h5totxt - generate comma-delimited text from 2d slices of HDF5 files
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 syntax HDF5FILE:DATASET
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
The most basic usage is something like ´h5totxt foo.h5´, which
will output comma-delimited text to stdout from the data in foo.h5.
- Display help on the command-line options and usage.
- Print the version number and copyright info for h5totxt.
- Verbose output.
- -o file
- 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
- 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 center.
- 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
- Transpose the data (interchange the dimension ordering). By default, no
transposition is done.
- -. numdigits
- Output numdigits digits after the decimal point (defaults to
- -d name
- 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, email@example.com.
Written by Steven G. Johnson. Copyright (c) 2005 by the Massachusetts Institute