mincdump - Convert minc files to ASCII form (CDL)
mincdump -c -h -v var1, -b lang -f lang -l len -n name -p f_digits ,d_digits file
mincdump is based upon the netCDF tool ncdump, modified to work with both MINC 1 (netCDF) and MINC 2 (HDF5) format files. It is intended for use primarily with scripts such as mincdiff and mincheader. Since it was not created at the Montreal Neurological Insititute it does not follow the usual conventions for MINC programs.
mincdump generates an ASCII representation of a specified minc file on standard output. The ASCII representation is in a form called CDL (LDQUOnetwork Common Data form LanguageRDQUO) that can be viewed, edited, or serve as input to ncgen. ncgen is a companion program that can generate a binary minc file from a CDL file. Hence ncgen and
mincdump can be used as inverses to transform the data representation between binary and ASCII representations. See ncgen for a description of CDL and netCDF representations.
mincdump defines a default format used for each type of netCDF data, but this can be changed if a `C_format’ attribute is defined for a netCDF variable. In this case,
mincdump will use the `C_format’ attribute to format each value. For example, if floating-point data for the netCDF variable `Z’ is known to be accurate to only three significant digits, it would be appropriate to use the variable attribute
Z:C_format = “%.3g”
mincdump may also be used as a simple browser for netCDF data files, to display the dimension names and sizes; variable names, types, and shapes; attribute names and values; and optionally, the values of data for all variables or selected variables in a netCDF file.
mincdump uses `_’ to represent data values that are equal to the `_FillValue’ attribute for a variable, intended to represent data that has not yet been written. If a variable has no `_FillValue’ attribute, the default fill value for the variable type is used if the variable is not of byte type.
Show the values of coordinate variables (variables that are also dimensions) as well as the declarations of all dimensions, variables, and attribute values. Data values of non-coordinate variables are not included in the output. This is the most suitable option to use for a brief look at the structure and contents of a netCDF file.
Show only the header information in the output, that is the declarations of dimensions, variables, and attributes but no data values for any variables. The output is identical to using the
-c option except that the values of coordinate variables are not included. (At most one of
-h options may be present.)
The output will include data values for the specified variables, in addition to the declarations of all dimensions, variables, and attributes. One or more variables must be specified by name in the comma-delimited list following this option. The list must be a single argument to the command, hence cannot contain blanks or other white space characters. The named variables must be valid netCDF variables in the input-file. The default, without this option and in the absence of the
-h options, is to include data values for all variables in the output.
A brief annotation in the form of a CDL comment (text beginning with the characters LDQUO//RDQUO) will be included in the data section of the output for each `row’ of data, to help identify data values for multidimensional variables. If lang begins with `C’ or `c’, then C language conventions will be used (zero-based indices, last dimension varying fastest). If lang begins with `F’ or `f’, then Fortran language conventions will be used (one-based indices, first dimension varying fastest). In either case, the data will be presented in the same order; only the annotations will differ. This option is useful for browsing through large volumes of multidimensional data.
Full annotations in the form of trailing CDL comments (text beginning with the characters LDQUO//RDQUO) for every data value (except individual characters in character arrays) will be included in the data section. If lang begins with `C’ or `c’, then C language conventions will be used (zero-based indices, last dimension varying fastest). If lang begins with `F’ or `f’, then Fortran language conventions will be used (one-based indices, first dimension varying fastest). In either case, the data will be presented in the same order; only the annotations will differ. This option may be useful for piping data into other filters, since each data value appears on a separate line, fully identified.
Changes the default maximum line length (80) used in formatting lists of non-character data values.
CDL requires a name for a netCDF data set, for use by
ncgen -b in generating a default netCDF file name. By default,
mincdump constructs this name from the last component of the pathname of the input netCDF file by stripping off any extension it has. Use the
-n option to specify a different name. Although the output file name used by
ncgen -b can be specified, it may be wise to have
mincdump change the default name to avoid inadvertantly overwriting a valuable netCDF file when using
mincdump, editing the resulting CDL file, and using
ncgen -b to generate a new netCDF file from the edited CDL file.
Specifies default precision (number of significant digits) to use in displaying floating-point or double precision data values for attributes and variables. If specified, this value overrides the value of the `C_format’ attribute for any variable that has such an attribute. Floating-point data will be displayed with float_digits significant digits. If double_digits is also specified, double-precision values will be displayed with that many significant digits. In the absence of any
-p specifications, floating-point and double-precision data are displayed with 7 and 15 significant digits respectively. CDL files can be made smaller if less precision is required. If both floating-point and double-presision precisions are specified, the two values must appear separated by a comma (no blanks) as a single argument to the command. If you really want every last bit of precision from the netCDF file represented in the CDL file for all possible floating-point values, you will have to specify this with
-p 9,17 (according to Theorem 15 of the paper listed under REFERENCES).
Look at the structure of the data in the netCDF file `foo.mnc’:
mincdump -c foo.mnc
Produce an annotated CDL version of the structure and data in the netCDF file `foo.mnc’, using C-style indexing for the annotations:
mincdump -b c foo.mnc > foo.cdl
Output data for only the variables `uwind’ and `vwind’ from the netCDF file `foo.mnc’, and show the floating-point data with only three significant digits of precision:
mincdump -v uwind,vwind -p 3 foo.mnc
Produce a fully-annotated (one data value per line) listing of the data for the variable `omega’, using Fortran conventions for indices, and changing the netCDF dataset name in the resulting CDL file to `omega’:
mincdump -v omega -f fortran -n omega foo.mnc > Z.cdl
Originally written by members of the Unidata Program at the University Corporation for Atmospheric Research.
Modified by Bert Vincent (email@example.com) for use with both netCDF and HDF5 files.
Copyright © University Corporation for Atmospheric Research
What Every Computer Scientist should Know About Floating-Point Arithmetic, D. Goldberg, ACM Computing Surveys, Vol. 23, No. 1, March 1991, pp. 5-48.
ncdump, ncgen, netcdf
Character arrays that contain a null-byte are treated like C strings, so no characters after the null byte appear in the output.
Multidimensional character string arrays are not handled well, since the CDL syntax for breaking a long character string into several shorter lines is weak.
There should be a way to specify that the data should be displayed in `record’ order, that is with the all the values for `record’ variables together that have the same value of the record dimension.