Provided by: h5utils_1.13.1-4build1_amd64 
NAME
h5topng - generate PNG images from 2d slices of HDF5 files
SYNOPSIS
h5topng [OPTION]... [HDF5FILE]...
DESCRIPTION
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 syntax HDF5FILE:DATASET.
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.
OPTIONS
-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 -mM options.
-o file
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 center.
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.
-s skewangle
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.
-c colormap
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 option.
-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 individually.
-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).
-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.
-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.
BUGS
Send bug reports to S. G. Johnson, stevenj@alum.mit.edu.
AUTHORS
Written by Steven G. Johnson. Copyright (c) 2004 by the Massachusetts Institute of Technology.
h5utils March 9, 2002 H5TOPNG(1)