values will be displayed with that many significant digits. In the absence of any '-p' specifications, floating-point and double-precision data are displayed with 7 and 15 significant digits respectively. CDL files can be made smaller if less precision is required. If both floating-point and double precisions are specified, the two values must appear separated by a comma (no blanks) as a single argument to the command. | |
-n name | CDL requires a name for a netCDF dataset, for use by 'ncgen -b' in generating a default netCDF dataset name. By default, ncdump constructs this name from the last component of the file name of the input netCDF dataset by stripping off any extension it has. Use the '-n' option to specify a different name. Although the output file name used by 'ncgen -b' can be specified, it may be wise to have ncdump change the default name to avoid inadvertently overwriting a valuable netCDF dataset when using ncdump, editing the resulting CDL file, and using 'ncgen -b' to generate a new netCDF dataset from the edited CDL file. |
foo.nc:
ncdump -c foo.ncProduce an annotated CDL version of the structure and data in the netCDF dataset
foo.nc, using C-style indexing for the annotations:
ncdump -b c foo.nc > foo.cdlOutput data for only the variables
uwind and vwind from the netCDF dataset foo.nc, and show the floating-point data with only three significant digits of precision:
ncdump -v uwind,vwind -p 3 foo.ncProduce a fully-annotated (one data value per line) listing of the data for the variable
omega, using FORTRAN conventions for indices, and changing the netCDF dataset name in the resulting CDL file to omega:
ncdump -v omega -f fortran -n omega foo.nc > Z.cdl