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MINCGEN(1) MINC User's Guide MINCGEN(1) 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 invok- ing mincgen, it merely checks the syntax of the input CDL file, produc- ing 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 de- fault file name will be constructed from the MINC name (speci- fied after the netcdf or hdf5 keyword in the input) by appending the `.mnc' extension. If a file already exists with the speci- fied name, it will be overwritten. -o minc_filename Name for the binary MINC file created. If this option is speci- fied, it implies the "-b" option. (This option is necessary be- cause 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, im- age), 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, vari- ables, and data, beginning with the keyword dimensions:, variables:, and data, respectively. The variable part may contain variable decla- rations and attribute assignments. A MINC dimension is used to define the shape of one or more of the mul- tidimensional 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 coordi- nates of the dimension it names. Dimensions need not have correspond- ing 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, at- tributes 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 asso- ciated 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 al- phanumeric 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 val- ues are supplied than are needed to fill a variable, it is extended with a type-dependent `fill value', which can be overridden by supply- ing 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 vari- able. 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 sup- ports the same primitive data types as C. The names for the primitive data types are reserved words in CDL, so the names of variables, dimen- sions, 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 in- teger 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 exter- nal representation is as 32-bit IEEE normalized single-precision float- ing point numbers. real is accepted as a synonym for float in CDL dec- larations. Doubles can hold values between about -1.7+308 and 1.7+308. Their ex- ternal representation is as 64-bit IEEE standard normalized double-pre- cision floating point numbers. CDL Constants Constants assigned to attributes or variables may be of any of the ba- sic MINC types. The syntax for constants is similar to C syntax, ex- cept that type suffixes must be appended to shorts and floats to dis- tinguish them from longs and doubles. A byte constant is represented by a single character or multiple char- acter 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 char- acters 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 in- terpreted as octal, except that if it begins with `0x', it is inter- preted 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 con- stant, 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 con- stant. 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 accept- able float constants: -2.0f 3.14159265358979f // will be truncated to less precision 1.f Floating point constants of type double are appropriate for represent- ing floating point data with about sixteen significant digits of preci- sion. 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 (C) 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 rep- resent an array of variable-length strings in one MINC variable. MINC and CDL do not yet support a type corresponding to a 64-bit inte- ger. $Date: 2008-10-12 05:07:12 $ MINCGEN(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | USAGE | AUTHOR | COPYRIGHTS | SEE ALSO | BUGS
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