Gnuplotting

Create scientific plots using gnuplot

Color maps from colorbrewer

June 5th, 2013 | 2 Comments

If you are looking for nice color maps which are especially prepared to work with cartographic like plots you should have a look at colorbrewer2.org. On that site hosted by Cynthia Brewer you can pick from a large set of well balanced color maps. The maps are ordered regarding their usage. Figure 1 shows example color maps for three different use cases.

Colorbrew color maps

Fig. 1 Examples of color maps from colorbrewer2.org ordered in three categories (code to produce this figure, data)

The diverging color maps are for data with extremes at both points of a neutral value, for example like the below and above sea level. The sequential color maps are for data ordered from one point to another and the qualitative color maps are for categorically-grouped data with now explicit ordering.
Thanks to Anna Schneider there is an easy way to include them (at least the ones with eight colors each) into gnuplot. Just go to her gnuplot-colorbrewer github site and download the color maps. Place them in the same path as your plotting file, or add the three pathes of the repository to your load pathes, for example by adding the following to your .gnuplot file.

set loadpath '~/git/gnuplot-colorbrewer/diverging' \
    '~/git/gnuplot-colorbrewer/qualitative' \
    '~/git/gnuplot-colorbrewer/sequential'
YlGnBu color map from colorbrewer

Fig. 2 Photoluminescence yield plotted with the YlGnBu color map from colorbrewer2.org (code to produce this figure, data)

After this you can pick the right color map for you on colorbrewer2.org, keep its name and load it before your plot command. For example in Fig. 2 we are plotting again the photoluminescence yield with the sequential color map named YlGnBu. First we load the color map, then switch the two poles of the color map by setting the palette to negative, and finally plotting the data.

load 'YlGnBu.plt'
set palette negative
plot 'matlab_colormap.txt' u ($1/3.0):($2/3.0):($3/1000.0) matrix with image
Paired color map from colorbrewer

Fig. 3 Eight lines plotted with the Paired color map from colorbrewer2.org (code to produce this figure)

The nice thing of the palettes coming with gnuplot-colorbrewer is that they also include the corresponding line colors. In Fig. 3 you see the Paired qualitative color map in action with lines.

load 'Paired.plt'
plot for [ii=1:8] f(x,ii) ls ii lw 2

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Default color map

May 21st, 2013 | No Comments

As you may have noted, gnuplot and Matlab have different default color maps. Designing such a default map is not easy, because they should handle a lot of different things (Moreland, 2009):
– The map yields images that are aesthetically pleasing
– The map has a maximal perceptual resolution
– Interference with the shading of 3D surfaces is minimal
– The map is not sensitive to vision deficiencies
– The order of the colors should be intuitively the same for all people
– The perceptual interpolation matches the underlying scalars of the map

In his paper Moreland developed a new default color map that was mentioned already in a user comment. In Fig. 1 the map is used to replot the photoluminescence yield plotted in an earlier entry.

Default color map after Moreland, 2009

Fig. 1 Photoluminescence yield plotted with the default color map after Moreland, 2009 (code to produce this figure, data)

To use the default color map proposed by Moreland, just download default.plt and store it to a path, that is available to gnuplot. For example store it under /home/username/.gnuplotting/default.plt and add the following line to your .gnuplot file.

set loadpath "/home/username/.gnuplotting"

After that you can just load the palette before your plot command via

load 'default.plt'
Default gnuplot color palette

Fig. 2 Photoluminescence yield plotted with gnuplots default color palette (code to produce this figure, data)

In Fig. 2 the same plot is shown using the default color map from gnuplot, which is a little bit dark in my opinion.

Default Matlab color palette

Fig. 3 Photoluminescence yield plotted with Matlabs default color palette (code to produce this figure, data)

Figure 3 shows the jet color map from Matlab, which is a classical rainbow map with all its pros and cons.

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Animation II – video

February 3rd, 2012 | No Comments

In the first post regarding animations we have created a bunch of png files and combined them to a single gif animation. Now we want to generate again a bunch of png files, but combine them to a movie.

Fig. 1 Video animation of Huygens principle (code to produce this figure, loop function)

We create the png files in analogy to the gif example, hence we will discuss only the generation of the movie here. In order to compose a avi file from the png files we are using Mencoder. Gnuplot is able to directly start Mencoder by its system command.

# Create movie with mencoder
ENCODER = system('which mencoder');
if (strlen(ENCODER)==0) print '=== mencoder not found ==='; exit
CMD = 'mencoder mf://animation/*.png -mf fps=25:type=png -ovc lavc -lavcopts vcodec=mpeg4:mbd=2:trell -oac copy -o huygen.avi'
system(CMD)

The first two lines check if Mencoder is available and quit gnuplot if not. The Mencoder command itselfs gets the directory containing the png files mf://animation/*.png, frames per second and input type-mf fps=25:type=png, video -ovc and audio -oac options, and finally of course the output file -o huygen.avi.

In order to generate a webm video file for a web site, ffmpeg can be used to convert the video.

$ ffmpeg -i huygen.avi huygen.webm

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Animation I – gif

October 21st, 2011 | 6 Comments

For presentation or teaching purposes it can be useful to show not only a figure, but an animation to illustrate something more clear. There exists different possibilities to do this in Gnuplot. Today we will have a look at how to create a gif animation.

Bessel function

Fig. 1 Animation of Bessel function (code to produce this figure, loop)

Fig. 1 shows a gif animation of a Bessel function of first kind and zeroth order. Gnuplot has a gif output terminal, but the result will be smoother if we first create png files with Gnuplot and then the animated gif file with another program. In order to create a set of png files we have to loop through the time value t and different output files.

# initializing values for the loop and start the loop
t = 0
end_time = 1
system('mkdir -p animation')
load 'bessel.plt'

The above code sets a start value for the running time variable t and the end_time variable at which the looping should be stopped. Then a folder for the output png files is created and the loop file bessel.plt is loaded. The content of this loop file is shown below.

# bessel loop
t = t + 0.02
outfile = sprintf('animation/bessel%03.0f.png',50*t)
set output outfile
splot u*sin(v),u*cos(v),bessel(u,t) w pm3d ls 1
if(t<end_time) reread;

Here we update the time t, create a file name with a different number and plot out Bessel function. Finally the last line checks if our time t is smaller than the end_time variable, and executes the loop again if this is the case.

After we have created the png files in the animation folder, we start GIMP and load all the files as layers (File > Open as Layers). After this we save all layers together as an animated gif file.

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