H5TOPNG(1) h5utils H5TOPNG(1)
h5utils h5utils
March 9, 2002
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-dimensional data set, the xy slice at z index zero is
extracted by default, but other slices can be extracted using the -xyz
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
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
This tells h5topng to use a particular slice of a two- or three-
dimensional dataset. e.g. -x causes a yz plane 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). The default behaviour is
equivalent to -z 0. See also the -0 option to shift the origin
of the slice coordinates to the dataset center.
-0 Shift the origin of the slice coordinates to the dataset center,
so that e.g. -0 -x 0 (or more compactly -0x0) returns the central
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H5TOPNG(1) h5utils H5TOPNG(1)
h5utils h5utils
March 9, 2002
x plane of the dataset instead of the edge x plane.
-X scalex, -Y scaley, -S scale
Scale the x and y dimensions 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, no
transposition is done.
-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
/opt/h5utils/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.) The colors in the color map
are linearly interpolated as necessary to provide an 8-bit color
palette.
-r Reverse the ordering of the color map.
-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
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H5TOPNG(1) h5utils H5TOPNG(1)
h5utils h5utils
March 9, 2002
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, which should have the same dimensions as the input
dataset, on all of the output images. 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).
-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) 1999, 2000, 2001, 2002 by
the Massachusetts Institute of Technology.
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