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 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¶
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.