1. Summary
  2. Files
  3. Support
  4. Report Spam
  5. Create account
  6. Log in

Plotting with PDL::Graphics::Gnuplot

From pdl

Revision as of 04:15, 16 November 2012 by Zowie (Talk | contribs)
Jump to: navigation, search

PDL::Graphics::Gnuplot is a plotting package for PDL. It is not currently included in the main PDL distribution - you can get it from CPAN, or from Github. It is a Perl-only layer that works with the standalone gnuplot plotting program. You can get gnuplot from the SourceForge site; it is also available pre-compiled for most common platforms (including Gnu/Linux, MacOS, and Microsoft Windows) via the usual package distribution channels for each platform.

Gnuplot can plot 2-D and 3-D lines, curves, surfaces, and scientific images in B/W, pseudocolor, or full RGBA color. It can render plots on many devices, including interactive screen display and publication-quality output formats such as PDF.

You can get full documentation for gnuplot itself at the gnuplot.info site, or for the module in its POD, which is quite extensive.

Here we include some cookbooks and recipes for simple plots.

Contents

Basics

You load PDL::Graphics::Gnuplot in the usual way. Two symbols are exported by default: gplot and gpwin. The former is a catch-all entry point for plotting stuff with usual subroutine-calling syntax. The latter is a constructor for the object oriented interface.

Plot syntax

The main entry point for plotting is the PDL::Graphics::Gnuplot::plot method, which is also exported by default as gplot. It accepts three kinds of arguments:

Plot options
these are named options that affect the appearance or behavior of the plot as a whole. They include things like 2D/3D selection, location of the legend (called the "key" by gnuplot), axis positioning and labeling, plot title, etc. You can set persistent plot options in the object itself with the options method, or just set transient ones on-the-fly in a call to plot. Plot options are supplied in a leading or trailing hash ref (or both) in the arg list.
Curve options
these are named options that affect an individual curve only, such as the curve style (set by the with option). Curve options can be run inline in the argument list, or can be supplied as a hash ref.
Data
Data for each plot are passed in as a collection of PDLs or array refs, called a "tuple". Each element of a "tuple" is called a "column", and represents some parameter of the data to be plotted -- e.g. ordinate, abscissa, color, glyph size, or error bar extent. Most types of plot use 1-D data; higher dimensions are threaded over, so you can pass in a 2-D column to generate many lines on a plot. Some types of plot use 2-D columns - for example, a grid mesh to be plotted in 3-D, or an image.

The argument list to plot thus contains:

  • an optional hash ref containing plot options;
  • Zero or more "curve blocks", each of which contains zero or more curve options followed by a tuple of data;
  • another optional hash ref containing plot options.

Because the size of a tuple is not known in advance (and different tuple sizes can change the style of plot), you *must* place either a curve option or an empty hash in between separate tuples. Curve options are cumulative, so you don't have to re-enter them for each curve block if they don't change. The empty hash between tuples serves to delimit curve blocks that have the same curve options.

The simplest plot

use PDL::Graphics::Gnuplot;
gplot( xvals(5)**2 );

That should produce a simple plot on your default output device. On most systems, it will appear on your screen and look more-or-less like this:

image:PGG-simple.png

Different systems will render the plot slightly differently because they use different output devices ("terminals") by default. On Linux it is X11; on MaxOS it is a program called AquaTerm. You can change the default output device with an environment variable.

Object Oriented plotting

It is recommended that you use the object-oriented interface. The exported constructor gpwin builds PDL::Graphics::Gnuplot objects, that represent a connection to a particular underlying gnuplot process. The objects store persistent options and other state, and you can use them to send the same plot to multiple devices (for example, to tweak a plot interactively so you like it, and then render it in a publication-quality form).

The constructor takes, as its first argument, the *name* of the output device (what gnuplot calles a "terminal") you want to use. The rest of the arguments are a collection of *terminal options* that modify the behavior of the terminal. Different terminals take different options. The enhanced option is a flag (on terminals that support it) indicating that you expect to use LaTeX-like markup for font and formatting information in text strings. Other common options include output (names an output file where appropriate), size (specifies an output size for the plot, in one of many convenient units), and font (names a system font and size to use by default for text markup on the plot).

use PDL::Graphics::Gnuplot;
$w = gpwin( wxt, enhanced=>1 ); # wxt is an anti-aliased X11 interactive terminal

Once you've defined an object, you can plot with it.

$x = xvals(51)/50;
$w = gpwin( png, output=>"PGG-points.png",size=>[320,240,'px'],font=>'Arial,9',enhanced=>1);
$w->plot( {key=>'top center'}, legend=>"x^2", with=>"points", $x, $x**2 );

should yield the following:

Image:PGG-points.png

Interactive plotting

There are several interactive output terminals. The wxt device is available on Gnu/Linux, MacOS, and Microsoft Windows, and allows you to pan and zoom the plot, and also to read off coordinates by placing the cursor over them. The wxt and x11 terminals also let you read mouse input into your script.

You can read mouse input like this:

$r = sin(rvals(51,51)/5) + sin(xvals(51,51)/10); # Generate some data
$w = gpwin(wxt);
$w->image($r);
($x,$y,$status) = $w->read_mouse();

The read_mouse() call will die unless $w is an interactive device that can accept mouse input. On return, $x and $y are the scientific coordinates of the click (in polar coordinates, they are actually *r* and *theta*); and $status is a hash containing mouse status. The "b" key points to the mouse button that was pressed, and the "m" key points to a string that indicates which, if any, modifier keys (like SHIFT) were pressed with the mouse button.

You can also read in a polygon with a simple event loop:

$r = sin(rvals(51,51)/5) + sin(xvals(51,51)/10); # Generate some data
$w = gpwin(wxt);
$w->image($r);
$p = $w->read_polygon();

read_polygon is a simple event loop that lets the user input a polygon with simple editing ("DEL" key works) and returns the coordinates of its vertices in a PDL. You can modify the event loop to do pretty much anything, by passing in code refs to carry out actions when specific buttons are pressed.


Display-and-save plots

If you are using object-oriented plotting, then you can generate and tweak your plot with an immediate display terminal like wxt, aqua, x11, or even dumb, then redirect the output to a publication-quality file format and replot directly to a file. You do it like this:

$w = gpwin(wxt); # or any immediate display device
$w->plot( with=>'points', xvals(5), xvals(5)**4 ); # or whatever
$w->output( png, output=>"foo.png" );  # or pdf, or jpg, or whatever format you want
$w->replot;

Remember that some formats, like pdf, require you to close the plot window before the plot is fully written to disk. (This is a requirement of gnuplot itself):

$w->close;

will close the file.

Basic examples of plot styles

Gnuplot treats plot styles on a per-curve basis, but the plot must be in 2-D or 3-D mode. The mode is set with the trid (synonym 3d) plot option flag (default value 0). If it is set to a true value the plot is in 3-D.

2-D plots

In 2-D, most of the plotting styles accept one-dimensional columns of data, each of which describes a curve or collection of points to be plotted. Feeding in columns with more dimensions causes those styles to thread, plotting multiple curves from the same tuple. In some cases, the plots behave differently depending on the number of columns in the tuple.

Lines, step functions, and filled curves

These curve styles are the workhorses of scientific plotting.

lines and linespoints
These are basic connect-the-dots styles with and without glyphs at the data points themselves.
 $x = xvals(101)/100;
 $y = cos( $x * 12 * 3.14 ) / (($x - 0.25)**2 + 0.2);
 
 $w = gpwin( png, output=>"lines.png",  size=>[5,3,'in'], font=>",11" );
 
 $w->plot( title=>"Lines and linespoints", xlab=>"X value", ylab=>"Y value",
          with=>"lines",       legend=>"lines",       $x,  $y,
          with=>"linespoints", legend=>"linespoints", $x, -$y
         );
 
 $w = gpwin( png, output=>"lines2.png",  size=>[5,3,'in'], font=>",11" );
 
 $w->plot( title=>"Lines and linespoints", xlab=>"Autogenerated X index", ylab=>"Y value",
          with=>"lines",       legend=>"lines",        $y,
          with=>"linespoints", legend=>"linespoints", -$y
         );


Image:lines.png Image:lines2.png

steps, fsteps, and histeps
The "steps" styles are useful for displaying data domain bins directly. The histeps style centers each range (Y) value on the corresponding domain location. The steps style places each range value between its associated domain point and the next one. The fsteps style places the range segment *before* the corresponding domain element.
$x = xvals(10);
$y = pdl(7,2,1,4,3,6,5,0,9,8);

$w = gpwin(png, output=>"steps.png", size=>[5,3,'in'], font=>",11");

$w->plot(title=>"Steps", xlab=>"X value", ylab=>"Y value", 
     with=>"histeps", legend=>"histeps", $x, $y,
     with=>"steps",   legend=>"steps",   $x+0.05, $y+0.05,
     with=>"fsteps",  legend=>"fsteps",  $x+0.10, $y+0.10
 );

Image:steps.png

filledcurves
There are several variants You can use filledcurves to draw a filled shape. If you feed in two columns of data, that is the default style:
$t = xvals(6) * 3.14159 * 4 / 5;
$x = cos($t); $y = sin($t);

$w = gpwin(png, output=>"star.png", size=>[4,3.5,'in'], font=>",11");
$w->plot( title=>"Star with filledcurves", justify=>1, xlab=>"X", ylab=>"Y",
         with=>filledcurves, $x, $y 
  );

Image:star.png

Other two-column variants include distance to an axis or line, and distance from a point:

$w = gpwin(png, output=>"filled.png", size=>[5,3,'in'], font=>",11");
 
$w->plot({title=>"Filled curves", xlab=>"X value", ylab=>"Y value",yrange=>[-1.5,1.5]},
       with=>"filledcurves y1=0",legend=>"filledcurves y1=0",xvals(10), sin(xvals(10)),
       with=>"filledcurves above x1",legend=>"filledcurves above x1", xvals(10),xvals(10)/10**2 - 0.5
  );

$w = gpwin(png, output=>"filled2.png", size=>[5,3,'in'],font=>",11");
 
$w->plot({title=>"Filled to a point", xlab=>"X value", ylab=>"Y value", yrange=>[0,8]}, 
       with=>"filledcurves xy=5,6", legend=>"filledcurves xy=5,6", xvals(31)/3, 1 - sin(xvals(31)/3)
   );

Image:filled.png Image:filled2.png

You can also fill the distance between two different curves, by feeding a third column into the tuple:

$x = xvals(10);
$yhi = sin($x) + 4 + $x/10;
$ylo = ($x**2)/50;
 
$w = gpwin(png, output=>"filled3.png", size=>[5,3,'in'], font=>",11");
$w->plot({yrange=>[0,8],title=>"Filled between curves", xlab=>"X value", ylab=>"Y value"},
    with=>"filledcurves", legend=>"filledcurves (3-tuple)", $x, $ylo, $yhi );

Image:filled3.png


Points and glyphs

Basic point plots are OK, but there's so much *more*...

points
glyphs at (x,y) locations. Shouldn't you be using one of the errorbars styles?
$w=gpwin(png, output=>"points.png", size=>[5,3,'in'],font=>',11');
$w->plot(title=>"Points. Yawn.",xlab=>"X value", ylab=>"Y value", 
     wi=>"points", le=>"sine",  xvals(46)*8,  sin(xvals(46)*3.14159*2/45),
     wi=>"points", le=>"flat",  xvals(46)*8, pdl(0)
 );

Image: points.png


dots
tiny points at (x,y) locations - useful for scatterplots. On pixelated devices like PNG or the screen, scatterplots can get overwhelmed quickly (this one does!) -- but on a high resolution device like a PDF, they are far more useful.
$a = rfits("/usr/local/src/PDL/m51.fits");
$b = $a->convolveND(ones(9,9)/81);
$w=gpwin(png, output=>"dots.png", size=>[4,4],font=>",11");
$w->plot(title=>"Image smear",xlab="Original image value", ylab=>"Smoothed image value",
      with=>'dots', $a->flat, $b->flat);

Image: dots.png

circles
useful for filled circles, outlined circles, or both.
$x = xvals(51);
$y = sin($x/5);
$r = cos($x/5) / 3;
$color = ($x-25)->abs;
$w = gpwin(png, output=>"circles.png", size=>[5,3,'in'],font=>',11');
$w->plot(title=>"Circles", xlab=>"X",ylab=>"Y",style=>"fill solid", 
       with=>"circles fillcolor palette", $x, $y, $r, $color);

Image: circles.png

ellipses
accepts x, y, major_diameter, minor_diameter, angle. If you omit the angle the major diameter is horizontal. If you omit the minor diameter, the ellipses are circles.

Notice that the major diameter as delivered doesn't have to be the actual major diameter of the ellipse -- the ellipses at the left hand side of the plot have a "major diameter" that is small than their "minor diameter".

$x = xvals(51)/50;
$y = $x**2;
$rmaj = sin($x*3.14159*2);
$rmin = cos($x*3.14159*2);
$w = gpwin(png,output=>"ellipses.png", size=>[5,5,'in'],font=>',11');
$w->plot(title=>"Ellipses", xlab=>"X value", ylab=>"Y value",j=>1,
   with=>"ellipses",$x,$y,$rmaj, $rmin);

Image: ellipses.png

labels
labels
vectors
vectors

Error bars

yerrorbars, xerrorbars, xyerrorbars
yerrorlines, xerrorlines, xyerrorlines
boxerrorbars
boxes with yerrorbars
boxxyerrorbars
boxes with xyerrorbars
candlesticks
candlesticks
financebars
financebars

Histograms

impulses
A line-style impulse plot. This is sort of a "trivial" histogram - if the plot is dense enough, it becomes an area plot.
$x = xvals(18) * 20 * 3.14159 / 180;
$y = sin($x);

$w = gpwin(png,output=>"impulses.png", size=>[5,3,'in'],font=>',11');
$w->plot({title=>"A simple impuse plot", 
         xlab=>"X value", ylab=>"Y value"},
         with=>'boxes', $x, $y);

Image:impulses.png

boxes
Basic box-style histogram plot. This is useful for histogram-style charts of a single variable (or multiple ones with overlays).
$x = xvals(18) * 20 * 3.14159 / 180;
$y = sin($x);

$w = gpwin(png,output=>"boxes.png", size=>[5,3,'in'],font=>',11');
$w->plot({title=>"A simple histogram with boxes", 
         xlab=>"X value", ylab=>"Y value",
         style=>"fill solid 0.3", boxwidth=>[0.8,'relative'] },
         with=>'boxes', $x, $y);

Image:boxes.png




histogram
histogram
newhistogram
newhistogram

Images

image
image
rgbimage
rgbimage
rgbalpha
rgbalpha
fits
image with FITS WCS header


FITS files and the World Coordinate System

Plotting time values

Polar plots

Contour plots

3-D plots

Lines and points

Here is an example for how to plot a collection of curves in a 3D plot. It plots xy for − 10 < = x < = 10 and y \in [0,1,2,3,4].

$x = sequence(101)->xlinvals(-10,10);
$y = sequence(1,5);
$z = $x**$y;
$z/=$z->maximum->transpose; #normalize z curves so we can see the differences
$yp = $y->(*$x->dim(0))->clump(2);
$view = [60,30,1,1];
$leg = [map{sprintf("x^%d",$_)}(0..4)];
$w=gpwin('png',(output=>'3dlines.png',size=>[8,5,'in'],enhanced=>1));
$w->plot({title=>"3D line plot (x^y)",view=>$view,trid=>1,xlabel=>"X", ylabel=>"y (power)",zlabel=>"x^y"},{legend=>$leg,with=>'lines linewidth 3'},$x,$yp,$z);
3D line plot

Cylindrical and spherical plots

Surface plots

Contour plots

Getting Fancy

Text Markup

Labels on your Plots

Fancy Axes and Tick Marks

Some complex examples

Rendering the Solar System

Here's an example two-panel rendering of the geometry of several spacecraft in on 16-Dec-2008. It shows two "overhead" views of the ecliptic plane, with relevant objects rendered as circles.

use PDL::NiceSlice;
$au = 1.496e8   #km per AU
$ace_heq    = pdl(1.0, 0) - pdl(1.408e6,-1.70e5) / $au;  # from ACE metadata
$wind_heq  = pdl(1.0, 0) - pdl(1.6e6,    -1.5e5)   / $au;  # from WIND metadata
$s_a_heq     = pdl(1.069e11, 0.965e11) / 1e3 / $au;       # from STEREO-A metadata
Personal tools