H5TOVTK(1) h5utils H5TOVTK(1)NAMEh5tovtk - convert datasets in HDF5 files to VTK format
SYNOPSISh5tovtk [OPTION]... [HDF5FILE]...
DESCRIPTIONh5tovtk 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 Univer‐
sity 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 sin‐
gle 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 cor‐
respond 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-dimen‐
sional dataset. e.g. -x uses the subset (with one less dimen‐
sion) 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)
