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h5totxt: generate comma-delimited text from 2d slices of HDF5 files

Synopsis

h5totxt [OPTION]... [HDF5FILE]...

Description

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 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.

Options

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

  • -V — Print the version number and copyright info for h5totxt.

  • -v — 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 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 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.)

  • -T — Transpose the data (interchange the dimension ordering). By default, no transposition is done.

  • -. numdigits — Output numdigits digits after the decimal point (defaults to 16).

  • -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.

Bugs

Report bugs by filing an issue at https://github.com/stevengj/h5utils

Authors

Written by Steven G. Johnson. Copyright © 2017 by the Massachusetts Institute of Technology.