How to plot network by gnuplot - gnuplot

I have a list of more than 100 points. I'd like to plot a figure like this picture. The lines connect any two points whose distance is less than 3.
1.53 2.40
5.39 3.02
4.35 1.29
9.58 8.34
6.59 1.45
3.44 3.45
7.22 0.43
0.23 8.09
4.38 3.49
https://www.codeproject.com/Articles/1237026/Simple-MLP-Backpropagation-Artificial-Neural-Netwo

You probably have to check every point against every other point whether the distance is less than your threshold. So, create a table with all these points, the vector between them and plot them with vectors. The following example creates some random points with random sizes and random colors.
Code:
### Plot connections between points which are closer than a threshold
reset session
set size square
# create some random test data
set print $Data
myColors = "0xe71840 0x4d76c3 0xf04092 0x47c0ad 0xf58b1e 0xe6eb18 0x59268e 0x36b64c"
myColor(n) = int(word(myColors,n))
do for [i=1:100] {
print sprintf("%g %g %g %d", rand(0), rand(0), rand(0)*2+1, myColor(int(rand(0)*8)+1))
}
set print
d(x1,y1,x2,y2) = sqrt((x2-x1)**2 + (y2-y1)**2)
myDist = 0.2
set print $Connect
do for [i=1:|$Data|-1] {
x1=real(word($Data[i],1))
y1=real(word($Data[i],2))
do for [j=i+1:|$Data|] {
x2=real(word($Data[j],1))
y2=real(word($Data[j],2))
if (d(x1,y1,x2,y2)<myDist) { print sprintf("%g %g %g %g", x1, y1, x2-x1, y2-y1) }
}
}
set print
set key noautotitle
plot $Connect u 1:2:3:4 w vec lc "grey" nohead, \
$Data u 1:2:3:4 w p pt 7 ps var lc rgb var
### end of code
Result:

You do not specify how to choose the node size or color. I show an example using a constant pointsize and taking the color from sequential linetypes
[![enter image description here][1]][1]$DATA << EOD
1.53 2.40
5.39 3.02
4.35 1.29
9.58 8.34
6.59 1.45
3.44 3.45
7.22 0.43
0.23 8.09
4.38 3.49
EOD
N = |$DATA|
do for [i=1:N] {
do for [j=i+1:N] {
x0 = real(word($DATA[i],1))
y0 = real(word($DATA[i],2))
x1 = real(word($DATA[j],1))
y1 = real(word($DATA[j],2))
if ((x1-x0)**2 + (y1-y0)**2 <= 9) {
set arrow from x0,y0 to x1,y1 nohead
}
}
}
unset border
unset tics
unset key
set pointsize 3
plot $DATA using 1:2:0 with points pt 7 lc variable

Related

Finding fitting range using gnuplot

I am new to Gnuplot, I have a non-linear data set and I want to fit the data within the linear range only. I normally do the fitting and specifies the fit range using the following command and redo the fitting process by changing the fit range manually until I get the optimum range for the fit:
fit [0.2:0.6]f(x) "data.txt" u 2:3:6 yerror via m1,m2
plot "<(sed -n '15,500p' data.txt)" u 2:3:6 w yerr title 'Window A',[0:.6] f(x) notitle lc rgb 'black'
Is it possible to iteratively run the fit within some data range to obtain the optimum data range for the fit in Gnuplot?
The data is typically like this one:
data
Your data (I named the file 'mas_data.txt') looks like the following (please always show/provide relevant data in your question).
Data: (how to plot with zoom-in)
### plotting data with zoom-in
reset session
FILE = 'mas_data.txt'
colX = 2
colY = 3
set key top left
set multiplot
plot FILE u colX:colY w lp pt 7 ps 0.3 lc rgb "red" ti "Data", \
set title "Zoom in"
set origin 0.45,0.1
set size 0.5, 0.6
set xrange [0:1.0]
plot FILE u colX:colY w lp pt 7 ps 0.3 lc rgb "red" ti "Data"
unset multiplot
### end of code
Regarding the "optimum" fitting range, you could try the following procedure:
find the absolute y-minimum of your data using stats (see help stats)
limit the x-range from this minimum to the maximum x-value
do a linear fit with f(x)=a*x+b and remember the standard error value for the slope (here: a_err)
reduce the x-range by a factor of 2
go back to 3. until you have reached the number of iteration (here: N=10)
find the minimum of Aerr[i] and get the corresponding x-range
The assumption is if the relative error (Aerr[i]) has a minimum then you will have the "best" fitting range for a linear fit starting from the minimum of your data.
However, I'm not sure if this procedure will be robust for all of your datasets. Maybe there are smarter procedures. Of course, you can also decrease the xrange in different steps. This procedure could be a starting point for further adaptions and optimizations.
Code:
### finding "best" fitting range
reset session
FILE = 'mas_data.txt'
colX = 2
colY = 3
stats FILE u colX:colY nooutput # do some statistics
MinY = STATS_min_y # minimum y-value
MinX = STATS_pos_min_y # x position of minimum y-value
Xmax = STATS_max_x # maximum x-value
XRangeMax = Xmax-MinX
f(x,a,b) = a*x + b
set fit quiet nolog
N = 10
array A[N]
array B[N]
array Aerr[N]
array R[N]
set print $myRange
do for [i=1:N] {
XRange = XRangeMax/2**(i-1)
R[i] = MinX+XRange
fit [MinX:R[i]] f(x,a,b) FILE u colX:colY via a,b
A[i] = a
Aerr[i] = a_err/a*100 # asymptotic standard error in %
B[i] = b
print sprintf("% 9.3g % 9.3f %g",MinX,R[i],Aerr[i])
}
set print
print $myRange
set key bottom right
set xrange [0:1.5]
plot FILE u colX:colY w lp pt 7 ps 0.3 lc rgb "red" ti "Data", \
for [i=1:N] [MinX:R[i]] f(x,A[i],B[i]) w l lc i title sprintf("%.2f%%",Aerr[i])
stats [*:*] $myRange u 2:3 nooutput
print sprintf('"Best" fitting range %.3f to %.3f', MinX, STATS_pos_min_y)
### end of code
Result:
Zoom-in xrange[0:1.0]
0.198 19.773 1.03497
0.198 9.985 1.09066
0.198 5.092 1.42902
0.198 2.645 1.53509
0.198 1.421 1.81259
0.198 0.810 0.659631
0.198 0.504 0.738046
0.198 0.351 0.895321
0.198 0.274 2.72058
0.198 0.236 8.50502
"Best" fitting range 0.198 to 0.810

Clip vectors on circle in gnuplot

I try to draw some vector fields in a circular region. Consider the following MWE
unset grid
unset tics
unset colorbox
unset border
set size square
besselj(n, x) = n > 1 ? 2*(n-1)/x*besselj(n-1,x) - besselj(n-2,x) : (n == 1 ? besj1(x) : besj0(x))
dbesselj(n, x) = n/x*besselj(n,x) - besselj(n+1,x)
rho(x,y) = sqrt(x**2+y**2)
phi(x,y) = atan2(y,x)
d = 1.0
l = 1.0
z = l/2
q = 1
set xrange [-d/2*1.1:d/2*1.1]
set yrange [-d/2*1.1:d/2*1.1]
Erho(x,y,n,ynp) = (-1/rho(x,y)) * besselj(n, (ynp*2/d)*rho(x,y)) * (-n*sin(n*phi(x,y))) * sin(q*pi*z/l)
Ephi(x,y,n,ynp) = (ynp*2/d) * dbesselj(n, (ynp*2/d)*rho(x,y)) * (cos(n*phi(x,y))) * sin(q*pi*z/l)
Ex(x,y,n,ynp) = rho(x,y) > d/2 ? NaN : cos(phi(x,y))*Erho(x,y,n,ynp) - sin(phi(x,y))*Ephi(x,y,n,ynp)
Ey(x,y,n,ynp) = rho(x,y) > d/2 ? NaN : sin(phi(x,y))*Erho(x,y,n,ynp) + cos(phi(x,y))*Ephi(x,y,n,ynp)
mag(x,y,n,ynp) = sqrt(Ex(x,y,n,ynp)**2 + Ey(x,y,n,ynp)**2)
set object circle at 0,0 size 0.5 fc black lw 3 front
set multiplot layout 1,2
set title 'TE_{01}'
set table 'tmp.dat'
set samples 16
set isosamples 16
plot '++' u 1:2:(Ex($1,$2,0,3.832)/50):(Ey($1,$2,0,3.832)/50) w vectors
unset table
set samples 250
set isosamples 250
plot '++' u 1:2:(mag($1,$2,0,3.832)) w image notitle, \
'tmp.dat' u 1:2:3:4 w vectors head filled lc black lw 1 notitle
set title 'TE_{11}'
set table 'tmp.dat'
set samples 16
set isosamples 16
plot '++' u 1:2:(Ex($1,$2,1,1.841)/20):(Ey($1,$2,1,1.841)/20) w vectors
unset table
set samples 250
set isosamples 250
plot '++' u 1:2:(mag($1,$2,1,1.841)) w image notitle, \
'tmp.dat' u 1:2:3:4 w vectors head filled lc black lw 1 notitle
unset multiplot
which plots the vector field as well as its magnitude inside the circle with diameter d. The result from this is
which is totally okay for the left image (TE01), but the right image (TE11) looks ugly because there are some vectors which are drawn outside the circle. My actually desired result is this
where I have no vectors outside of the black circle. How can I achieve that?
I know there is the clip function in gnuplot, but this does not allow to specify the shape to be used for clipping.
Here is what you can try. Define your own clip function, e.g. a circle.
First you need to check whether a data point is outside of your circle or not.
Clip(x,y) returns NaN if it is outside and 0 if it is inside.
Now, when you plot simply add the value of the clip function to your value. Your data will be clipped within a circle because something +0 remains unchanged and something +NaN will be NaN and will not be plotted. It is sufficient if you do this just for x (vector start) and x + delta x (vector end).
Code:
### clip function in circle form
reset session
set size square
# create some test data
set samples 25
Scaling = 0.5
set table $Data
plot [-5:5] '++' u 1:2:(Scaling*$1/sqrt($1**2+$2**2)): \
(Scaling*$2/sqrt($1**2+$2**2)) : (sqrt($1**2+$2**2)) with table
unset table
set palette rgb 33,13,10
CenterX = 0
CenterY = 0
Radius = 3.5
Clip(x,y) = sqrt((x-CenterX)**2 + (y-CenterY)**2) > Radius ? NaN : 0
set xrange[-6:6]
set yrange[-6:6]
set multiplot layout 1,3
plot $Data u 1:2:3:4:5 w vec lc pal not
plot $Data u ($1+Clip($1,$2)):2:($3+Clip($1+$3,$2+$4)):4:5 w vec lc pal not
CenterX = 1
CenterY = 1
plot $Data u ($1+Clip($1,$2)):2:($3+Clip($1+$3,$2+$4)):4:5 w vec lc pal not
unset multiplot
### end of code
Result:

Plot transparent 3D boxes using gnuplot

I have a data file "data.txt" which contains the coordinates of the borders of several boxes in three dimensions. Each line represents a single box. The file contains over 100 boxes.
x_Min x_Max y_Min y_Max z_Min z_Max
-0.2 0.2 -0.2 0.2 -0.2 0.2
0.2 0.4 -0.2 0.2 -0.2 0.2
....
...
..
Now I want to plot that. In two dimensions it is very easy by using
plot "boxes.txt" u 1:2:3:4 w boxxyerrorbars
With (x-Value):(y-Value):(Half Width):(Half Height).
Than I get this:
But how can I achieve this in three dimensions? I didn't find any solution for this problem.
In case you are still interested in a gnuplot solution...
If it is sufficient to just draw the edges of the boxes you can use the plotting style with vectors. You simply need to select the necessary columns and plot all edges in 3 loops. Here gnuplot's integer division (e.g. 1/2=0) is helpful.
However, if you want to plot surfaces and hide surfaces if they are covered by another box you'd better use with pm3d (check help pm3d). Then, however, you have to re-shape your input data.
Script:
### plot edges of boxes in 3D
reset session
$Data <<EOD
x_Min x_Max y_Min y_Max z_Min z_Max
-0.2 0.2 -0.2 0.2 -0.2 0.2
0.3 0.4 -0.1 0.2 -0.1 0.2
-1.5 -0.5 -1.2 -0.4 -0.9 0.0
0.5 1.0 -1.0 -0.5 -0.5 -0.1
0.0 0.3 -1.4 -1.1 -1.0 -0.7
EOD
set xyplane relative 0
set view equal xyz
set view 60,30,1.7
set xtics 0.5
set ytics 0.5
set ztics 0.5
set key noautotitle
splot for [i=0:3] $Data u 1:i/2+3:i%2+5:($2-$1):(0):(0):0 w vec lc var nohead, \
for [i=0:3] '' u i/2+1:3:i%2+5:(0):($4-$3):(0):0 w vec lc var nohead, \
for [i=0:3] '' u i/2+1:i%2+3:5:(0):(0):($6-$5):0 w vec lc var nohead
### end of script
Result:
I actually found a solution using Python and Matplotlib.
import numpy as np
import matplotlib.pyplot as plt
import random
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.gca(projection='3d')
DIM = 3;
# Unit cube
cube = [[[0.0,1.0],[0.0,0.0],[0.0,0.0]],\
[[0.0,0.0],[0.0,1.0],[0.0,0.0]],\
[[0.0,0.0],[0.0,0.0],[0.0,1.0]],\
[[1.0,1.0],[0.0,1.0],[0.0,0.0]],\
[[1.0,0.0],[1.0,1.0],[0.0,0.0]],\
[[1.0,1.0],[0.0,0.0],[0.0,1.0]],\
[[1.0,1.0],[1.0,1.0],[0.0,1.0]],\
[[0.0,0.0],[1.0,1.0],[0.0,1.0]],\
[[0.0,0.0],[0.0,1.0],[1.0,1.0]],\
[[0.0,1.0],[0.0,0.0],[1.0,1.0]],\
[[1.0,1.0],[0.0,1.0],[1.0,1.0]],\
[[0.0,1.0],[1.0,1.0],[1.0,1.0]]]
# Number of Cubes
numb_Cubes = 5
# Array with positions [x, y, z]
pos = [[0 for x in range(DIM)] for y in range(numb_Cubes)]
for k in range(numb_Cubes):
for d in range(DIM):
pos[k][d] = random.uniform(-1,1)
# Size of cubes
size_of_cubes = [0 for y in range(numb_Cubes)]
for k in range(numb_Cubes):
size_of_cubes[k] = random.random()
# Limits
xmin, xmax = -1, 1
ymin, ymax = -1, 1
zmin, zmax = -1, 1
for n in range(numb_Cubes):
for k in range(len(cube)):
x = np.linspace(cube[k][0][0]*size_of_cubes[n]+pos[n][0], cube[k][0][1]*size_of_cubes[n]+pos[n][0], 2)
y = np.linspace(cube[k][1][0]*size_of_cubes[n]+pos[n][1], cube[k][1][1]*size_of_cubes[n]+pos[n][1], 2)
z = np.linspace(cube[k][2][0]*size_of_cubes[n]+pos[n][2], cube[k][2][1]*size_of_cubes[n]+pos[n][2], 2)
ax.plot(x, y, z, 'black', lw=1)
ax.set_xlim([xmin,xmax])
ax.set_ylim([ymin,ymax])
ax.set_zlim([zmin,ymax])
The result I get:
I am still interested in a solution for gnuplot or a faster solution for Python.

GNU plot: How to plot a sphere and imported file on the same frame?

I am very new to GNU plot. Now, I am trying to plot a sphere and imported .txt file at the same frame. However, I cannot figure out a suitable way. Here are my attempts:
Using only splot.
set parametric ; unset pm3d ; splot [-pi:pi] [-pi/2:pi/2] cos(u)*cos(v), cos(u)*sin(v), sin(u) ; unset parametric ; splot "traj_3dtest.txt" u 2:3:4
But there is only splot "traj_3dtest.txt" u 2:3:4 in output file.
Using multiplot
set parametric
splot cos(u)*cos(v), cos(u)*sin(v), sin(u)
splot "traj_3dtest.txt" u 2:3:4
But the output shows that overlapped two plot, prnt_scrn_1
Here are also extra question: how to plot the spherical "surface"? I mean, I don't want a sphere with contours but a gray surface.
NOTE: the data file format
# T X Y Z Vx Vy Vz
1.00 -0.429 -0.847 0.314 -.09755 -.29510 -.15748
2.00 -0.429 -0.848 0.314 -.09752 -.29504 -.15750
3.00 -0.429 -0.848 0.313 -.09749 -.29497 -.15752
4.00 -0.429 -0.848 0.313 -.09746 -.29491 -.15755
If you want both in the same frame, but not overlapping:
splot cos(u)*cos(v), cos(u)*sin(v), sin(u), "traj_3dtest.txt" u 2:3:4
From your multiplot example, you'd have the two plots with separate axis:
set multiplot layout 2,1
splot cos(u)*cos(v), cos(u)*sin(v), sin(u)
splot "traj_3dtest.txt" u 2:3:4
or
set multiplot
set origin 0,0.5
set size 1,0.5
splot cos(u)*cos(v), cos(u)*sin(v), sin(u)
set origin 0,0
set size 1,0.5
splot "traj_3dtest.txt" u 2:3:4

Drawing a plane on a cartesian plane using gnuplot

I'm trying to reproduce a figure I've found on a linear algebra book using gnuplot. This is the original image
You can see an intersection between two planes described by the two equations:
2u + v + w = 5
4u - 6v = -2.
I suppose that in order to plot the first equation using gnuplot I have to transform it in the form:
splot 5 - 2*x - y
where u -> x; v -> y and w -> z which is the free variable. But the result is very different from what expected. Any clue?
The approach you outline makes sense, however, the results may be far from what you expect.
I propose you draw single lines, using the arrow function in gnuplot.
This example will generate a plot very similar to the one you showed (only one plane, though):
set term gif
set output "demo_plane.gif"
# define your axis limits:
xmax = 6.5
xmin = -1.5
ymax = 8.5
ymin = -1.5
zmax = 5.5
zmin = -0.5
set xrange [xmin:xmax]
set yrange [ymin:ymax]
set zrange [zmin:zmax]
# remove the original axis
unset border
unset xtics
unset ytics
unset ztics
# define you data points:
x1 = 3.0
y1 = -1.0
z1 = 0.0
x2 = -1.0
y2 = 7.0
z2 = 0.0
x3 = -3.0
y3 = 7.0
z3 = 4.0
x4 = 1.0
y4 = -1.0
z4 = 4.0
# define 'arrow' without head:
set arrow 1 from x1,y1,z1 \
to x2,y2,z2 nohead
set arrow 2 from x2,y2,z2 \
to x3,y3,z3 nohead
set arrow 3 from x3,y3,z3 \
to x4,y4,z4 nohead
set arrow 4 from x4,y4,z4 \
to x1,y1,z1 nohead
# draw new axis manually (again, using arrow):
set arrow 5 from 0,0,0 \
to 6,0,0
set arrow 6 from 0,0,0 \
to 0,6,0
set arrow 7 from 0,0,0 \
to 0,0,5
# annotate axis labels:
set label "u" at 6.25,0,0
set label "v" at 0,6.25,0
set label "w" at 0,0,5.25
# plot will not show when empty, include dummy plot command:
set parametric
splot x1, y1, z1 not
With a little rotation you will get a figure like this:

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