So I'm trying to plot three parametric functions using the gnuplot;
unfortunately, I cannot get around some garbage that is generated in the output plot. I tried to isolate the problem by splitting a function j into j1 and j2, just changing the position of the minus sign. Unexpectedly, the functions j1 and j2 jump strangely when close to the origin. I currently use version 4.6 of gnuplot, any suggestions?
CODE BELOW:
set parametric
j1(x) = -((1.0/27.0*(1.+9.*x))/2.0)**(1./3.) #negative portion
j2(x) = (-(1.0/27.0*(1.+9.*x))/2.0)**(1./3.)
k(x) = ((-x/3.0)**(3./2.))**(1./3.)
l(x) = -((-x/3.0)**(3./2.))**(1.0/3.0)
tt(x) = sqrt(-x/3.)
set trange [-1.0/3.0:0]
set yrange [0:1.0/3.0]
set xrange [-1./6.:1./3]
plot j1(t),tt(t) w l ls 1, j2(t),tt(t) w l ls 1, k(t),tt(t) w l ls 2, l(t),tt(t) w l ls 3
The problem comes from selecting the cube root of a negative number. Gnuplot can work with complex numbers, and in the complex number system there are three cube roots of any number†. For a real number, one of these is real and two are complex. Gnuplot is selecting the first‡ one which is complex for a negative number (for a positive number, the first one is real).
print (-8)**(1/3.0) # prints {1.0, 1.73205080756888}
The solution is to construct our own cube root function
cuberoot(x) = sgn(x)*abs(x)**(1/3.0)
This will select take the cube root of the absolute value (always positive) and make the result have the same sign as the original.
We can then use it in our functions
j1(x) = -cuberoot((1.0/27.0*(1.+9.*x))/2.0) #negative portion
j2(x) = cuberoot(-(1.0/27.0*(1.+9.*x))/2.0)
leaving the rest of the code alone.
Without custom cuberoot function
With custom cuberoot function
† For the given example of -8, they are 1 + 1.7320508i, -2, and 1 - 1.7320508i.
‡ When ordered in increasing order by complex argument (restricted to the interval [0,2π) ).
Related
I am trying to plot a function that contains discontinuities in gnuplot. As a result, gnuplot automatically draws a vertical line connecting the jump discontinuities. I would like to remove this line. I have looked around and found two solutions, none of which worked: One solution was to use smooth unique when plotting, and the other one was to define the function in a conditional form and remove the discontinuity manually. The first solution simply did not make any changes to the plot (at least visually). The second solution seemed to move the location of the jump discontinuity to left or right, not get rid of the vertical line. Please note that I would like to plot with lines. I know with points works, but I do not wish to plot with points.
set sample 10000
N=50
l1(x)=2*cosh(1/x)
l2(x)=2*sinh(1/x)
Z(x)=l1(x)**N+l2(x)**N
e(x)=(-1/Z(x))*(l2(x)*l1(x)**(N-1)+l1(x)*l2(x)**(N-1))
plot e(x)
Produces:
If all you need to do is to remove the vertical line at the singularity you could use conditional plotting:
plot (x<0 ? 1/x : 1/0) w l ls 1, (x>0 ? 1/x : 1/0) w l ls 1
However, your function is more complicated: it cannot be numerically evaluated in a region around 0:
set grid
set xrange [-0.3:0.3]
plot e(x) with linespoints
If Mathematica is to be trusted, the function e(x) goes to 1 and -1 as x approaches 0 from the left and the right, respectively. However, you see in the picture above that gnuplot fails to properly evaluate the function already at x=0.1. print e(0.1) gives -0.0, and print e(0.05) already gives NaN. In this region the numerator and denominator of the function e(x) get too large to be handled with floating point numbers.
You can either exclude this region using conditional plotting,
plot (x<-0.15 ? e(x) : 1/0) w l ls 1, (x>0.15 ? e(x) : 1/0) w l ls 1
or you have to rewrite the function e(x) so you avoid extremely large values in its evaluation (if that is possible). Alternatively you can use a software package that can switch to higher precision, such as Mathematica.
You can redefine your function e(x) to avoid calculations of large exponentials like
e(x) = -(l2(x)/l1(x) + (l2(x)/l1(x))**(N-1))/(1 + (l2(x)/l1(x))**N)
Now you always calculate l2(x)/l1(x) before taking the power.
For your high sampling rate of 10000, this still gives some undefined points near the singularity, so that you have not connecting line. For lower sampling rates of e.g. 1000 you would also see a line crossing zero. To avoid that you can use an odd sampling rate:
set sample 1001
N=50
l1(x)=2*cosh(1/x)
l2(x)=2*sinh(1/x)
Z(x)=l1(x)**N+l2(x)**N
e(x) = -(l2(x)/l1(x) + (l2(x)/l1(x))**(N-1))/(1 + (l2(x)/l1(x))**N)
set autoscale yfix
set offsets 0,0,0.05,0.05
plot e(x) with lines
Late answer... but you can use the same principle as
here:
How to remove line between "jumping" values, in gnuplot?
or here:
Avoid connection of points when there is empty data
Just find the condition for where you want the line to be interrupted.
The condition in this case would be for example:
If two successive values y0 and y1 have different signs then make the line color fully transparent according to the color scheme 0xaarrggbb, e.g. 0xff123456, actually it doesn't matter what comes after 0xff, because 0xff means fully transparent.
Script:
### remove connected "jump" in curve
reset session
N=50
l1(x)=2*cosh(1/x)
l2(x)=2*sinh(1/x)
Z(x)=l1(x)**N+l2(x)**N
e(x)=(-1/Z(x))*(l2(x)*l1(x)**(N-1)+l1(x)*l2(x)**(N-1))
set key noautotitle
set grid x,y
plot y1=NaN '+' u 1:(y0=y1, y1=e(x)):(sgn(y0)!=sgn(y1)?0xff123456:0xff0000) w l lc rgb var
### end of code
Result: (identical independent of the number of samples)
I calculated the eigenvalues of the Hamiltonian for the 1D-hydrogen atom in atomic units with the Fourier-Grid-Hamiltonian method in a nice little Fortran program.
All the eigenvalues found between -1 and 0 (the bound states) are saved into a file line by line like this:
-0.50016671392950229
-0.18026105614262633
-0.11485673263086937
-4.7309305955423042E-002
-4.7077108902158216E-002
As the number of found eigenvalues differs depends on the stepsize my program uses, the number of entries in the file can vary (in theory, there are infinite ones).
I now want to plot the values from the file as a line parallel to the x-axis with the offset given by the values read from file.
I also want to be able to plot the data only up to a certain line number, as the values get really close to each other the further you come to zero and they cannot be distinguished by eye anymore.
(Here e.g. it would make sence to plot the first four entries, the fifth is already too close to the previous one)
I know that one can plot lines parallel to the x axis with the command plot *offset* but I don't know how to tell gnuplot to use the data from the file. So far I had to manually plot the values.
As a second step I would like to plot the data only in a certain x range, more concrete between the points of intersection with the harmonic potential used for the numeric solution V(x) = -1/(1+abs(x))
The result should look like this:
scheme of the desired plot (lookalike)
The closest I got to, was with
plot -1/(1+abs(x)),-0.5 title 'E0',-0.18 title 'E1', -0.11 title 'E2'
which got me the following result:
my plot
Hope you guys can help me, and I'm really curios whether gnuplot actually can do the second step I described!
As for the first part of your question, you can for example use the xerrorbars plotting style as:
set terminal pngcairo
set output 'fig.png'
unset key
set xr [-1:1]
set yr [-1:0]
unset bars
plot '-' u (0):($1<-0.1?$1:1/0):(1) w xerrorbars pt 0 lc rgb 'red'
-0.50016671392950229
-0.18026105614262633
-0.11485673263086937
-4.7309305955423042E-002
-4.7077108902158216E-002
e
The idea here is to:
interpret the energies E as points with coordinates (0,E) and assign to each of them an x-errorbar of width 1 (via the third part of the specification (0):($1<-0.1?$1:1/0):(1))
"simulate" the horizontal lines with x-errorbars. To this end, unset bars and pt 0 ensure that Gnuplot displays just plain lines.
consider only energies E<-0.1, the expressions $1<-0.1?$1:1/0 evaluates otherwise to an undefined value 1/0 which has the consequence that nothing is plotted for such E.
plot '-' with explicit values can be of course replaced with, e.g., plot 'your_file.dat'
This produces:
For the second part, it mostly depends how complicated is your function V(x). In the particular case of V(x)=-1/(1+|x|), one could infer directly that it's symmetric around x=0 and calculate the turning points explicitly, e.g.,
set terminal pngcairo
set output 'fig.png'
fName = 'test.dat'
unset key
set xr [-10:10]
set yr [-1:0]
unset bars
f(x) = -1 / (1+abs(x))
g(y) = (-1/y - 1)
plot \
f(x) w l lc rgb 'black', \
fName u (0):($1<-0.1?$1:1/0):(g($1)) w xerrorbars pt 0 lc rgb 'red', \
fName u (0):($1<-0.1?$1:1/0):(sprintf("E%d", $0)) w labels offset 0, char 0.75
which yields
The idea is basically the same as before, just the width of the errorbar now depends on the y-coordinate (the energy). Also, the labels style is used in order to produce explicit labels.
Another approach may be to get data from "energy.dat" (as given in the question) with system and cat commands (so assuming a Un*x-like system...) and select V(x) and E at each x via max:
set key bottom right
set yr [-1:0.2]
set samples 1000
Edat = system( "cat energy.dat" )
max(a,b) = ( a > b ) ? a : b
V(x) = -1/(1+abs(x))
plot for [ E in Edat ] \
max(V(x),real(E)) title sprintf("E = %8.6f", real(E)) lw 2, \
V(x) title "V(x) = -1/(1+|x|)" lc rgb "red" lw 2
If we change the potential to V(x) = -abs(cos(x)), the plot looks pretty funny (and the energy levels are of course not correct!)
More details about the script:
max is not a built-in function in Gnuplot, but a user-defined function having two formal arguments. So for example, we may define it as
mymax( p, q ) = ( p > q ) ? p : q
with any other names (and use mymax in the plot command). Next, the ? symbol is a ternary operator that gives a short-hand notation for an if...else construct. In a pseudo-code, it works as
function max( a, b ) {
if ( a > b ) then
return a
else
return b
end
}
This way, max(V(x),real(E)) selects the greater value between V(x) and real(E) for any given x and E.
Next, Edat = system( "cat energy.dat" ) tells Gnuplot to run the shell command "cat energy.dat" and assign the output to a new variable Edat. In the above case, Edat becomes a string that contains a sequence of energy values read in from "energy.dat". You can check the contents of Edat by print( Edat ). For example, it may be something like
Edat = "-0.11 -0.22 ... -0.5002"
plot for [ E in Edat ] ... loops over words contained in a string Edat. In the above case, E takes a string "-0.11", "-0.22", ..., "-0.5002" one-by-one. real(E) converts this string to a floating-point value. It is used to pass E (a character string) to any mathematical function.
The basic idea is to draw a truncated potential above E, max(V(x),E), for each value of E. (You can check the shape of such potential by plot max(V(x),-0.5), for example). After plotting such curves, we redraw the potential V(x) to make it appear as a single potential curve with a different color.
set samples 1000 increases the resolution of the plot with 1000 points per curve. 1000 is arbitrary, but this seems to be sufficient to make the figure pretty smooth.
I have a large set of data points from x = 1 to x = 10e13 (step size is fixed to about 3e8).
When I try to plot them using a logscale I certainly get an incredible huge point-density towards the end. Of course this affects my output plots since postscript and svg files (holding each and every data point) are getting really big.
Is there a way to tell gnuplot to decrease the data density dynamically?
Sample data here. Shows a straight line using logarithmic x-axis.
Usually, for this kind of plots, one can use a filter function which selects the desired points and discards all others (sets their value to 1/0:
Something like:
plot 'sample.dat' using (filter($1) ? $1 : 1/0):2
Now you must define an appropriate filter function to change the data density. Here is a proposal, with pseudo-data, although you might for sure find a better one, which doesn't show this typical logarithmic pattern:
set logscale x
reduce(x) = x/(10**(floor(log10(x))))
filterfunc(x) = abs(log10(sc)+(log10(x) - floor(log10(x))) - log10(floor(sc*reduce(x))))
filter(x) = filterfunc(x) < 1e-5 ? x : 1/0
set multiplot layout 1,2
sc = 1
plot 'sample.data' using (filter($1)):2 notitle
sc = 10
replot
The variable sc allows to change the density. The result is (with 4.6.5) is:
I did some work inspired by Christoph's answer and able to get equal spacing in log scale. I made a filtering, if you have numbers in the sequence you can simply use Greatest integer function and then find the nearest to it in log scale by comparing the fraction part. Precision is tuned by precision_parameter here.
precision_parameter=100
function(x)=(-floor(precision_parameter*log10(x))+(precision_parameter*log10(x)))
Now filter by using the filter function defined below
density_parameter = 3.5
filter(x)=(function(x) < 1/(log10(x))**density_parameter & function(x-1) > 1/(log10(x))**density_parameter ) ? x : 1/0
set datafile missing "NaN"
Last line helps in plotting with line point. I used x and x-1 assuming the xdata is in arithmetic progression with 1 as common difference, change it accordingly with your data. Just replace x by filter(x) in the plot command.
plot 'sample_data.dat' u (filter($1)):2 w lp
I try to plot the orbital velocity with gnuplot, but somehow gnuplot gets completely different results than me. Now from experience I think my values are correct but I checked it with Google's calculator and get my results.
I use the formula from Wikipedia and Google gets a velocity at apoapsis of about 2.2 km/s. Now gnuplot itself gets a velocity of about 3.2 km/s.
set xlabel "Altitude above sea level (meters)"
set ylabel "Orbital velocity (meters per second)"
set title "Velocity of an 80×100 km orbit around Kebrin"
set terminal png size 800,640
set output "orbitv.png"
set xrange [80000:100000]
G=6.674*10**-11
M=5.2915793*10**22
R=600000
plot sqrt(G*M*(2/(x+R)-1/(90000+R))) title 'Orbital velocity' with lines
I'm wondering were did I make the mistake? I copied the formula directly to Google and replaced G, M and R with the constant values and x with 100000 and get the result linked above.
This problem has to do with how gnuplot handles integers when doing arithmetic. When you have an expression like 1/(90000 + R), if R is an integer, gnuplot evaluates 1/(690000) = 0, which is perfectly valid integer arithmetic. The solution is to add a period to a number so that gnuplot knows to cast it as a floating-point number:
R = 600000. # short option
R = 600000.0 # clearer option
Another solution is to use e-notation for big numbers:
R = 6e5
Gnuplot treats that as a float. This also helps prevent order-of-magnitude/number-of-zeroes errors.
Incidentally, python and other languages have the same problem with integer arithmetic--watch out!
I know how to create a histogram (just use "with boxes") in gnuplot if my .dat file already has properly binned data. Is there a way to take a list of numbers and have gnuplot provide a histogram based on ranges and bin sizes the user provides?
yes, and its quick and simple though very hidden:
binwidth=5
bin(x,width)=width*floor(x/width)
plot 'datafile' using (bin($1,binwidth)):(1.0) smooth freq with boxes
check out help smooth freq to see why the above makes a histogram
to deal with ranges just set the xrange variable.
I have a couple corrections/additions to Born2Smile's very useful answer:
Empty bins caused the box for the adjacent bin to incorrectly extend into its space; avoid this using set boxwidth binwidth
In Born2Smile's version, bins are rendered as centered on their lower bound. Strictly they ought to extend from the lower bound to the upper bound. This can be corrected by modifying the bin function: bin(x,width)=width*floor(x/width) + width/2.0
Be very careful: all of the answers on this page are implicitly taking the decision of where the binning starts - the left-hand edge of the left-most bin, if you like - out of the user's hands. If the user is combining any of these functions for binning data with his/her own decision about where binning starts (as is done on the blog which is linked to above) the functions above are all incorrect. With an arbitrary starting point for binning 'Min', the correct function is:
bin(x) = width*(floor((x-Min)/width)+0.5) + Min
You can see why this is correct sequentially (it helps to draw a few bins and a point somewhere in one of them). Subtract Min from your data point to see how far into the binning range it is. Then divide by binwidth so that you're effectively working in units of 'bins'. Then 'floor' the result to go to the left-hand edge of that bin, add 0.5 to go to the middle of the bin, multiply by the width so that you're no longer working in units of bins but in an absolute scale again, then finally add back on the Min offset you subtracted at the start.
Consider this function in action:
Min = 0.25 # where binning starts
Max = 2.25 # where binning ends
n = 2 # the number of bins
width = (Max-Min)/n # binwidth; evaluates to 1.0
bin(x) = width*(floor((x-Min)/width)+0.5) + Min
e.g. the value 1.1 truly falls in the left bin:
this function correctly maps it to the centre of the left bin (0.75);
Born2Smile's answer, bin(x)=width*floor(x/width), incorrectly maps it to 1;
mas90's answer, bin(x)=width*floor(x/width) + binwidth/2.0, incorrectly maps it to 1.5.
Born2Smile's answer is only correct if the bin boundaries occur at (n+0.5)*binwidth (where n runs over integers). mas90's answer is only correct if the bin boundaries occur at n*binwidth.
Do you want to plot a graph like this one?
yes? Then you can have a look at my blog article: http://gnuplot-surprising.blogspot.com/2011/09/statistic-analysis-and-histogram.html
Key lines from the code:
n=100 #number of intervals
max=3. #max value
min=-3. #min value
width=(max-min)/n #interval width
#function used to map a value to the intervals
hist(x,width)=width*floor(x/width)+width/2.0
set boxwidth width*0.9
set style fill solid 0.5 # fill style
#count and plot
plot "data.dat" u (hist($1,width)):(1.0) smooth freq w boxes lc rgb"green" notitle
As usual, Gnuplot is a fantastic tool for plotting sweet looking graphs and it can be made to perform all sorts of calculations. However, it is intended to plot data rather than to serve as a calculator and it is often easier to use an external programme (e.g. Octave) to do the more "complicated" calculations, save this data in a file, then use Gnuplot to produce the graph. For the above problem, check out the "hist" function is Octave using [freq,bins]=hist(data), then plot this in Gnuplot using
set style histogram rowstacked gap 0
set style fill solid 0.5 border lt -1
plot "./data.dat" smooth freq with boxes
I have found this discussion extremely useful, but I have experienced some "rounding off" problems.
More precisely, using a binwidth of 0.05, I have noticed that, with the techniques presented here above, data points which read 0.1 and 0.15 fall in the same bin. This (obviously unwanted behaviour) is most likely due to the "floor" function.
Hereafter is my small contribution to try to circumvent this.
bin(x,width,n)=x<=n*width? width*(n-1) + 0.5*binwidth:bin(x,width,n+1)
binwidth = 0.05
set boxwidth binwidth
plot "data.dat" u (bin($1,binwidth,1)):(1.0) smooth freq with boxes
This recursive method is for x >=0; one could generalise this with more conditional statements to obtain something even more general.
We do not need to use recursive method, it may be slow. My solution is using a user-defined function rint instesd of instrinsic function int or floor.
rint(x)=(x-int(x)>0.9999)?int(x)+1:int(x)
This function will give rint(0.0003/0.0001)=3, while int(0.0003/0.0001)=floor(0.0003/0.0001)=2.
Why? Please look at Perl int function and padding zeros
I have a little modification to Born2Smile's solution.
I know that doesn't make much sense, but you may want it just in case. If your data is integer and you need a float bin size (maybe for comparison with another set of data, or plot density in finer grid), you will need to add a random number between 0 and 1 inside floor. Otherwise, there will be spikes due to round up error. floor(x/width+0.5) will not do because it will create pattern that's not true to original data.
binwidth=0.3
bin(x,width)=width*floor(x/width+rand(0))
With respect to binning functions, I didn't expect the result of the functions offered so far. Namely, if my binwidth is 0.001, these functions were centering the bins on 0.0005 points, whereas I feel it's more intuitive to have the bins centered on 0.001 boundaries.
In other words, I'd like to have
Bin 0.001 contain data from 0.0005 to 0.0014
Bin 0.002 contain data from 0.0015 to 0.0024
...
The binning function I came up with is
my_bin(x,width) = width*(floor(x/width+0.5))
Here's a script to compare some of the offered bin functions to this one:
rint(x) = (x-int(x)>0.9999)?int(x)+1:int(x)
bin(x,width) = width*rint(x/width) + width/2.0
binc(x,width) = width*(int(x/width)+0.5)
mitar_bin(x,width) = width*floor(x/width) + width/2.0
my_bin(x,width) = width*(floor(x/width+0.5))
binwidth = 0.001
data_list = "-0.1386 -0.1383 -0.1375 -0.0015 -0.0005 0.0005 0.0015 0.1375 0.1383 0.1386"
my_line = sprintf("%7s %7s %7s %7s %7s","data","bin()","binc()","mitar()","my_bin()")
print my_line
do for [i in data_list] {
iN = i + 0
my_line = sprintf("%+.4f %+.4f %+.4f %+.4f %+.4f",iN,bin(iN,binwidth),binc(iN,binwidth),mitar_bin(iN,binwidth),my_bin(iN,binwidth))
print my_line
}
and here's the output
data bin() binc() mitar() my_bin()
-0.1386 -0.1375 -0.1375 -0.1385 -0.1390
-0.1383 -0.1375 -0.1375 -0.1385 -0.1380
-0.1375 -0.1365 -0.1365 -0.1375 -0.1380
-0.0015 -0.0005 -0.0005 -0.0015 -0.0010
-0.0005 +0.0005 +0.0005 -0.0005 +0.0000
+0.0005 +0.0005 +0.0005 +0.0005 +0.0010
+0.0015 +0.0015 +0.0015 +0.0015 +0.0020
+0.1375 +0.1375 +0.1375 +0.1375 +0.1380
+0.1383 +0.1385 +0.1385 +0.1385 +0.1380
+0.1386 +0.1385 +0.1385 +0.1385 +0.1390
Different number of bins on the same dataset can reveal different features of the data.
Unfortunately, there is no universal best method that can determine the number of bins.
One of the powerful methods is the Freedman–Diaconis rule, which automatically determines the number of bins based on statistics of a given dataset, among many other alternatives.
Accordingly, the following can be used to utilise the Freedman–Diaconis rule in a gnuplot script:
Say you have a file containing a single column of samples, samplesFile:
# samples
0.12345
1.23232
...
The following (which is based on ChrisW's answer) may be embed into an existing gnuplot script:
...
## preceeding gnuplot commands
...
#
samples="$samplesFile"
stats samples nooutput
N = floor(STATS_records)
samplesMin = STATS_min
samplesMax = STATS_max
# Freedman–Diaconis formula for bin-width size estimation
lowQuartile = STATS_lo_quartile
upQuartile = STATS_up_quartile
IQR = upQuartile - lowQuartile
width = 2*IQR/(N**(1.0/3.0))
bin(x) = width*(floor((x-samplesMin)/width)+0.5) + samplesMin
plot \
samples u (bin(\$1)):(1.0/(N*width)) t "Output" w l lw 1 smooth freq