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beginning of ncdump documentation in doxygen

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@ -582,7 +582,8 @@ libdispatch/nc4.c libdispatch/dcompound.c libdispatch/dv2i.c \
libdispatch/dvlen.c libdispatch/denum.c libdispatch/dopaque.c \
libdispatch/dtype.c libsrc4/nc4file.c \
man4/mainpage.doc man4/tutorial.doc COPYRIGHT man4/install.doc man4/dispatch.doc \
man4/guide.doc man4/types.doc man4/notes.doc
man4/guide.doc man4/types.doc man4/notes.doc man4/cdl.doc \
ncdump/ncdump.c
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is

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/**
\file
Documentation for Common Data Language
\page CDL
\section CDL Syntax
Below is an example of CDL, describing a netCDF dataset with several
named dimensions (lat, lon, time), variables (z, t, p, rh, lat, lon,
time), variable attributes (units, _FillValue, valid_range), and some
data.
\code
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;
}
\endcode
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 for a classic model file consists of three optional
parts: dimensions, variables, and data. The variable part may contain
variable declarations and attribute assignments. For the enhanced
model supported by netCDF-4, a CDL decription may also includes
groups, subgroups, and user-defined types.
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 classic
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). Any number of dimensions can be declared of unlimited length in
CDL for an enhanced model 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 or containing group. 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 one-dimensional arrays of values. For example,
“units” might be an attribute represented by a string 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 or
metadata (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, if not explicitly specified, 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. In the netCDF-4
enhanced model, attributes may be declared to be of user-defined type,
like variables.
In CDL, just as for netCDF, the names of dimensions, variables and
attributes (and, in netCDF-4 files, groups, user-defined types,
compound member names, and enumeration symbols) consist of arbitrary
sequences of alphanumeric characters, underscore '_', period '.', plus
'+', hyphen '-', or at sign '@', but beginning with a letter or
underscore. However names commencing with underscore are reserved for
system use. Case is significant in netCDF names. A zero-length name is
not allowed. Some widely used conventions restrict names to only
alphanumeric characters or underscores. Names that have trailing space
characters are also not permitted.
Beginning with versions 3.6.3 and 4.0, names may also include UTF-8
encoded Unicode characters as well as other special characters, except
for the character '/', which may not appear in a name (because it is
reserved for path names of nested groups). In CDL, most special
characters are escaped with a backslash '\' character, but that
character is not actually part of the netCDF name. The special
characters that do not need to be escaped in CDL names are underscore
'_', period '.', plus '+', hyphen '-', or at sign '@'. For the formal
specification of CDL name syntax See Format. Note that by using
special characters in names, you may make your data not compliant with
conventions that have more stringent requirements on valid names for
netCDF components, for example the CF Conventions.
The names for the primitive data types are reserved words in CDL, so
names of variables, dimensions, and attributes must not be primitive
type names.
The optional data section of a CDL description is where netCDF
variables may be initialized. The syntax of an initialization is
simple:
\code
variable = value_1, value_2, ...;
\endcode
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 among primitive types are supported.
A special notation for fill values is supported: the ‘_’ character
designates a fill value for variables.
\section CDL Data Types
The CDL primitive data types for the classic model are:
- char Characters.
- byte Eight-bit integers.
- short 16-bit signed integers.
- int 32-bit signed integers.
- long (Deprecated, synonymous with int)
- float IEEE single-precision floating point (32 bits).
- real (Synonymous with float).
- double IEEE double-precision floating point (64 bits).
NetCDF-4 supports the additional primitive types:
- ubyte Unsigned eight-bit integers.
- ushort Unsigned 16-bit integers.
- uint Unsigned 32-bit integers.
- int64 64-bit singed integers.
- uint64 Unsigned 64-bit singed integers.
- string Variable-length string of characters
Except for the added data-type byte, CDL supports the same primitive
data types as C. For backward compatibility, in declarations primitive
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
numeric data, and the zero byte has no special significance, as it may
for character data. The short type holds values between -32768 and
32767. The ushort type holds values between 0 and 65536. The int type
can hold values between -2147483648 and 2147483647. The uint type
holds values between 0 and 4294967296. The int64 type can hold values
between -9223372036854775808 and 9223372036854775807. The uint64 type
can hold values between 0 and 18446744073709551616.
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 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
string type holds variable length strings.
\section CDL Notation for Data Constants
This section describes the CDL notation for constants.
Attributes are initialized in the variables section of a CDL
description by providing a list of constants that determines the
attribute's length and type (if primitive and not explicitly
declared). CDL defines a syntax for constant values that permits
distinguishing among different netCDF primitive types. The syntax for
CDL constants is similar to C syntax, with type suffixes appended to
bytes, 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:
\code
'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
\endcode
Character constants are enclosed in double quotes. A character array
may be represented as a string enclosed in double quotes. Multiple
strings are concatenated into a single array of characters, permitting
long character arrays to appear on multiple lines. To support multiple
variable-length string values, a conventional delimiter such as ','
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:
\code
"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"
\endcode
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:
\code
2s // a short 2
0123s // octal
0x7ffs // hexadecimal
\endcode
The 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:
\code
-2
0123 // octal
0x7ff // hexadecimal
1234567890L // deprecated, uses old long suffix
\endcode
The 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:
\code
-2.0f
3.14159265358979f // will be truncated to less precision
1.f
.1f
\endcode
The 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:
\code
-2.0
3.141592653589793
1.0e-20
1.d
\endcode
*/

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@ -1,8 +1,10 @@
/*********************************************************************
* Copyright 2008, University Corporation for Atmospheric Research
* See netcdf/README file for copying and redistribution conditions.
* $Id: ncdump.c 400 2010-08-27 21:02:52Z russ $
*********************************************************************/
/** \file
Attribute functions
These functions read and write attributes.
Copyright 2008 University Corporation for Atmospheric
Research/Unidata. See \ref copyright file for more info. */
#include <config.h>
#include <stdio.h>
@ -2002,6 +2004,186 @@ void adapt_url_for_cache(char **pathp) {
return;
}
/**
The ncdump 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.
As of netCDF version 4.1, ncdump can also access DAP data sources if
DAP support is enabled in the underlying netCDF library. Instead of
specifying a file name as argument to ncdump, the user specifies a URL
to a DAP source.
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:
\code
Z:C_format = "%.3g"
\endcode
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:
\code
ncdump [ -c | -h] [-v var1,...] [-b lang] [-f lang]
[-l len] [ -p fdig[,ddig]] [ -s ] [ -n name] [input-file]
\endcode
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.
-s Specifies that special virtual attributes should be output for the
file format variant and for variable properties such as compression,
chunking, and other properties specific to the format implementation
that are primarily related to performance rather than the logical
schema of the data. All the special virtual attributes begin with '_'
followed by an upper-case letter. Currently they include the global
attribute “_Format” and the variable attributes “_Fletcher32”,
“_ChunkSizes”, “_Endianness”, “_DeflateLevel”, “_Shuffle”, “_Storage”,
and “_NoFill”. The ncgen utility recognizes these attributes and
supports them appropriately.
-t Controls display of time data, if stored in a variable that uses a
udunits compliant time representation such as “days since 1970-01-01”
or “seconds since 2009-03-15 12:01:17”. If this option is specified,
time values are displayed as human-readable date-time strings rather
than numerical values, interpreted in terms of a “calendar” variable
attribute, if specified. Calendar attribute values interpreted with
this option include the CF Conventions values “gregorian” or
“standard”, “proleptic_gregorian”, “noleap” or “365_day”, “all_leap”
or “366_day”, “360_day”, and “julian”.
\section Examples
Look at the structure of the data in the netCDF dataset foo.nc:
\code
ncdump -c foo.nc
\endcode
Produce an annotated CDL version of the structure and data in the
netCDF dataset foo.nc, using C-style indexing for the annotations:
\code
ncdump -b c foo.nc > foo.cdl
\endcode
Output 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:
\code
ncdump -v uwind,vwind -p 3 foo.nc
\endcode
Produce 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:
\code
ncdump -v omega -f fortran -n omega foo.nc > Z.cdl
\endcode
Examine the translated DDS for the DAP source from the specified URL.
\code
ncdump -h http://test.opendap.org:8080/dods/dts/test.01
\endcode
*/
int
main(int argc, char *argv[])
{