Gnuplotting

Create scientific plots using gnuplot

March 2nd, 2015 | 4 Comments

If you are a regular gnuplot user you most probably want to reuse some common settings. I normally avoid it on this blog to have easy scripts that run as standalone files, but during my work I use a lot of small config files.

Bessel functions

Fig. 1 Bessel functions from order zero up to six plotted with the dark2 line colors. (code to produce this figure, dark2.pal, xyborder.cfg, grid.cfg, mathematics.cfg)

Let us start with the Bessel function example from the last blog entry. As you can see in Fig. 1, it is a 2D plot, including axes, a grid, line colors, and definitions of higher order Bessel functions. All of those could be easily stored in small config files and reused in other plots.
As an example I will start with the axes. Here, I have four different config files, called xyborder.cfg, xborder, yborder.cfg, noborder.cfg, which do exactly what their names would suggest. Here are the first and last file:

# xyborder.cfg
set style line 101 lc rgb '#808080' lt 1 lw 1
set border 3 front ls 101
set tics nomirror out scale 0.75
set format '%g'
# noborder.cfg
set border 0
set style line 101 lc rgb '#808080' lt 1 lw 1
unset xlabel
unset ylabel
set format x ''
set format y ''
set tics scale 0

In the main plotting file I then just have to load the setting I like to have and I’m done. The same can be done for adding a grid, the right line color definitions and the extra Bessel functions leading to the following excerpt from the main plotting file:

# set path of config snippets
set loadpath './config'
# load config snippets
load 'dark2.pal'
load 'xyborder.cfg'
load 'grid.cfg'
load 'mathematics.cfg'

The set loadpath command tells gnuplot the directory where it can find all the configuration snippets. If you want to see an overview, look at my gnuplot configuration snippets and at the collection of palettes and line colors.

If you want to include more complicated settings, you have to use the macro setting of gnuplot. Fig. 2 is a reproduction of an earlier entry plotting a vector field with arrows. It included an lenghty definition of how to plot these arrows. If you want to do it several time and define the arrows in the same way every time you should also put it into a config file, this time as a variable (macro). In our example it looks like

color_arrows = 'u ($1-dx($1,$2)/2.0):($2-dy($1,$2)/2.0):(dx($1,$2)):(dy($1,$2)):\
(v($1,$2)) with vectors head size 0.08,20,60 filled lc palette'

In the main file the only thing we have then to do is

set macros
load 'noborder.cfg'
load 'moreland.pal'
load 'arrows.cfg'

# [...] 

plot '++' @color_arrows

Important is the first line that enables the use of macros in gnuplot which is disabled by default.

December 1st, 2012 | 6 Comments

In an earlier entry we created a vector field from measured data. Now we will visualize functions with the vector plotting style. As functions we have two 1/r potentials which define the amplitude of the vectors, as can be seen in Fig. 1. It is often better to indicate the amplitude by a color instead of by the length of the single vectors, especially if there are big changes. For the exact functions have a look into the corresponding file.

Vector field showing two sources

Fig. 1 Vector field of two sources with the opposite charge. The color indicates the amplitude. (code to produce this figure)

By analogy to the data vector field we have again a dx, and dy function for the length of the vectors.

dx(x,y) = scaling*ex(x,y)/enorm(x,y)
dy(x,y) = scaling*ey(x,y)/enorm(x,y)

Now we need a trick, because we have to fill the u 1:2:3:4 for the vector style with our function data. The four columns are then x,y,dx,dy of the vectors, where dx, dy are the lengths of the vector in x and y direction. Here the special filename ++ is a big help. It gives us x and y points as a first and second column, which we could address by $1 and $2. The number of points for the two axes are handled by the samples and isosamples command.

set samples 17    # x-axis
set isosamples 15 # y-axis
plot '++' u ($1-dx($1,$2)/2.0):($2-dy($1,$2)/2.0):\
    (dx($1,$2)):(dy($1,$2)):(v($1,$2)) \
    with vectors head size 0.08,20,60 filled lc palette

To place the vector at the center of the single x, y points, we move the starting point of the vectors to x-dx/2, y-dy/2.

October 17th, 2012 | 5 Comments

Some data could be nicely visualized by representing them as arrows. For example, assume that we have done an experiment where we played something to a subject through three loudspeakers and the subject should name the direction where he or she perceived it. In Fig. 1 we show the named direction by the direction of the arrows. The color of the arrow indicates the deviation from the desired direction. A white and not visible arrow means no deviation and a dark red one a deviation of 40° or more.

Vector field showing localization data

Fig. 1 Vector field showing localization results. The arrows are pointing towards the direction the subject had named. The color indicates the deviation from the desired direction. (code to produce this figure, set_loudspeakers.gnu, data)

In gnuplot the with vectors command enables the arrows in the plot. It requires four parameters, x, y, dx, dy, where dx and dy controls the endpoint of the arrow as offset values to x,y. In our example the direction is stored as an angle, hence the following functions do the conversion to dx,dy. 0.1 defines the length of the arrows.

xf(phi) = 0.1*cos(phi/180.0*pi+pi/2)
yf(phi) = 0.1*sin(phi/180.0*pi+pi/2)

An optional fifth parameter controls the color of the vector together with the lc palette setting. The arrows start at x-dx,y-dy and point to x+dx,y+dy.

plot 'localization_data.txt' \
    u ($1-xf($3)):($2-yf($3)):(2*xf($3)):(2*yf($3)):4 \
    with vectors head size 0.1,20,60 filled lc palette