NAME¶
mincgen - Generate a MINC file from a CDL file.
SYNOPSIS¶
mincgen [-b]
[-n] [-o minc_filename] input_file
DESCRIPTION¶
mincgen generates a MINC file. The input to
mincgen is a
description of a MINC file in a small language known as CDL (network Common
Data form Language), described below. If no options are specified in invoking
mincgen, 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 MINC file.
mincgen may be used with the companion program
mincdump to perform
some simple operations on MINC files. For example, to rename a dimension in a
MINC file, use
mincdump to get a CDL version of the MINC file, edit the
CDL file to change the name of the dimensions, and use
mincgen to
generate the corresponding MINC file from the edited CDL file.
OPTIONS¶
- -b
- Create a (binary) MINC file. If the -o option is
absent, a default file name will be constructed from the MINC name
(specified after the netcdf or hdf5 keyword in the input) by
appending the `.mnc' extension. If a file already exists with the
specified name, it will be overwritten.
- -o minc_filename
- Name for the binary MINC file created. If this option is
specified, it implies the " -b" option. (This option is
necessary because MINC files cannot be written directly to standard
output, since standard output is not seekable.)
EXAMPLES¶
Check the syntax of the CDL file `
foo.cdl':
From the CDL file `
foo.cdl', generate an equivalent binary MINC file
named `
x.mnc':
USAGE¶
CDL Syntax Summary¶
Below is an example of CDL syntax, describing a MINC file with several named
dimensions (xspace, yspace, and zspace), variables (zspace, image), variable
attributes (valid_range, signtype), 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 MINC specification in CDL
dimensions:
xspace = 8;
yspace = 8;
zspace = 5;
variables:
float xspace;
float yspace;
float zspace(zspace);
short image(zspace,yspace,xspace);
double image-min(zspace)
double image-max(zspace)
// variable attributes
image:valid_range = 0,5;
data:
image-min = -1,-1,-1,-1,-1;
image-max = 1,1,1,1,1;
image =
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5;
zspace = 0,2,3.5,7,10;
}
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 MINC
dimension is used to define the shape of one or more of the
multidimensional variables contained in the MINC file. A MINC dimension has a
name, a size, and possibly several other attributes.
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 file 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 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
long 32-bit signed integers
int (synonymous with long)
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
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.
Shorts can hold values between -32768 and 32767.
Longs can hold values between -2147483648 and 2147483647.
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.
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.
CDL Constants¶
Constants assigned to attributes or variables may be of any of the basic MINC
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 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
mincdump 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. MINC
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:
-2s // a short -2
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
0123 // octal
0x7ff // 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
AUTHOR¶
Originally written by members of the Unidata Program at the University
Corporation for Atmospheric Research.
Modified by Bert Vincent (bert@bic.mni.mcgill.ca) for use with both netCDF and
HDF5 files.
COPYRIGHTS¶
Copyright © University Corporation for Atmospheric Research
SEE ALSO¶
ncdump(1),
ncgen(1),
netcdf(3)
BUGS¶
The CDL syntax makes it easy to assign what looks like an array of
variable-length strings to a variable, but the strings will simply be
concatenated into a single array of characters, since MINC cannot represent an
array of variable-length strings in one MINC variable.
MINC and CDL do not yet support a type corresponding to a 64-bit integer.
