gnuplot - Properly clipping a 3D plot (splot) - plot

Disclaimer: I am totally new to Gnuplot, so I am probably missing something obvious...
For a presentation that I have to give, I am trying to use Gnuplot for creating an interactive version of this plot.
Up to now, I have come up with the following code:
set hidden3d
set isosamples 40
set border 4095
set xrange [-1 : 5]
set yrange [-3 : 3]
set zrange [-10 : 10]
set xtics 2
set ytics 2
set ztics 2
f(x,y) = x**2 + y**2 * (1 - x)**3
splot f(x,y)
pause -1
However, at the boundary of the plot (specifically, at the boundary with respect to the z-axis) the plot gets truncated in a way that I find quite ugly; see below. What I would like is essentially that all the lines get drawn as if my plot range would be (e.g.) -50 : 50, but then in the end only the "intersection" of the plot with the box [-1:5] x [-3:3] x [-10:10] should actually be shown. What seems to be happening right now is that any "plot segment" that has at least one point outside the box determined by xrange-zrange gets not drawn at all.
(How) can I change this?

Answering from the future, sort of, so this may not count...
Versions of gnuplot through 5.2 cannot do exactly what you want. However the development version 5.3 does this by default so long as you use a pm3d surface rather than a hidden3d surface. Here is your plot as rendered by the current development code:
set border 4095
unset colorbox
set view 56, 15, .75, 1.75
set samples 40, 40
set isosamples 40, 40
set xyplane 0
set grid x y z vertical
set pm3d depthorder border linewidth 0.100
set pm3d clip z
set pm3d lighting primary 0.8 specular 0.3 spec2 0.3
set xrange [-1 : 5]
set yrange [-3 : 3]
set zrange [-10 : 10]
set xtics 1 offset 0,-0.5
set ytics 1 offset 0,-0.5
set ztics 5
f(x,y) = x**2 + y**2 * (1 - x)**3
splot f(x,y) with pm3d fillcolor "cyan"
The key is the command set pm3d clip z. This will be the default in future versions but is not supported in version 5.2. You can build from the current git source repository on gnuplot.sf.net or wait for the release of version 5.4 expected in Spring 2020.

Maybe you can the following line of code to force the zrange.
set ticslevel 0

Related

How to label zrange in multiplot graph in gnuplot?

I am plotting multiplot surfaces.
I found this code 1 very helpful to plot my graph.
However, I want to label the z-axis throughout all surfaces in one plot.
I tried this set zrange[0.5:b+0.5], but nothing showed up. then I tried min_z and max_z, still, nothing showed up.
though I calculated and checked the range by the following the command.
print min_z,max_z.
can anyone please tell me how can I choose zrange with my own choice? like 1 ,2 3 4 5.
I will expand my comment as a possible answer. Multiplot is not needed for this style of plot. Here is an approximate recreation of the figure you linked to.
If you want to customize the axis labels along z, you can add a command to change the format like this: set ztic format "%.2f", and/or add additional commands of the form: set ztic add ( pi/2 "z = π/2" )
f(x,y,z) = besj0(x*x/z + y*y/z) / z
set palette cubehelix
set xyplane 0
set view 64,58
set ztics 0.2
unset key
splot for [i=1:6] z=(1.+i/6.), '++' using 1:2:(z):(f(x,y,z)) with pm3d
Answer expanded to show plotting from a series of files
Plotting from a series of files is essentially the same. The splot command again inserts a constant z value to create a plane, taking the data coordinates [x,y] from columns 1 and 3 and the f(x,y) value from column 4.
Here is an example:
set palette defined( 0 "dark-red", 1 "yellow" )
set xyplane 0
set view 74, 62, 0.85, 1.8
set border 16 # z axis only
unset xtics; unset ytics
unset key
file(i) = sprintf("map%d.dat",i)
set ztics ("File 1" 1, "File 2" 2, "File 3" 3, "File 4" 4)
splot for [i=1:4] file(i) using 1:2:(i):3 with image

Gnuplot: Making pm3d palette repeat when out of range

The plan is to plot the phase of a 2D-complex function using pm3d map and a repeating color-palette in a continous way. To be more specific, the palette is only defined on [-pi, pi], while the phase itself might run out of this range. The color-palette shall repeat for those values.
My current attempt was to force the function to stay inside the range and start over from the other side when crossing a border by subtracting or adding multiples of 2*pi.
This, however, resulted in artifacts whenever such a phase-jump occured in the function. Note those blue-ish pixel-rings in the plot:
This was the code used to generate this plot:
set pm3d map
set palette model HSV defined ( 0 0 1 1, 1 1 1 1 )
set samples 100; set isosamples 100
set xrange [-4:4]
set yrange [-4:4]
set cbrange [-pi:pi]
set cblabel "Phase"
phaseCont(u,v) = 2*pi* ((u/4)**2 + (v/4)**2)
phaseClip(u,v) = phaseCont(u,v) - (floor(phaseCont(u,v)/(2*pi) + 0.5) * 2*pi)
set terminal png
set output "phaseplot.png"
splot phaseClip(x,y) with pm3d
unset output
It makes sense the artifacts appear as interpolation happens, but it's not what I'm going for, of course.
Is there a way to create beautiful 2D-plots with repeating color-patterns?
Gnuplot cannot define infinitey repeating color palettes. In your case, the disturbing interpolation comes from the default pm3d interpolation, which calculates the average of all four corners to determine the color (see show pm3d).
To avoid that kind of interpolation use e.g.
set pm3d corners2color c1
to determine the color from one corner only. Especially in your case that shouldn't matter, because you can always increase the sampling of your function to get smoother results:
set pm3d map
set palette model HSV defined ( 0 0 1 1, 1 1 1 1 )
set samples 500; set isosamples 500
set xrange [-4:4]
set yrange [-4:4]
set cbrange [-pi:pi]
set pm3d corners2color c1
set cblabel "Phase"
phaseCont(u,v) = 2*pi* ((u/4)**2 + (v/4)**2)
phaseClip(u,v) = phaseCont(u,v) - (floor(phaseCont(u,v)/(2*pi) + 0.5) * 2*pi)
set terminal pngcairo
set output "phaseplot.png"
splot phaseClip(x,y) with pm3d

Gnuplot 3D plotting from file, not enough detailed values on x-,y-, and z-ticks

I have a simple data I want to plot as 3D plot (3 columns divided by a comma):
33.26,0.0000001,1
67.02,0.0000010,2
101.64,0.0000100,3
137.53,0.0001000,4
175.06,0.0010000,5
214.59,0.0100000,6
256.47,0.1000000,7
301.09,1.0000000,8
348.78,10.0000000,9
399.92,100.0000000,10
454.87,1000.0000000,11
513.99,10000.0000000,12
577.65,10000.0000000,13
646.22,10000.0000000,14
720.05,10000.0000000,15
799.51,10000.0000000,16
884.96,10000.0000000,17
976.77,10000.0000000,18
1075.29,10000.0000000,19
1180.89,10000.0000000,20
1293.92,10000.0000000,21
1414.77,10000.0000000,22
1431.83,10000.0000000,23
1449.15,10000.0000000,24
1466.97,10000.0000000,25
1485.79,10000.0000000,26
1505.97,10000.0000000,27
1527.88,10000.0000000,28
1551.87,10000.0000000,29
1578.3,10000.0000000,30
1607.56,10000.0000000,31
1639.98,10000.0000000,32
1675.95,10000.0000000,33
1715.82,10000.0000000,34
1759.96,10000.0000000,35
1808.72,10000.0000000,36
1862.49,10000.0000000,37
1921.6,10000.0000000,38
1986.44,10000.0000000,39
2057.35,10000.0000000,40
2134.71,10000.0000000,41
2218.87,10000.0000000,42
2310.2,10000.0000000,43
2409.06,10000.0000000,44
2515.83,10000.0000000,45
I wrote a simple script to plot the above data:
#!/usr/bin/gnuplot
set palette rgbformulae 33,13,10
set datafile separator ","
set terminal postscript eps size 10.5, 5.62 enhanced color font 'Helvetica,20' linewidth 2
set output 'test.eps'
set xlabel "time [s] (no operation)" offset -4, 0, 0
set xtics left offset 0,-0.3 rotate by 45 right
set xrange [0:400]
set ylabel "ranges" offset 2, 0, 0
set ytics left offset 0,-0.5
set zlabel "devices" offset -4, 0, 0
set zrange [0:50]
set autoscale
set title " "
set key inside left top;
set dgrid3d 30,30
set hidden3d
set style line 1 linecolor rgb '00FF00' linetype 4 linewidth 1
splot "data.csv" u 1:2:3 title "" with lines palette
And my output:
As you all can see, the output image (or, I should say), the x,y and z ticks on axis x,y, and z are not enough detailed. It is hard to say that the output image was plotted with this data.
Is there a way that would let me manipulate the x,y, and z ticks, to be taken from file, in some elegant way?
I also would like the image to be more readable with new x,y, and z ticks, so I think that the 10000.0000000 value should appear only once, when it appeared for the first time in data file.
Thank you.
Not exactly an answer to your question, and it is my personal opinion, but you might be interested in the ideas:
The data seems not to be grid data, so I would not use a surface plot of any kind.
Plotting only the datapoints in 3d does not give a useful picture, it is only a single line somewhere in space. I would try to use a 2D plot which contains the height information as color.
I would use a logscale for the y-axis.
This leads to the following script:
set terminal pngcairo
set output 'test.png'
set datafile separator ","
set palette rgbformulae 33,13,10
# Set margins to keep colorbox label inside the picture
set lmargin screen 0.12
set rmargin screen 0.85
set xlabel "time [s] (no operation)"
set ylabel "ranges"
set cblabel "devices"
unset key
set yrange [1e-8:1e5]
set ytics format "1e%+T"
set logscale y
set view map
set cbrange [0:50]
set zrange [0:50]
splot "data.csv" u 1:2:3 w p pt 7 palette ,\
"data.csv" every 5::4 u ($1+0):($2/3):(0):($3 != 30 ? 3 : "") with labels
It also prints the z-labels of some datapoints, skipping 30 for spacing reasons.
This is the result:

Plotting an IR Spectrum with Gnuplot

I have an infrared spectrum for a compound of interest that I would like to plot, and I have a spectrum.dat file with all of the data points. It is of the form:
# X Y
300 100
301 100
302 99
303 70
...
3999 98
4000 100
I would like to plot this using an x axis typical of IR spectra, but I am having trouble doing so. If you are unfamiliar, this is what a typical IR spectrum might look like (aside from the labels on the graph itself). Notice that the x-axis is reversed, and that it abruptly doubles its scaling above 2000 units (reciprocal centimeters). Is there a way to coerce Gnuplot into plotting my data this way? I so far have managed to come up with the following script:
# Make an SVG of size 800x500
set terminal svg size 800,500 fname 'CMU Sans Serif' fsize '10'
set output 'ir.svg'
# Color definitions
set border linewidth 1.5
set style line 1 lc rgb '#a0a0a0' lt 1 lw 2 pt 7 # gray
# Format graph
unset key
set xlabel 'Wavenumbers'
set ylabel 'Transmittance'
set xrange [4000:300]
# Plot data
plot 'spectrum.dat' with lines ls 1
This reverses the x-axis nicely, but I can't figure out how to change the scaling in such an unusual way.
As a chemist I am motivated to answer...
As far as I know gnuplot doesn't easily allow for arbitrary axis scaling (unless anyone has bright ideas about how to use set link). My strategy in this kind of situation is to plot the two halves separately and have them join seamlessly:
#!/usr/bin/env gnuplot
set terminal png size 800,500
set output 'ir.png'
set xlabel 'Wavenumbers' offset 20
set ylabel 'Transmittance'
set tics out nomirror
set key bottom right
set bmargin 4
set yrange [0:1]
set multiplot layout 1,2 title 'IR Spectrum of Cholesterol'
# left half of plot
set xrange [4000:2000]
set rmargin 0
set border 7
plot 'cholesterol.txt' notitle
# right half of plot
set xrange [1999:300]
set lmargin 0
set rmargin 2
set border 13
unset xlabel
unset ylabel
unset ytics
plot 'cholesterol.txt' title 'Cholesterol'
unset multiplot
My one quibble is that the 2000 is written twice and looks bolder on my screen, but I will leave fidgeting with the tics to you.
andyras' answer is a nice one, this is an arguably simpler (more elegant :-P) solution in terms of layout options. This should also be a more universal solution. If there are not too many tics (read below the figure if there are too many), then this could be done scaling the curve itself beyond 2000, and then adding all the tics by hand. Since I don't have IR spectrum data available I will use the dummy file "+" and plot log(x) from 4000 to 500:
xmax=4000 ; xmin = 500
pivot = 2000 ; rescfactor = 2.
rescale(x) = (x >= pivot ? x : pivot + rescfactor*(x-pivot))
set xrange [rescale(xmax):rescale(xmin)]
set xtics ("4000" 4000, "3000" 3000, "2000" 2000, \
"1500" rescale(1500), "1000" rescale(1000), "500" rescale(500))
plot "+" u (rescale($1)):(log($1)) w l
In your case you just substitute log($1) by 2 or whatever you're plotting.
In newer versions of gnuplot (starting from 4.4) adding the tics can be done automatically using a loop:
xmax = 4000 ; xmin = 500 ; step = 500
set xtics (sprintf("%i",xmax) rescale(xmax)) # Add the first tic by hand
set for [i=xmin:xmax-step:step] xtics add (sprintf("%i",i) rescale(i))
Starting from gnuplot 4.6 also a different for construction can be made using do for:
do for [i=xmin:xmax-step:step] {set xtics add (sprintf("%i",i) rescale(i))}

Gnuplot plot 2D matrix with image, want to draw borders for each cell

I want to plot a 18x18 matrix with gnuplot. Here is my codes:
set size ratio 1
set palette gray negative
set xrange[-0.5:17.5]
set yrange[-0.5:17.5]
set cbrange[-0.2:0.8]
set xtics 0,1,17
set ytics 0,1,17
set xtics offset -0.5,0
set title "Resolusition Matrix for E"
plot "Mat" matrix w image noti
Then I got a fig like this:
Now I would like to add borders to each cell, which will look like this:
Thank you.
For your case you can set one minor tic, which then lies on the border between two pixels, and draw a grid on them:
set size ratio 1
set palette gray negative
set autoscale xfix
set autoscale yfix
set xtics 1
set ytics 1
set title "Resolution Matrix for E"
set tics scale 0,0.001
set mxtics 2
set mytics 2
set grid front mxtics mytics lw 1.5 lt -1 lc rgb 'white'
plot "Mat" matrix w image noti
Note, that set grid front also brings the tics to the front. To avoid that you can scale the tics to 0. For the minor tics you must use a very small number, 0 would omit the grid lines on the minor tics.
The result with 4.6.3 is:
EDIT: In order to control the grid lines and tic labels independently, you can use the unused x2 and y2 to draw the grid (inspired by an answer to How do I draw a vertical line in gnuplot?):
set size ratio 1
set palette gray negative
# grid lines
set x2tics 1 format '' scale 0,0.001
set y2tics 1 format '' scale 0,0.001
set mx2tics 2
set my2tics 2
# labeling
set xtics 5 out nomirror
set ytics 5 out nomirror
set grid front mx2tics my2tics lw 1.5 lt -1 lc rgb 'white'
set xrange[-0.5:39.5]
set yrange[-0.5:39.5]
set x2range[-0.5:39.5]
set y2range[-0.5:39.5]
plot "Mat" matrix w image notitle
With gnuplot version 4.6, this requires setting explicit ranges, so that the x and x2 (unused!) are equal. The information might be extracted with stats from the data file.
Using version 5 allows you to use set link. Instead of all the set *range stuff. You could use:
set autoscale fix
set link x
set link y
Result:

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