10

Is there an easier way to create this in pgfplots than plotting the matrix image externally and using addplot graphics (as on p.42 of the pgfplots manual)? A mesh plot (as suggested for plotting matrixes here) might not support the number of data points I'd like to use, plotting 1000x500 points this way won't work, or create a giantic output file.

Getting the upper/lower limits for the colorbar and the palette right isn't that straightforward when using two plotting programs (the gnuplot print statement can be redirected into a file, which allows generating TeX-code from gnuplot, so the limits as determined by gnuplot could be imported as macros etc.)

Since pgfplots can call gnuplot for line-data already, passing commands and reading back the output, could I use this to write the gnuplot code to generate the image directly into my TeX file instead of having to run an external script and manage the temporary files manually?

set terminal tikz standalone externalimages
set output "plot.tex"
plot "data.dat" matrix with image
set print "plot-params.tex"
print sprintf("\cb{%g}{%g}",GPVAL_CB_MIN,GPVAL_CB_MAX)

The style of gnuplot's tikz output doesn't match pgfplots' style and draws the color bars as a series of boxes instead of a gradient but it automatically generates the pixel data as plot.0.png in the correct size, which makes it a bit easier to use with addplot graphics.

This gets worse when multiple such plots should be combined using multiplot/groupplots.

gnuplot output

  • is it possible to provide a sample(small size) data.dat to see the structure of data and how was it generated ? – texenthusiast Apr 27 '13 at 18:35
  • Here is a 131x131 data set I'd like to plot. The (error)values are slightly higher every 32rows/columns, to make that point I'll need to plot at least 100 each. Using a log scale on the values, and drawing the color ticks accordingly would be nice too. – pascal Apr 27 '13 at 18:54
  • Are you interested in my answer 1.Fully gnuplot approach using gnuplottex due to large datasets ? BTW Did you use LuaLaTeX as it has handle more points( memory capacity) than pdfLaTeX1. Also see Jake's Answer:pgfplot: plotting a large dataset – texenthusiast Apr 27 '13 at 22:02
  • 1
    @pascal: If you don´t mind to share your 1000x500 set (or some king of its draft), I can plot it with the Asymptote (or you can try it yourself, with minor corrections to the answer with the plot of bigdata.dat). – g.kov Apr 30 '13 at 10:08
6

gnuplot lua/tikz terminal driver

"The lua terminal driver creates data intended to be further processed by a script in the lua programming language. At this point only one such lua script, gnuplot-tikz.lua, is available. It produces a TeX document suitable for use with the latex TikZ package. Other lua scripts could be written to process the gnuplot output for use with other TeX packages, or with other non-TeX tools. set term tikz is shorthand for set term lua tikz. As decribed above, it uses the generic lua terminal and an external lua script to produce a latex document" from gnuplot 4.6 documentation

Examples:

A tikz terminal can export full-plot.tex of plot like in this TeXample.net example and gnuplottikz example

Hoping this works for you.

Using pgfplots (invoking gnuplot) and it's groupplot library. on 131*131 matrix dataset provided by OP

\documentclass[preview=true,12pt,border=2pt]{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=newest}
\usepgfplotslibrary{groupplots} 
%\usepgfplotslibrary{external}
%\tikzexternalize% activate externalization!
% same matrix data used for all four figures for illustration
% code compiled with lualatex -shell-escape, gnuplot 4.4.3 and pgfplots 1.8 
% Matrix dataset(131*131) in "mat-data.dat" (provided by OP in comment). 
\begin{document}
\begin{tikzpicture}
\begin{groupplot}[view={0}{90},colorbar,colormap/bluered,colorbar style={%
ytick={-19,-18,-17,-16,-15,-14,-13,-12,-11}},label style={font=\small},group style={group size=2 by 2,horizontal sep=3cm},
height=3.5cm,width=3.5cm,footnotesize]
\nextgroupplot % First Figure
\addplot3[raw gnuplot,surf,shader=interp]
            gnuplot[id={surf}]{%
set pm3d map interpolate 0,0;
splot 'mat-data.dat' matrix using 1:2:(log($3));}; %natural logarithm
\nextgroupplot % Second Figure
\addplot3[raw gnuplot,surf,shader=interp]
            gnuplot[id={surf}]{%
set pm3d map interpolate 0,0;
splot 'mat-data.dat' matrix using 1:2:(log($3));};
\nextgroupplot % Third Figure
\addplot3[raw gnuplot,surf,shader=interp]
            gnuplot[id={surf}]{%
set pm3d map interpolate 0,0;
splot 'mat-data.dat' matrix using 1:2:(log($3));};
\nextgroupplot % Fourth Figure
\addplot3[raw gnuplot,surf,shader=interp]
            gnuplot[id={surf}]{%
set pm3d map interpolate 0,0;
splot 'mat-data.dat' matrix using 1:2:(log($3));};
\end{groupplot}
\end{tikzpicture}
\end{document}

code compiled with lualatex -shell-escape, gnuplot 4.4.3 and pgfplots 1.8

enter image description here

Alternative Approach(option 4 above): Using fully gnuplot based on gnuplottex package

code compiled with pdflatex -shell-escape, gnuplot 4.4.3 and gnuplottex(version October 2, 2012)

enter image description here

\documentclass[preview=true,border=2pt]{standalone}
\usepackage{gnuplottex} 
\begin{document}    
\begin{gnuplot}[terminal=epslatex,terminaloptions={font ",7"}]
set tmargin 0       # set white top margin in multiplot figure
set bmargin 1       # set white bottom margin in multiplot figure  
set lmargin 0
set rmargin 0 
set xrange [0:130]; # x and y axis range 
set yrange [0:130];
set cbrange [-19:-12]; # colorbox range  
unset key;             # disables plot legend or  use "notitle"  
set palette model RGB defined (0 '#0000B4',1 '#00FFFF',2 '#64FF00',3 '#FFFF00',4 '#FF0000',5 '#800000');         # hex colormap matching pgfplots "colormap/bluered"  
set pm3d map;       # `splot` for drawing palette-mapped 3d colormaps/surfaces
set pm3d interpolate 0,0; # interpolate optimal number of grid points into finer mesh, and          
                          # color each quadrangle with 0,0
set multiplot layout 2,2 rowsfirst scale 0.9,1.2;  # subplots 2 by 2
# First Figure
splot 'mat-data.dat' matrix using 1:2:(log($3)); # matrix data with log(z-axis)
# Second Figure
splot 'mat-data.dat' matrix using 1:2:(log($3)); 
# Third Figure
splot 'mat-data.dat' matrix using 1:2:(log($3)); 
# Fourth Figure
splot 'mat-data.dat' matrix using 1:2:(log($3)); 
unset multiplot;
\end{gnuplot}
\end{document}

Alternative Approach: Reading from mat-data.dat file directly in pgfplots

I have failed to get result in this way. Anybody can give their feedback. \addplot3[surf,mesh/cols=131,mesh/ordering=rowwise,shader=interp] file {mat-data.dat};

  • 1
    thanks for the different solutions; I tried the raw gnuplot one but in 4.6 with set pm3d map interpolate 0,0; splot 'data' matrix[which implicitly adds with pm3d] I get an error “Tabular output of this 3D plot style not implemented”. Using with points does output a list of col:row:value, but doesn't interpolate. The message I'm seeing seems to have been introduced in 2012/06/08, no mention of pm3d in this file, maybe a regression or something else wrong on my end? – pascal Apr 29 '13 at 18:17
  • 1
    @pascal pgfplots(incase of raw gnuplot) uses gnuplot to generate the filename.surf.table this .table is plotted by pgfplots. In gnuplot 4.6 i got the same error Tabular output of this 3D plot style not implemented,May be mail to pgfplots developer or gnuplot guys to see any work around. Also gnuplot lua/tikz is new feature give it a try. Generally it takes time for all dependencies to come to same stage, sometimes we are well ahead of times. gnuplot,pgfplots are ever evolving :). see robust python based matplotlib mayavi . – texenthusiast Apr 29 '13 at 18:48
  • 1
    While set pm3d interpolate currently doesn't seem to work with tables, interpolating using set dgrid3d 64,64 exp works. – pascal Apr 30 '13 at 1:03
  • @pascal Thanks :),Is it possible to share your gnuplot 4.6 compatible code via paste.ubuntu.com or add to your answer ? to benefit of future visitors we can add to the post. – texenthusiast Apr 30 '13 at 2:55
4

Below is my current solution using an external script. It uses gnuplot to generate the raster data and prints the code that should be piped into a file and included into the document.

#!/bin/bash
cat <<EOF
  \begin{tikzpicture}
  \begin{groupplot}[
    group stype={group size=2 by 2},
    colorbar, colormap/bluered
  ]
EOF

function plot_matrix {
  matrix=${1/.dat/.png}
  gnuplot <<EOF
    set terminal tikz externalimages
    set output "temp.tex"
    unset xtics
    unset ytics # messes up xrange,yrange
    plot "$1" matrix w image
    # gnuplot uses <index> <r:0-1> <g> <b> syntax
    set palette defined (0 0 0 0.7, 1 0 1 1, 2 0.4 1 0, 3 1 1 0, 4 1 0 0, 5 0.5 0 0)
    set print '-' # default is stderr
    cb = sprintf('point meta min=%g,point meta max=%g',GPVAL_CB_MIN,GPVAL_CB_MAX)
    ra = sprintf('xmin=%g,xmax=%g,ymin=%g,ymax=%g',GPVAL_X_MIN,GPVAL_X_MAX,GPVAL_Y_MIN,GPVAL_Y_MAX)
    print sprintf('\nextgroupplot[%s,%s,$2]',cb,ra)
    print sprintf('\addplot graphics[%s]{$matrix};',ra)
EOF
  rm 'temp.tex'
  mv 'temp.01.png' $matrix
}

plot_matrix "a.dat" "ylabel={Y1}"
plot_matrix "b.dat" ""
plot_matrix "c.dat" "ylabel={Y2}"
plot_matrix "d.dat" ""

cat <<EOF
  \end{groupplot}
  \end{tikzpicture}
EOF
  • My opinion only: I generally avoid \addplot graphics due to the mentioned issues in your Q,instead i plot entirely in pgfplots or gnuplot. May be this is a right application to use,anyone who used can share their experience. – texenthusiast Apr 27 '13 at 22:17
  • This is the same problem why I avoid drawing the colorbar gradients with gnuplot: approximating a surface with small rectangles often produces rendering artefacts, i.e. lines of white or lighter pixels in a surface that should appear closed, because the rectangles are rendered on top of each other anti-aliased, and when half-covered pixels don't add up to the intended color exactly it shows a gap. This is not an issue with raster images... – pascal Apr 27 '13 at 22:49
4

enter image description here

As another option, the Asymptote can handle bigger images. p.asy:

real unit=0.5mm;
unitsize(unit);
import graph;
import palette;

file fin=input("bigdata.dat");
real[][] v=fin.dimension(0,1310);
v=transpose(v);

int n=v.length;
int m=v[0].length;

write(n,m);

scale(Linear,Linear,Log);

pen[] Palette=
  Gradient(
    rgb(0,0,0.1)
    ,rgb(0,0,1)
    ,rgb(1,0,0)
    ,rgb(0,1,0)
    ,rgb(1,0.1,0)
    ,rgb(1,1,0)
  );

picture bar;
bar.unitsize(unit);

bounds range=image(v, (0,0),(n,m),Palette);

palette(bar,"$A$",range,(0,0),(50,n),Right,Palette,
  PaletteTicks(scale(10)*"$%0.1e$",pTick=black+5pt,Step=0.5e-6)
);

xaxis(0,m,RightTicks(scale(10)*"$%0f$",Step=200,step=100,beginlabel=false,black+5pt));
yaxis(0,n,LeftTicks(scale(10)*"$%0f$",Step=200,step=100,black+5pt));

add(bar.fit(),point(E),E);

The original 131x131 matrix data.dat was scaled to 1310x1310 by this helper pre.asy:

file fin=input("data.dat");
real[][] v=fin.dimension(0,131);
v=transpose(v);

int n=v.length;
int m=v[0].length;

real[][] w=new real[10n][10m];

file fout=output("bigdata.dat");
string s;

for(int i=0;i<10n;++i){
  s="";
  for(int j=0;j<10m;++j){
    w[i][j]=v[rand()%n][rand()%m]*0.618+v[i%n][j%n]*0.382;
    w[i][j]*=((real)(i+1)/10n+(real)(j+1)/10m)/2;
    s=format("%#.5e ",w[i][j]);
    write(fout,s);
  }
  write(fout,'\n');
}

Edit: There is nothing special in pre.asy, it was used just to get a bigger dataset bigdata.dat (1310x1310, about 20Mb), to check how asy can handle it. Btw, it the OP already has the 1000x500 file, it would be better to try it instead.

Comments on pre.asy:

file fin=input("data.dat");
real[][] v=fin.dimension(0,131);  // read data file into the matrix v[][]
v=transpose(v);                   

int n=v.length;                   // n - number of rows
int m=v[0].length;                // m - number of columns

This is a standard sequence to read a matrix from the data file. Now, declare a new matrix w, ten times bigger:

real[][] w=new real[10n][10m];

Declare the output file fout and string s:

file fout=output("bigdata.dat");
string s;

Next, there are C-like for loops to run through all indices of the new bigger matrix:

for(int i=0;i<10n;++i){
  s="";
  for(int j=0;j<10m;++j){

Now, put something into the current element w[i][j]:

    w[i][j]=v[rand()%n][rand()%m]*0.618+v[i%n][j%n]*0.382;
    w[i][j]*=((real)(i+1)/10n+(real)(j+1)/10m)/2;

some random element of the original small matrix is used, but it can be anything. In fact, it could be possible to calculate the entire matrix here, if the data used by OP are not coming from the sensors or use some really tricky algorithms.

    s=format("%#.5e ",w[i][j]); // format the value 
                                // according to scientific notation
                                // with 5 digits, e.g. `4.75586e-08`
    write(fout,s);              // write it to the file
  }
  write(fout,'\n');             // write a new line symbol
}

That's it.

And for the sake of comparison, this is the original 131x131 matrix, with (natural) log applied to the values, and a palette similar (I hope) to colormap/bluered in pgfplots:

real unit=0.5mm;
unitsize(unit);
import graph;
import palette;

file fin=input("data.dat");
real[][] v=fin.dimension(0,131);
v=transpose(v);

int n=v.length;
int m=v[0].length;

write(n,m);

for(int i=0;i<n;++i){
  for(int j=0;j<m;++j){
    v[i][j]=log(v[i][j]);
  }
}

//\pgfplotsset{
//colormap={bluered}{
//rgb255(0cm)=(0,0,180); rgb255(1cm)=(0,255,255); rgb255(2cm)=(100,255,0);
//rgb255(3cm)=(255,255,0); rgb255(4cm)=(255,0,0); rgb255(5cm)=(128,0,0)}
//}

pen[] Palette=
  Gradient(
    rgb(0,0,180.0/255)
    ,rgb(0,1,1)
    ,rgb(100.0/255,1,0)
    ,rgb(1,1,0)
    ,rgb(1,0,0)
    ,rgb(128.0/255,0,0)
  );

picture bar;
bar.unitsize(unit);

bounds range=image(v, (0,0),(n,m),Palette);

palette(bar,range,(0,0),(5,n),Right,Palette,
  PaletteTicks(scale(1)*"$%0f$",pTick=black+0.5pt,Step=1,beginlabel=false)
);

xaxis(0,m,RightTicks(scale(1)*"$%0f$",Step=20,step=10,beginlabel=false,black+0.5pt));
yaxis(0,n,LeftTicks(scale(1)*"$%0f$",Step=20,step=10,black+0.5pt));

add(bar.fit(),point(E),E);

enter image description here

  • is it possible to take a log(values) and replot with similar palette to colormap/bluered in pgfplots to see colormap comparison with other answers. How was the data scaled(using linear/spline interpolation), can you help others by giving details on pre.asy does ? Thanks a lot. – texenthusiast Apr 29 '13 at 22:37
  • @texenthusiast: comments and the image for comparison added. – g.kov Apr 30 '13 at 7:27
  • Thanks for the edit,I have asked OP for small size for it's easiness to share. may be you can ask him for the full dataset to plot them in asy and suggest him the data-sharing tools. BTW OP asked for subplots(2*2), see his answer, is subplots possible in .asy and is slight interpolation possible to remove the pixelation on plot ?. – texenthusiast Apr 30 '13 at 7:42
  • 1
    @texenthusiast:I would say, just about any kind of interpolation is possible, see for example GaussianBlur. – g.kov Apr 30 '13 at 10:17

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