NAME¶
h5fromtxt - convert text input to an HDF5 file
SYNOPSIS¶
h5fromtxt [
OPTION]... [
HDF5FILE]
DESCRIPTION¶
h5fromtxt takes a series of numbers from standard input and outputs a
multi-dimensional numeric dataset in an 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,
h5fromtxt creates a dataset called "data", 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.
All characters besides the numbers (and associated decimal points, etcetera) in
the input are ignored. By default, the data is assumed to be a two-dimensional
MxN dataset where M is the number of rows (delimited by newlines) and N is the
number of columns. In this case, it is an error for the number of columns to
vary between rows. If M or N is 1 then the data is written as a
one-dimensional dataset.
Alternatively, you can specify the dimensions of the data explicitly via the
-n size option, where
size is e.g. "2x2x2". In
this case, newlines are ignored and the data is taken as an array of the given
size stored in row-major ("C") order (where the last index varies
most quickly as you step through the data). e.g. a 2x2x2 array would be have
the elements listed in the order: (0,0,0), (0,0,1), (0,1,0), (0,1,1), (1,0,0),
(1,0,1), (1,1,0), (1,1,1).
A simple example is:
-
- h5fromtxt foo.h5 <<EOF
1 2 3 4
5 6 7 8
EOF
which reads in a 2x4 space-delimited array from standard input.
OPTIONS¶
- -h
- Display help on the command-line options and usage.
- -V
- Print the version number and copyright info for
h5fromtxt.
- -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.
- -n size
- Instead of trying to infer the dimensions of the array from
the rows and columns of the input, treat the data as a sequence of numbers
in row-major order forming an array of dimensions size. size
is of the form MxNxLx... (with M, N, L being numbers) and may be of any
dimensionality.
- -T
- Transpose the input when it is written, reversing the
dimensions.
- -d name
- Write to dataset name in the output; otherwise, the
output dataset is called "data" by default. Alternatively, use
the syntax HDF5FILE:DATASET.
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.