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h5tovtk: convert datasets in HDF5 files to VTK format

Synopsis

h5tovtk [OPTION]... [HDF5FILE]...

Description

h5tovtk is a program to generate VTK data files from multidimensional datasets in HDF5 files. VTK, the Visualization ToolKit, is an open-source, freely available software system for 3D computer graphics, image processing, and visualization. VTK itself is a programming library, but it is also the basis for a number of end-user graphical visualization programs.

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 datasets; by default, h5tovtk takes the first dataset, but this can be changed via the -d option, or by using the syntax HDF5FILE:DATASET.

1d/2d/3d datasets are converted into 3d VTK datasets. Normally, a single scalar VTK dataset is output, but vectors and fields can be output via the -o option below.

A typical invocation is of the form h5tovtk foo.h5, which will output a VTK data file foo.vtk 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 h5tovtk.

  • -v — Verbose output.

  • -o file — Save all the input datasets to a single VTK file. If there is only one dataset, it is output to a VTK scalar dataset; if there are three datasets, they are output as a VTK vector dataset; all other numbers of datasets are combined into a VTK field dataset.

  • Otherwise, the default behavior is to save each dataset to a separate VTK file, with the .h5 suffix of the input filename replaced by .vtk in the output filename.

  • Only three-dimensional datasets may be written to the VTK file. If you have a four (or more) dimensional data set, then you must take a three-dimensional "slice" of the multi-dimensional data. To do this, you specify coordinates in one (or more) slice dimension(s), via the -xyzt options.

  • -1, -2, -4 — Use 1 , 2, or 4 bytes to store each data point in the output file. Fewer bytes require less storage and memory, but will decrease the resolution in the values. -1 will break up the data values into one of 256 possible values (on a linear scale from the minimum to the maximum value in your data), -2 will allow 65536 possible values, and -4 (the default) will use 4-byte floating-point numbers for an "exact" representation.

  • -a — Output in ASCII format; otherwise, VTK’s more compact, but less readable and somewhat less portable binary format is used.

  • -n — For binary output (see -a above), by default the data is written in bigendian byte order, which is normally the order that VTK expects. However, some external tools and a few VTK classes use the native byte ordering instead (which may not be bigendian), and the -n option causes h5tovtk to output binary data in the native ordering.

  • -m min, -M max — When -1 or -2 are used, the input data are converted to a linear integer scale. Normally, the bottom and top of this scale correspond to the minimum and maximum values in the data. Using the -m and -M options, you can make the bottom and top of the scale correspond to min and max instead, respectively. Data values below or above this range will be treated as if they were min or max respectively. See also the -Z option.

  • -Z — For -1 or -2 output, center the linear integer scale on the value zero in the data.

  • -r — Invert the output values (map the minimum to the maximum and vice versa).

  • -x ix, -y iy, -z iz, -t it — This tells h5tovtk to use a particular slice of a multi-dimensional dataset. e.g. -x uses the subset (with one less dimension) 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.)

  • -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.