Ubuntu Manpage: mincgen - Generate a MINC file from a CDL file.

Provided by: minc-tools_2.3.00+dfsg-3build2_amd64

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

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 $                                MINCGEN(1)