---
name: "h5totxt"
section: "1"
platform: "linux"
package: "h5utils"
version: "1.13.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/h5totxt"
---

# h5totxt(1)

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

## NAME

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

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.