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
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.
- -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.
Send bug reports to S. G. Johnson, stevenj@alum.mit.edu.
Written by Steven G. Johnson. Copyright (c) 2004 by the
Massachusetts Institute of Technology.