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’:
mincgen foo.cdl
From the CDL file ‘foo.cdl’, generate an equivalent binary MINC file
named ‘x.mnc’:
mincgen -o x.mnc foo.cdl
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.
$Date: 2008/10/12 05:07:12 $