H5TOVTK(1) h5utils H5TOVTK(1)
NAME
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 Uni-
versity 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 out-
put 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 dimen-
sion(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 corre-
spond 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 cor-
respond 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
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.
h5utils March 9, 2002 H5TOVTK(1)