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h5math - combine/create HDF5 files with math expressions




h5math takes any number of HDF5 files as input, along with a mathematical expression, and
combines them to produce a new HDF5 file.

HDF5 is a free, portable binary format and supporting library developed by the National
Center for Supercomputing Applications at the University of Illinois in Urbana-Champaign.
A single h5 file can contain multiple data sets; by default, h5math creates a dataset
called "h5math", but this can be changed via the -d option, or by using the syntax
HDF5FILE:DATASET. The -a option can be used to append new datasets to an existing HDF5
file. The same syntax is used to specify the dataset used in the input file(s); by
default, the first dataset (alphabetically) is used.

A simple example of h5math's usage is:

h5math -e "d1 + 2*d2" out.h5 foo.h5 bar.h5:blah

which produces a new file, out.h5, by adding the first dataset in foo.h5 with twice the
"blah" dataset in bar.h5. In the expression (specified by -e), the first input dataset
(from left to right) is referred to as d1, the second as d2, and so on.

In addition to input datasets, you can also use the x/y/z coordinates of each point in the
expression, referenced by "x" "y" and "z" variables (for the first three dimensions) as
well as a "t" variable that refers to the last dimension. By default, these are integers
starting at 0 at the corner of the dataset, but the -0 option will change the x/y/z origin
to the center of the dataset (t is unaffected), and the -r res option will specify the
"resolution", dividing the x/y/z coordinates by res.

All of the input datasets must have the same dimensions, which are also the dimensions of
the output. If there are no input files, and you are defining the output purely by a
mathematical formula, you can specify the dimensions of the output explicitly via the -n
size option, where size is e.g. "2x2x2".

Sometimes, however, you want to use only a smaller-dimensional "slice" of multi-
dimensional data. To do this, you specify coordinates in one (or more) slice
dimension(s), via the -xyzt options.


-h Display help on the command-line options and usage.

-V Print the version number and copyright info for h5math.

-v Verbose output.

-a If the HDF5 output file already exists, append the data as a new dataset rather
than overwriting the file (the default behavior). An existing dataset of the same
name within the file is overwritten, however.

-e expression
Specify the mathematical expression that is used to construct the output (generally
in " quotes to group the expression as one item in the shell), in terms of the
variables for the input datasets and the coordinates as described above.

Expressions use a C-like infix notation, with most standard operators and
mathematical functions (+, sin, etc.) being supported. This functionality is
provided (and its features determined) by GNU libmatheval.

-f filename
Name of a text file to read the expression from, if no -e expression is specified.
Defaults to stdin.

-x ix, -y iy, -z iz, -t it
This tells h5math to use a particular slice of a multi-dimensional dataset. e.g.
-x uses the subset (with one less dimension) at an x index of ix (where the indices
run from zero to one less than the maximum index in that direction). Here, x/y/z
correspond to the first/second/third dimensions of the HDF5 dataset. The -t option
specifies a slice in the last dimension, whichever that might be. See also the -0
option to shift the origin of the x/y/z slice coordinates to the dataset center.

-0 Shift the origin of the x/y/z slice coordinates to the dataset center, so that e.g.
-0 -x 0 (or more compactly -0x0) returns the central x plane of the dataset instead
of the edge x plane. (-t coordinates are not affected.)

This also shifts the origin of the x/y/z variables in the expression so that 0 is
the center of the dataset.

-r res Use a resolution res for x/y/z (but not t) variables in the expression, so that the
data "grid" coordinates are divided by res. The default res is 1.

For example, if the x dimension has 21 grid steps, setting a res of 20 will mean
that x variables in the expression run from 0.0 to 1.0 (or -0.5 to 0.5 if -0 is
specified), instead of 0 to 20.

-r does not affect the coordinates used for slices, which are always integers.

-n size
The output dataset must be the same size as the input datasets. If there are no
input datasets (if you are defining the output purely by a formula), then you must
specify the output size manually with this option: size is of the form MxNxLx...
(with M, N, L being integers) and may be of any dimensionality.

-d name
Write to dataset name in the output; otherwise, the output dataset is called "data"
by default. Also use dataset name in the input; otherwise, the first input dataset
(alphabetically) in a file is used. Alternatively, use the syntax HDF5FILE:DATASET
(which overrides the -d option).

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