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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 $                        MINCGEN(1)