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H5TOTXT(1) h5utils H5TOTXT(1)


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 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.


Display help on the command-line options and usage.
Print the version number and copyright info for h5totxt.
Verbose output.
Send text output to file rather than to stdout (the default).
Use the string sep to separate columns of the output rather than a comma (the default).
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 affected.)
Transpose the data (interchange the dimension ordering). By default, no transposition is done.
-. numdigits
Output numdigits digits after the decimal point (defaults to 16).
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,


Written by Steven G. Johnson. Copyright (c) 2005 by the Massachusetts Institute of Technology.

March 9, 2002 h5utils