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mincgen - Generate a MINC file from a CDL file.


mincgen [-b] [-n] [-o minc_filename] input_file


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.


-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.)


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


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

xspace = 8;
yspace = 8;
zspace = 5;

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;
image-min = -1,-1,-1,-1,-1;
image-max = 1,1,1,1,1;
image =
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:
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:
3.14159265358979f // will be truncated to less precision

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:

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