Is it possible to change the opacity of the key's background in gnuplot? I can only find the option to toggle between opaque or transparent.
Here is an example using python's matplotlib - https://matplotlib.org/3.2.0/_images/dflt_style_changes-14.png
This is possible in the development version (5.5) and in the most recent release version (5.4.2) but not in earlier versions.
set key box opaque fillcolor "0x7faaaaaa"
There is a cumbersome workaround for filling the key box with a custom color:
Set custom background color for key in Gnuplot.
However, it seems like semi-transparent colors are not accepted as terminal background.
Well, either you want to see the data and place the legend next to it
or you cover the data with the legend, then the data is not "important".
Putting a semi-transparent legend box on top of data seems to me a bit of a strange mix of both.
The only workaround I see currently is to manually place a semi-transparent box on top of the plot and behind the legend.
The only way I succeeded so far to get this into the right layer stacking order is to plot a box with boxxyerror and add the legend via keyentry. You can put the coordinates and size of the box e.g. into the datablock $myBox. A pretty ugly workaround, but I'm happy to learn about better solutions.
Code:
### manual workaround for semi-transparent fill of key box
reset session
set style fill solid 1.0
set key center at 0,-0 noautotitle box
$myBox <<EOD
0 -0 1.25 1.25
EOD
plot x w filledcurves x1 lc rgb 0xccff0000, \
-x w filledcurves x1 lc rgb 0xcc0000ff, \
$myBox u 1:2:3:4 w boxxy lc rgb 0x77ffffff noautoscale, \
keyentry w filledcurves x1 lc rgb 0xccff0000 ti "x" , \
keyentry w filledcurves x1 lc rgb 0xcc0000ff ti "-x"
### end of code
Result: (wxt terminal)
Related
To generate vector graphics figures with LaTeX labels, I use gnuplot and the cairolatex terminal, creating the image via plot "data.txt" u 1:2:3 matrix with image notitle followed by:
latex figuregen.tex
dvips -E -ofile.eps figuregen
# Correct the bounding box automatically:
epstool --copy --bbox file.eps filename.eps
## Create a pdf:
ps2pdf -dPDFSETTINGS=/prepress -dSubsetFonts=true -dEmbedAllFonts=true -dMaxSubsetPct=100 -dCompatibilityLevel=1.3 -dEPSCrop filename.eps filename.pdf
Here is a zoom on a specific region of the original eps image:
White regions actually correspond to NaN values in the data file.
Now using the pdf file converted from eps:
In the pdf version, there are now unwanted outlines around all the NaN pixels, creating an awful lot of noise in the higher portion of the image.
I want to have these images as pdf, free of artefacts, and preserve high-quality LaTeX labels. I suspect that there might be a ps2pdf option to deactivate this kind of unwanted behaviour but I just cannot find it.
I tried things such as: -dGraphicsAlphaBits=1, -dNOINTERPOLATE, -dALLOWPSTRANSPARENCY, -dNOTRANSPARENCY, -dCompatibilityLevel=1.4 or -dCompatibilityLevel=1.5, but without success.
I also tried fixing this directly in gnuplot, but without success (see e.g. below).
Would any of you know how to solve this issue?
Thank you very much for your time!
EDIT
What's even more surprising and problematic is that these artefacts also appear when printed.
Note however that they do not appear at extreme levels of zoom in evince when only a small part of the data set is plotted.
MWE:
# plot.plt
set size ratio -1
set palette defined ( 0 '#D73027', 1 '#F46D43', 2 '#FDAE61', 3 '#FEE090', 4 '#FFFFD9', 5 '#E0F3F8', 6 '#ABD9E9', 7 '#74ADD1', 8 '#4575B4' )
#set yr [300:0] ### no artefacts if zoom is higher than 1310% in evince
set yr [400:100] ### no artefacts if zoom is higher than 1780% in evince
#set yr [450:0] ### artefacts at all zoom levels if we show more data, or all of it
set term cairolatex dashed color; set output "temp.tex"
plot "data.txt" u 1:2:3 matrix with image notitle
set output #Closes the temporary output file.
!sed -e 's|/Title|%/Title|' -e 's|/Subject|%/Subject|' -e 's|/Creator|%/Creator|' -e 's|/Author|%/Author|' < temp.tex > graph.tex
and, for completeness:
% figuregen.tex
\documentclass[dvips]{article}
\pagestyle{empty}
\usepackage[dvips]{graphicx} %
\begin{document}
\input graph.tex
\end{document}
If needed, part of the data can be found in text form here; enough to reproduce the issue: https://paste.nomagic.uk/?e0343cc8f759040a#DkRxNiNrH6d3QMZ985CxhA21pG2HpVEShrfjg84uvAdt
EDIT 2
In fact, same artefact issues appear when using set terminal cairolatex pdf
set terminal cairolatex standalone pdf size 16cm,10.5cm dashed transparent
set output "plot.tex"
directly with pdflatex
gnuplot<plot.plt
pdflatex plot.tex
(Note, this is using Gnuplot Version 5.2 patchlevel 6).
The actual problem is, that NaN values are set to transparent black pixels (#00000000).
The transparency causes these gray outline artifacts, depending on the zooming level. If you zoom close enough, then you see no artifacts.
But as soon as the image pixels are smaller than your monitor pixels, the values are interpolated for screen display. Its seems that pdf viewers like evince (I tested also okular and mupdf) interpolate both color and alpha channels, so that the alpha value of the Nan pixels is changed, and the underlying black appears as gray border around the color pixels.
I tried several ways. The easiest one, which actually worked for me was to use the tikz terminal with option externalimages which saves images created with image as separate png file.
These png file also contains transparency, and the final result has the same artifacts.
But you can use imagemagick's convert to change the transparent NaN pixels of the png to white with
convert temp.001.png -alpha off -fill white -opaque black temp.001.png
So, a fully working plot file is
# plot.plt
set size ratio -1
set palette defined ( 0 '#D73027', 1 '#F46D43', 2 '#FDAE61', 3 '#FEE090', 4 '#FFFFD9', 5 '#E0F3F8', 6 '#ABD9E9', 7 '#74ADD1', 8 '#4575B4' )
set ytics 100
set yrange reverse
set term tikz standalone externalimages background "white"; set output "temp.tex"
plot "data.txt" u 1:2:3 matrix with image notitle
# temp.001.png is the external image which contains only the 'with image' part
# We must remove the #00000000 color, which represents the NaN pixels
# I couldn't replace the colors directly, but I could first remove the alpha channel
# and then change black to white, because no other black pixel appear
!convert temp.001.png -alpha off -fill white -opaque black temp.001.png
set output #Closes the temporary output file.
!sed -e 's|/Title|%/Title|' -e 's|/Subject|%/Subject|' -e 's|/Creator|%/Creator|' -e 's|/Author|%/Author|' < temp.tex > graph.tex
!pdflatex graph.tex
Mupdf screen shot for graph.pdf:
Note, that I used standalone to be able to directly compile the resulting file, so that I could check the result.
A more cumbersome alternative would be to "manually" plot with image to a png file, and include that in a second plot, like I described in Big data surface plots: Call gnuplot from tikz to generate bitmap and include automatically? Then you can have more influence on how the png is generated.
Just for the records, with image pixels seems to do the "trick" and will create a file without grey surrounding of NaN datapoints. Tested with gnuplot 5.2.6.
plot FILE u 1:2:3 matrix with image pixels notitle
Code:
### avoid shading around NaN datapoints
reset session
set size ratio -1
FILE = "data.txt"
set palette defined ( 0 '#D73027', 1 '#F46D43', 2 '#FDAE61', 3 '#FEE090', 4 '#FFFFD9', 5 '#E0F3F8', 6 '#ABD9E9', 7 '#74ADD1', 8 '#4575B4' )
set term cairolatex dashed color
set output "temp.tex"
plot FILE u 1:2:3 matrix with image pixels notitle
set output
### end of code
Result: (a PNG of a screenshot, since it looks like I cannot add a PDF here)
How do i change the dimensions of an inset axes object?
I'm creating a plot like this:
I would like the inset to be wider, the zoomed_inset_axes method defaults to the same aspect ratio as the underlying data (sensibly i guess), but it seems to resist any attempt I make to change it...
I'm using it like this:
axins.axis(args.inset_extent)
os = axins.get_position()
pos = [pos.x0, pos.y0, pos.width * 2, pos.height]
axins.set_position(pos)
I've tried the which kwarg of set_position too, and that also appears to do nothing.
How can i set the position of the inset plot, and more importantly change it's aspect ratio?
It's part of a reasonably long plotting script, the full code is here, and a couple of example basis sets to try it are here: 6-31G.dat and 3-21G.dat.
Just download them into their own dir, and put the basis set files in a dir called basis_sets, and then use the command:
./basis_sets.py -r -2 2 -b 6-31G 3-21G -a C --inset --inset-zoom 6 --inset-extent -0.03 0.03 6.7 7.7
(./basis_sets.py --help prints out usage guide)
So i found another function in there, just called inset_axes.
It's used a little differently, but does exactly what i want, and the mark_inset helper function still works too, which is nice.
So now i have:
ax = inset_axes(ax, width=XX, height=XX, loc=XX)
ax.axis([x0, x1, y0, y1])
istead of the zoom one and it is much more flexible.
Is there a way to define an alpha channel in a palette in either gnuplot or matplotlib?
I'm trying to combine two scalar fields into one plot and so far came up with nothing.
There is a way to set line colors with an alpha channel in the development version (4.7) of gnuplot. You can set the alpha channel as the high bits of an RGB color specification. For example,
plot x lc rgb '#AAAAAAAA'
draws a translucent gray line.
However, I'm not sure there is a way to do this for a palette.
I'm using gnuplot to generate the following surface plot.
The important part of the command file I'm using is:
set terminal pdfcairo size 3,3;
In particular the size 3,3 resizes the plot to the way I want but crops out part of the z-axis label in the process. If I use a wider size like size 4,3 or don't use the size option at all then the z-axis labels fit as follows:
It seems that gnuplot doesn't take the width of the label into consideration when resizing the plot.
Is there a way to maybe move the plot to the right before resizing to 3,3 so that there's room to scientific notation?
You can set the lmargin option:
set lmargin 10
(or whatever size doesn't crop the label).
I'm struggling with a problem when making plots with filledcurves. Between the filled areas, there seems to be a "gap". However, these artifacts do not appear on the print, but depend on the viewer and zoom-options. In Gnuplot I use the eps terminal, the eps-files look great, but the lines appear when I'm converting to pdf. The conversion it either done directly after plotting or when converting the latex-document from dvi to pdf. As most of the documents are here on the display nowadays, this is an issue. The problem also appears when I'm directly using the pdfcairo terminal in Gnuplot, so it's not caused by the conversion (tried epstopdf and ps2pdf) alone.
I attached a SCREENSHOT of a plot displayed in "acroread" (same problem in other pdf-viewers).
Has anybody an idea how to get rid of it but keeping the graphic vectorized?
I just ran into the same issue. Apparently the filling between two curves
is done as a set of polygons that do not exactly touch one another, thus
the thin white lines visible on some PDF viewers.
One way to fix the issue is to draw over these polygon boundaries. First
define min and max functions in gnuplot:
min(x, y) = x < y ? x : y
max(x, y) = x > y ? x : y
Then, assuming that column 1 of "datafile" contains your x values and
that columns 2 and 3 contain the y values of curves 2 and 3, write:
plot "datafile" using 1:2:3 with filledcurves lc rgb "gray", \
"" using 1:2:(min($2, $3)):(max($2, $3)) with yerrorbars ps 0 lt 1 \
lc rgb "gray" lw 0.5
The first plot instruction fills the spaces between the curves in gray.
The second plot instruction draws points of zero size (ps 0) at each
x value (1) on curve (2) with thin (lw 0.5), continuous (lt 1), gray
(lc rgb "gray"), vertical errorbars (yerrorbars) from the lower to
the higher of curves 2 and 3.
This covers the white lines. To get best results you may need to
experiment with the thickness of the bars (e.g., lw 0.6, lw 0.2).
This issue is fixed with gnuplot 5.2, see https://sourceforge.net/p/gnuplot/patches/749/
The actual problem was, that filled curves were previously plotted as many quadrilaterals, which leads to artifacts (white stripes) in many viewers due to antialiasing.
Since version 5.2 filled curves are rendered as single polygon, which prevents these problems (see issue linked above).
The problem is still present in Gnuplot 5.0.4 and at least the cairolatex terminal which I use to output PDFs.
I also wanted to color the area between two curves, in my case defined as functions.
When I used something like
f(x) = 2 + sin(x)
g(x) = cos(x)
plot '+' using 1:(f($1)):(g($1)) with filledcurves closed
I got the same vertical white lines as in the question.
A simple solution for curves where one is always above the other is to let Gnuplot fill the area from the upper curve to the x-axis with the desired color and then paint it over with white from the lower curve downwards:
f(x) = 2 + sin(x)
g(x) = cos(x)
plot f(x) with filledcurves x1, g(x) w filledc x1 fs lc rgb "white"
Apparently this filledcurves style (not between curves but between a curve and an axis) avoids the trapezoid artifacts.
This can be readily extended for plotting data files and multiple stacked cures like in the question. Just paint from top to bottom and finish with white for the empty area between the lowest curve and the x-axis.
For overlapping curves a construction of minimum and maximum curves like in the answer from françois-tonneau might do the trick.
If you're talking about the red and cyan bits the gap could be an illusion caused by the Red + Cyan = White on a RGB screen. Maybe there's no gap, but the border areas appear as white due to the proximity of the pixels.
Take the screenshot and blow it up so you can see the individual pixels around the perceived gap.
If this is the case, maybe selecting a different colour scheme for the adjacent colurs would get rid of the effect. I certainly can't see anything matching your description on anywhere but the red and cyan bits.
From https://groups.google.com/forum/#!topic/comp.graphics.apps.gnuplot/ivRaKpu5cJ8, it seemed to be a pure Gostscript issue.
Using the eps terminal of Gnuplot and converting the eps file to pdf with
epstopdf -nogs <file.eps> -o <file.pdf>
solved the problem on my system. From the corresponding Man page, the "-nogs" option instructs epstopdf not to use Gostscript.