Gnuplot filled curves adds unwanted "bottom" border - time-series

I am trying to visualize a time series data set on one plot as a pseudo 3d figure. However, I am having some trouble getting the filledcurves capability working properly. It seems to be adding an unwanted border at the "bottom" of my functions and I do not know how to fix this.
This is my current set up: I have nb_of_frames different files that I want to plot on one figure. Without the filledcurves option, I can do something like this
plot for [i=1:nb_of_frames] filename(i) u ($1):(50.0 * $2 + (11.0 - (i-1)*time_step)) w l linewidth 1.2 lt rgb "black" notitle
which produces a figure like this:
no fill options
Instead of doing this, I want to use the filledcurves option to bring my plots "forward" and highlight the function that is more "forward" which I try to do with:
plot for [i=1:nb_of_frames] filename(i) u ($1):(50. * $2 + (11. - (i-1)*time_step)) w filledcurves fc "white" fs solid 1.0 border lc "black" notitle
This produces a figure as follows:
This is very close to what I want, but it seems that the border option adds a line underneath the function which I do not want. I have tried several variants of with filledcurves y1=0.0 with different values of y1, but nothing seems to work.
Any help would be appreciated. Thank you for your time.

Here is another workaround for gnuplot 5.2.
Apparently, gnuplot closes the filled area from the last point back to the first point. Hence, if you specifiy border, then this line will also have a border which is undesired here (at least until gnuplot 5.4rc2 as #Ethan says).
A straightforward solution would be to plot the data with filledcurves without border and then again with lines. However, since this is a series of shifted data, this has to be plotted alternately. Unfortunately, gnuplot cannot switch plotting styles within a for loop (at least I don't know how). As a workaround for this, you have to build your plot command in a previous loop and use it with a macro # (check help macros) in the plot command. I hope you can adapt the example below to your needs.
Code:
### filledcurves without bottom border
reset session
set colorsequence classic
$Data <<EOD
1 0
2 1
3 2
4 1
5 4
6 5
7 2
8 1
9 0
EOD
myData(i) = sprintf('$Data u ($1-0.1*%d):($2+%d/5.)',i,i)
myFill = ' w filledcurves fc "0xffdddd" fs solid 1 notitle'
myLine = ' w l lc rgb "black" notitle'
myPlotCmd = ''
do for [i=11:1:-1] {
myPlotCmd = myPlotCmd.myData(i).myFill.", ".myData(i).myLine.", "
}
plot #myPlotCmd
### end of code
Result:

I can reproduce this in gnuplot 5.2.8 but not in the output from the release candidate for version 5.4. So I think that some bug-fix or change was applied during the past year or so. I realize that doesn't help while you are using verion 5.2, but if you can download and build from source for the 5.4 release candidate that would take care of it.
Update
I thought of a work-around, although it may be too complicated to be worth it.
You can treat this as a 2D projection of a 3D fence plot constructed using plot style with zerrorfill. In this projection the y coordinate is the visual depth. X is X. Three quantities are needed on z: the bounding line, the bottom, and the top. I.e. 5 fields in the using clause: x depth zline zbase ztop.
unset key
set view 90, 180
set xyplane at 0
unset ytics
set title "3D projection into the xz plane\nplot with zerrorfill" offset 0,-2
set xlabel "X axis" offset 0,-1
set zlabel "Z"
splot for [i=1:25] 'foo.dat' using ($1+i):(i/100.):($2-i):(-i):($2-i) \
with zerrorfill fc "light-cyan" lc "black" lw 2

Related

Remove unnecessary margin in epslatex/gnuplot

I would like to remove unnecessary margins (gray part in the figure below) in a PDF figure generated by epslatex (gnuplot).
Following are scripts and commands to create the figure.
set term epslatex standalone
set output "figure.tex"
set xlabel "\\LARGE $x$"
set ylabel "\\LARGE $y$"
set format x "\\Large{%.1f}"
set format y "\\Large{%.1f}"
set key left top Left
set size square
set xrange [0.0:1.0]
set yrange [0.0:1.0]
plot x with lines dt 1 lw 5.0 lc rgb "red" title "\\Large $y = x$",\
x*x with lines dt 2 lw 5.0 lc rgb "green" title "\\Large $y = x^2$",\
x*x*x with lines dt 3 lw 5.0 lc rgb "blue" title "\\Large $y = x^3$"
and commands
$ gnuplot sample.gp
$ pdflatex figure.tex
Instead of pdflatex, xelatex would also work. I would like to directly convert to PDF file.
It will be super good if we can remove these margins without too much effort (such as removing the margin manually one-by-one).
Thanks!
If you check help latex, it will tell you that default size is 5 x 3 inches.
Since you set size square, there will be for sure an "unwanted" left and right margin.
What you can do to at least minimize the margins is to set the terminal size to square size as well, e.g. to 3 x 3 inches.
However, keep in mind the graph size is square but x and y axes have tics and labels which require space depending on numbers and labels which might be different for x and y.
set term epslatex standalone size 3 in, 3 in
From help latex:
Syntax:
set terminal {latex | emtex} {default | {courier|roman} {<fontsize>}}
{size <XX>{unit}, <YY>{unit}} {rotate | norotate}
By default the plot will inherit font settings from the embedding
document. You have the option of forcing either Courier (cmtt) or
Roman (cmr) fonts instead. In this case you may also specify a
fontsize. Unless your driver is capable of building fonts at any size
(e.g. dvips), stick to the standard 10, 11 and 12 point sizes.
...
Maybe, there are LaTeX commands to crop the graph to its bounding box.
Thanks to #AlainMarigot help, I change the system to Lua tikz with the option tightboundingbox.
Looks good, but not exactly same as epslatex.

Gnuplot multiplot positions all text incorrectly in epslatex terminal

I am trying to use the multiplot feature of gnuplot to make a inset graphic on the main plot. I can generate the plot exactly as I want with term='wxt' except for the axis labels, which require LaTeX formatting for generating the desired symbols. When I submit the same commands to term='epslatex', the plot is fine, but all text (axis and tic mark labels) is positioned incorrectly.
I thought using the set size & origin commands might have confused the epslatex terminal output, so I attempted to use the layout command and make the plots side by side just to see if the text would print correctly. It did not.
I'm using gnuplot 4.6 patch 4, and Linux Mint 17.
My script is below. The commented sections indicate the original script that used set size and origin commands to manually place the second plot as a inset, rather than side by side.
set term epslatex color font ",16"
unset key
set termoption dash
set style line 1 lc rgb 'blue' lw 2 lt 1
set style line 2 lc rgb 'red' lw 2 lt 3
set style line 3 lc rgb 'green' lw 2 lt 5
set style line 4 lc rgb 'magenta' lw 2 lt 7
set style line 5 lc rgb 'black' lw 1 lt 0
set output "gr-thresholds.tex"
#set size 1,1
# set multiplot
set multiplot layout 1,2
# bigger plot
set autoscale
set ytics scale default autofreq
set xrange[0:14]
set yrange[0:1.7]
set xlabel 'r (\AA)'
set ylabel '$g(r)$'
#set size 1,1
#set origin 0,0
plot "foo1.csv" w l ls 2, \
"foo2.csv" w l ls 3 , \
"foo3.csv" w l ls 1, \
"foo4.csv" w l ls 4
#small inset
#set size 0.4, 0.4
#set origin 0.5,0.15
set xrange[1.2:2.2]
set yrange[0:0.8]
set ytics 0, 0.2, 2
set xlabel ""
set ylabel ""
plot "foo1.csv" w l ls 2, \
"foo2.csv" w l ls 3 , \
"foo3.csv" w l ls 1, \
"foo4.csv" w l ls 4
unset multiplot
set output
The figure that was generated:
It might be a problem with the way you generate a pdf. The two commands dvipdfm and dvipdf produce different outcomes.
If I take your code, but plot sin(x) instead, and use the following in the terminal:
$ latex file.tex
$ dvipdfm file.dvi
I also get a mismatch between the axes and the plots.
If I use dvipdf however everything looks fine:
$ dvipdf file.dvi
Ok,
Per Tom Fenech's suggestion, I made a minimum code sample to reproduce the error, and the issue that arose is a machine state problem. To generate my graphs, I had run the script twice, once using term wxt and then again using term epslatex.
The problem is that somewhere the state of the gnuplot environment is changed and is not reset by this script. Specifically, the first time through, the default placement of the text labels is fine. The second time through, the range and labels are still attached to the size and origin from the last plot, which is the inset. I thought this was due to the order of the commands set origin/size relative to x/ylabel and x/y range, but simply running the below code twice without restarting gnuplot will generate two different plots. The first time is exactly what I wanted, the second time will skew the labels as shown above.
So I have a "solution", but it is fragile. I would appreciate if someone could explain what I need to do to make this script run multiple times without restarting each time.
Cheers,
--Jim
set term epslatex color font ",16"
unset key
f(x) = sin(x)
set output "sin.tex"
set multiplot
set size 1,1
set origin 0,0
set xrange[0:14]
set yrange[0:6]
set xlabel 'r (\AA)'
set ylabel '$g(r)$'
plot f(x)
#small inset
set size 0.4, 0.4
set origin 0.5,0.15
set xrange[1:3]
set yrange[0:4]
set ytics 0, 0.2, 2
set xlabel ""
set ylabel ""
plot f(x)
unset multiplot
set output

How to remove unknown slits when using filledcurve in Gnuplot (epslatex)?

I'm now trying to use filledcurve in gnuplot 4.6, patchlevel 1. Following shows the sample script:
set term epslatex
set output "figure.tex"
set xlabel "\\huge{x-axis}"
set ylabel "\\huge{y-axis}"
set format xy "\\LARGE{%.0f}"
set xrange [0.0:10.0]
set yrange [0.0:100.0]
set xtics 2.0
set ytics 20.0
set xtics offset 0, -0.3
f1(x) = x**1
f2(x) = x**2
f3(x) = x**3
set nokey
plot '+' using 1:(f2($1)):(f3($1)) with filledcurve lt 1 lc rgb "gray60",\
'+' using 1:(f1($1)):(f2($1)) with filledcurve lt 1 lc rgb "gray40",\
'+' using 1:(0.0):(f1($1)) with filledcurve lt 1 lc rgb "gray20"
I don't known why, but it seems that there are white annoying slits between bars. It cannot be get rid of even if I increase the number of set samples.
Is there any idea to remove these slits?
Unfortunately, this is a viewer problem related to the drawing of adjacent filled polygons, see also problematic Moire pattern in image produced with gnuplot pm3d and pdf output or the bug report #1259 cairolatex pdf fill patterns.
In your case you can use a workaround:
When you have only two columns in the using statement, the area is drawn as closed polygon and doesn't show these artifacts (filledcurves closed). So you must fill the area between each curve and the x1 axis (with filledcurves x1).
Because of a bug in the clipping of curves which exceed the y-range, you must do the clipping of the f3 curve yourself (i.e. use f3($1) > 100 ? 100 : f3($1)). This bug is fixed in the development version.
So you script is:
set term epslatex standalone
set output "figure.tex"
set xlabel "\\huge x-axis"
set ylabel "\\huge y-axis"
set format xy "\\LARGE %.0f"
set xrange [0.0:10.0]
set yrange [0.0:100.0]
set xtics 2.0
set ytics 20.0
set xtics offset 0, -0.3
f1(x) = x**1
f2(x) = x**2
f3(x) = x**3
set nokey
plot '+' using 1:(f3($1) > 100 ? 100 : f3($1)) with filledcurve x1 lt 1 lc rgb "gray60",\
'+' using 1:(f2($1)) with filledcurve x1 lt 1 lc rgb "gray40",\
'+' using 1:(f1($1)) with filledcurve x1 lt 1 lc rgb "gray20"
set output
system('latex figure.tex && dvips figure.dvi && ps2pdf figure.ps')
with the result (using 4.6.1):
Note also, that LaTeX commands like \huge don't take arguments, but are switches. Test e.g. \huge{A}BC, this will make all letter huge. Usually you must limit the scope of \huge with brackets like {\huge ABC}, but if the whole label is affected, it is enough to use set xlabel "\\huge x-axis". That doesn't change anything in your case, but may give you troubles in other circumstances :)

Gnuplot: Black and White contour plot

I have the following gnuplot plot embedded in my Latex document:
\begin{gnuplot}[terminal=epslatex,terminaloptions={color size 14.5cm, 9cm}]
set view map
unset surface
unset key
unset xtics
unset ytics
unset ztics
set contour base
set cntrparam levels discrete 2,4,8,16,32,64,128,256,512
set isosamples 100
splot y**2 + 0.1*x**2 notitle
\end{gnuplot}
The plot is alright. All I want to achive is that the contour lines all have the same style, i.e. line type and the same colour, black if possible.
Thanks for any advices.
I don't know about the latex terminal, but you could try:
splot y**2 + 0.1*x**2 notitle lc rgb "#000000"
http://www.gnuplot.info/demo/contours.html (see the section where they draw all the contours in the same color -- It's the last example on that page)
EDIT
It looks like the coloring of the contours is controlled by {un}set clabel. So if you just add unset clabel to your script, then the contours should probably show up black (with the lc rgb "#000000" that I had above. Note that unset clabel implies unset key. To achieve this with the ability to add a key is a little more tricky...
in case you ever need to keep the labels...
You'll likely need to set term push to save the current terminal. set term unknown to make the output go nowhere. set table "junk.dat" and then issue your plot commmand as normal. This will write the contours to a file "junk.dat" which can then be splotted with lines after a set term pop to restore the old terminal settings (you'll probably need some variant of title columnhead and maybe an index/every as well to get the labels to appear correctly...) -- I'm not actually sure if the set term push/pop commands are necessary in this case. Anyway, plotting things to tables with gnuplot is something that I've done a number of times for a number of different applications. It's a great tool to keep in mind.

How to concatenate a datafile with four columns

My data file has four columns because opencv saves elements in an n x 4 form in xml when exporting a cv::Mat to xml.
How can I concatenate these four columns into one?
reset
set terminal postscript eps enhanced
set output 'imp.eps'
set pm3d
set palette model HSV defined ( 0 0 1 1, 1 1 1 1 )
set style data histogram
set colorbox user
set origin 0.0,0.10
set size ratio 0 1,0.8
set colorbox horizontal origin graph 0.0, -0.15, 0 size graph 1, 0.05, 0 noborder
set xrange [0:4096]
plot 'var_imp_first_run.data' using 1
set output
I have 4094 elements, and this example creates an histogram where the first 1024 is plotted. I need to append column 2 from x=1024:2048. Please ignore the colorbox stuff; I'm just playing around to learn gnuplot.
I found out that following solve my problem above.
set xrange [0:4096]
plot newhistogram at 0, 'var_imp_first_run.data' every:: 7 using 1,\
newhistogram at 1024,'var_imp_first_run.data' every:: 7 using 2,\
newhistogram at 2048,'var_imp_first_run.data' every:: 7 using 3,\
newhistogram at 3072,'var_imp_first_run.data' every:: 7 using 4;
Then I found out that it was not what I wanted, because the data are arranged as entries,
x1,x2,x3,x4
x5,x6,x7,x8
and so on.
So what I really need is a histogram that plots the rows before columns. Is it possible?
If you want it to read
x1
x2
x3
instead of
x1,x2,x3
Then (assuming you are on *nix) use
plot 'cat var_imp_first_run.data | tr "," "\n" |' using 1
This is calling the following command and reading the output via the pipe at the end:
cat var_imp_first_run.data | tr "," "\n"
Here, tr is just transcribing commas as newlines.

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