NAME¶
h5math - combine/create HDF5 files with math expressions
SYNOPSIS¶
h5math [
OPTION]...
OUTPUT-HDF5FILE
[
INPUT-HDF5FILES...]
DESCRIPTION¶
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.
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).
BUGS¶
Send bug reports to S. G. Johnson, stevenj@alum.mit.edu.
AUTHORS¶
Written by Steven G. Johnson. Copyright (c) 2005 by the Massachusetts Institute
of Technology.