h5topng - generate PNG images from 2d slices of HDF5 files
h5topng [OPTION]... [HDF5FILE]...
h5topng is a utility to generate images in PNG (Portable Network
Graphics) format from two-dimensional slices of datasets in HDF5 files.
It is designed for quick-and-dirty visualization of scientific data,
and for batch processing thereof via shell scripts.
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, h5topng takes the first
dataset, but this can be changed via the -d option, or by using the
For a three- or four-dimensional dataset you must specify coordinates
in one or two slice dimensions, respectively, to get a two-dimensional
slice, via the -xyzt options. Yet more options control things like the
colormap and magnification. Still, the most basic usage is something
like ´h5topng foo.h5´, which will output a file foo.png containing an
image from the two-dimensional data in foo.h5.
-h Display help on the command-line options and usage.
-V Print the version number and copyright info for h5topng.
-v Verbose output. This output includes the minimum and maximum
values encountered in the data, which is useful to know for the
Send PNG output to file rather than to the filename with .h5
replaced with .png (the default).
-x ix, -y iy, -z iz, -t it
This tells h5topng 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
Instead of specifying a single index as an argument to these
options, you can also specify a range of indices in a Matlab-
like notation: start:step:end or start:end (step defaults to 1).
This loops over that slice index, from start to end in steps of
step, producing a sequence of output PNG files (with the slice
index appended to the filename, before the ".png").
-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.)
-X scalex, -Y scaley, -S scale
Scale the x and y dimensions of the image by scalex and scaley
respectively. The -S option scales both x and y. The default
is to use scale factors of 1.0; i.e. the image has the same
dimensions (in pixels) as the data. Linear interpolation is
used to fill in the pixels when the scale factors are not 1.0.
Skew the image by skewangle (in degrees) to the left or right.
The result is a parallelogram, with the leftover space in the
(square) image filled with either black or white pixels,
depending upon the color map.
-T Transpose the data (interchange the image axes). By default,
the first (x) coordinate of the data corresponds to the columns,
and the second (y) coordinate corresponds to the rows;
transposition reverses this convention.
Use a color map colormap rather than the default gray color map
(a grayscale ramp from white to black). colormap is normally
the name of one of the color maps provided with h5topng (in the
/usr/share/h5utils/colormaps directory), or can instead be the
name of a color-map file.
Three useful included color maps are hot (black-red-yellow-
white, useful for intensity data), bluered (blue-white-red,
useful for signed data), and hsv (a multi-color "rainbow"). If
you use the bluered color map for signed data, you may also want
to use the -Z option so that the center of the color scale
(white) corresponds to zero.
A color-map file is a sequence of whitespace-separated R G B A
quadruples, where each value is in the range 0.0 to 1.0 and
indicates the fraction of red/green/blue/alpha. (An alpha of 0
is transparent and of 1 is opaque; this is only used for the -a
option, below.) The colors in the color map are linearly
interpolated as necessary to provide a continuous color ramp.
-r Reverse the ordering of the color map. You can also accomplish
this by putting a "-" before the colormap name in the -c or -a
-Z Center the color scale on the value zero in the data.
-m min, -M max
Normally, the bottom and top of the color map correspond to the
minimum and maximum values in the data. Using these options,
you can make the bottom and top of the color map correspond to
min and max instead. Data values below or above this range will
be treated as if they were min or max respectively. See also
the -Z and -R options.
-R When multiple files are specified, set the bottom and top of the
color maps according to the minimum and maximum over all the
data. This is useful to process many files using a consistent
color scale, since otherwise the scale is set for each file
-C file, -b val
Superimpose contour outlines from the first dataset in the file
HDF5 file on all of the output images. (If the contour dataset
does not have the same dimensions as the output data, it is
peridically "tiled" over the output.) You can use the syntax
file:dataset to specify a particular dataset within the file.
The contour outlines are around a value of val (defaults to
middle of value range in file).
-A file, -a colormap:opacity
Translucently overlay the data from the first dataset in the
file HDF5 file, which should have the same dimensions as the
input dataset, on all of the output images, using the colormap
colormap with opacity (from 0 for completely transparent to 1
for completely opaque) opacity multiplied by the opacity (alpha)
values in the colormap. (If the overlay dataset does not have
the same dimensions as the output data, it is peridically
"tiled" over the output.) You can use the syntax file:dataset
to specify a particular dataset within the file.
Some predefined colormaps that work particularly well for this
feature are yellow (transparent white to opaque yellow) gray
(transparent white to opaque black), yarg (transparent black to
opaque white), green (transparent white to opaque green), and
bluered (opaque blue to transparent white to opaque red). You
can prepend "-" to the colormap name to reverse the colormap
order. (See also -c, above.) The default for -a is yellow:0.3
(yellow colormap multiplied by 30% opacity).
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.
-8 Use 8-bit (indexed) color for the PNG output, instead of 24-bit
(direct) color (the default). (This shrinks the image size
slightly, with some degradation in quality.) Not supported in
conjunction with the -A (translucent overlay) option.
Send bug reports to S. G. Johnson, email@example.com.
Written by Steven G. Johnson. Copyright (c) 2004 by the Massachusetts
Institute of Technology.