h5totxt - generate comma-delimited text from 2d slices of HDF5 files
h5totxt [OPTION]... [HDF5FILE]...
h5totxt is a utility to generate comma-delimited text (and similar
formats) from one-, two-, or more-dimensional slices of numeric
datasets in HDF5 files. This way, the data can easily be imported into
spreadsheets and similar programs for analysis and visualization.
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, h5totxt takes the first
dataset, but this can be changed via the -d option, or by using the
By default, the entire dataset is dumped to the output. in row-major
order. For 3d datasets, this corresponds to a sequence of yz slices,
in order of increasing x, separated by blank lines. If -T is
specified, outputs in the transposed (column-major) order instead
Often, however, you want only a one- or two-dimensional slice of multi-
dimensional data. To do this, you specify coordinates in one or more
slice dimensions, via the -xyzt options.
The most basic usage is something like ´h5totxt foo.h5´, which will
output comma-delimited text to stdout from the data in foo.h5.
-h Display help on the command-line options and usage.
-V Print the version number and copyright info for h5totxt.
-v Verbose output.
Send text output to file rather than to stdout (the default).
-s sep Use the string sep to separate columns of the output rather than
a comma (the default).
-x ix, -y iy, -z iz, -t it
This tells h5totxt to use a particular slice of a multi-
dimensional dataset. e.g. -x causes a yz plane (of a 3d
dataset) to be used, 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
-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.)
-T Transpose the data (interchange the dimension ordering). By
default, no transposition is done.
Output numdigits digits after the decimal point (defaults to
Use dataset name from the input files; otherwise, the first
dataset from each file is used. Alternatively, use the syntax
HDF5FILE:DATASET, which allows you to specify a different
dataset for each file. You can use the h5ls command (included
with hdf5) to find the names of datasets within a file.
Send bug reports to S. G. Johnson, firstname.lastname@example.org.
Written by Steven G. Johnson. Copyright (c) 2005 by the Massachusetts
Institute of Technology.