This is an overview of the capabilities of =gnuplotlib=. The [[https://github.com/dkogan/gnuplotlib/][documentation]]
provides a complete API reference.

* Tutorial
** Specifying the data in one dataset

First, a trivial plot: let's plot a sinusoid

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
gp.plot(np.sin(th))
#+END_SRC

#+RESULTS:
[[file:guide-1.svg]]

This was a trivial plot, and was trivially-easy to make: we called =plot()= with
one argument, and we got a plot.

Here each point we plotted was 2-dimensional (has an x value an a y value), but
we passed in only one number for each point. =gnuplotlib= noted the missing
value and filled in sequential integers (0, 1, 2, ...) for the x coordinate.

If we pass in two arrays, =gnuplotlib= will use one for the x, and the other for
the y. Let's plot =sin(theta)= vs. =cos(theta)=, i.e. a circle:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-np.pi, np.pi, 100)
gp.plot(np.cos(th), np.sin(th))
#+END_SRC

#+RESULTS:
[[file:guide-2.svg]]

Hmmm. We asked for a circle, but this looks more like an ellipse. Why? Because
gnuplot is autoscaling the x and y axes independently to fill the plot window.
If we ask for the autoscaling to scale the axes /together/, we get a circle:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-np.pi, np.pi, 100)
gp.plot(np.cos(th), np.sin(th),
        square = True)
#+END_SRC

#+RESULTS:
[[file:guide-3.svg]]

Here we used the =square= /plot option/. More on those later. We just plotted
something where each point is represented by 2 values: x and y. When making 2D
plots, this is the most common situation, but others are possible. What if we
want to color-code our points using another array to specify the colors? You
pass in the new array, you tell =gnuplotlib= that you now have /3/ values per
point (the =tuplesize=), and you tell =gnuplot= how you want this plot to be
made:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-np.pi, np.pi, 100)
gp.plot(np.cos(th), np.sin(th),
        # The angle (in degrees) is shown as the color
        th * 180./np.pi,
        tuplesize = 3,
        _with     = 'linespoints palette',
        square    = True)
#+END_SRC

#+RESULTS:
[[file:guide-4.svg]]

=_with= is a /curve option/ that indicates how this dataset should be plotted.
It's =_with= and not =with= because the latter is a built-in keyword in Python.
=gnuplotlib= treats all =_xxx= options identically to =xxx=, so =plot(..., _with
= 'xxx')= and =plot(..., **{'_with': 'xxx'})= and =plot(..., **{'with': 'xxx'})=
are identical.

Styles in =_with= are strings that are passed on to =gnuplot= verbatim. So the
full power of =gnuplot= is available, and there's nothing =gnuplotlib=-specific
to learn. =gnuplot= has plenty of documentation about styling details.

Earlier we saw that a missing x array can be automatically filled-in with
integers 0, 1, 2, ... This is available with fancier plots also. The rule is:

- Normally we should be given exactly =tuplesize= arrays
- If we are given exactly =tuplesize-1= arrays, use 0, 1, 2, ... for the x
- If we are given exactly =tuplesize-2= arrays, use a regularly spaced xy grid
  with 0, 1, 2, ... in x and in y

These are the only allowed mismatches between =tuplesize= and how much data is
received. This allows flexibility in the passing of data, and some level of
validation of input. Example. Let's color-code the sinusoid by passing in /two/
arrays. The =tuplesize= is still 3, but we have an implicit x.

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
gp.plot(np.sin(th),
        # use the cosine as the color
        np.cos(th),
        tuplesize = 3,
        _with     = 'linespoints palette')
#+END_SRC

#+RESULTS:
[[file:guide-5.svg]]

Finally, so far we have been passing in each dimension in a separate array. But
it is often far more convenient to pass in a single array where each point is
represented in a row corresponding to the last dimension in that array. This is
specifiable by passing in a negative =tuplesize=, and most easily explained with
an example. The circle plot from earlier can be made in this way:

#+BEGIN_SRC python :python python3 :results output :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps

th     = np.linspace(-np.pi, np.pi, 100)
points = nps.transpose(nps.cat(np.cos(th), np.sin(th)))

print(points.shape)
#+END_SRC

#+RESULTS:
: (100, 2)

I.e. we have 100 rows, each one of length 2.

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

# shape (100,)
th     = np.linspace(-np.pi, np.pi, 100)
# shape (100, 2)
points = nps.transpose(nps.cat(np.cos(th), np.sin(th)))
gp.plot(points,
        tuplesize = -2,
        square    = True)
# instead of
# gp.plot(points[:,0], points[:,1],
#         tuplesize = 2,
#         square    = True)
#+END_SRC

#+RESULTS:
[[file:guide-7.svg]]

** Specifying multiple datasets
So far we were plotting a single dataset at a time. However, often we want to
plot multiple datasets in the same plot, together. Note that the code and
documentation uses the terms "dataset" and "curve" interchangeably.

As before, the whole plot is made with a single call to =plot()=. In its most
explicit form, each dataset is specified as a /tuple/. /plot options/ apply to
the whole plot, and are given as kwargs to the =plot()= call. /curve options/
apply to each dataset, and are passed as a =dict= in the last element of each
dataset tuple. So each =plot= command looks like

#+BEGIN_SRC python :results none :exports code
plot( curve, curve, ..., plot_options )
#+END_SRC

#+RESULTS:

where each =curve= is a =tuple=:

#+BEGIN_SRC python :results none :exports code
curve = (array, array, ..., curve_options)
#+END_SRC

#+RESULTS:

The data in each dataset is interpreted as described in the previous section.

Let's plot a sine and a cosine together, using the default styling for one, and
a specific styling for another. And let's set some common options.

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
gp.plot( (
           th, np.sin(th),
         ),
         (
           th, np.cos(th),
           dict(_with  = "points pt 7",
                legend = "cosine")
         ),

         xlabel = "Angle (rad)",
         title  = "Sine and cosine",
         unset  = 'grid')
#+END_SRC

#+RESULTS:
[[file:guide-10.svg]]

The =plot()= kwargs are the plot options, but curve options are allowed there as
well. These will be used as the default curve options for all curves that omit
those specific options. For instance, if I want to plot lots of things with
lines, except /one/, I can do this:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
gp.plot( ( np.sin(th), ),
         ( np.cos(th), ),
         ( th,         ),
         ( -th, dict(_with = 'points ps 0.5') ),
         _with = 'lines')
#+END_SRC

#+RESULTS:
[[file:guide-11.svg]]

If we have just one dataset, each tuple can be inlined, which is why something
like =gp.plot(x, y)= works.

Unlike =matplotlib=, here we make a single =plot()= call instead of making a
separate call for each dataset and for each format setting. You can still
construct the plot piecemeal, however, but you use normal Python directives to
do that. For instance, the previous plot can be created instead like this:

#+BEGIN_SRC python :results none :exports code
datasets = []

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
datasets.append(( np.sin(th), ),)
datasets.append(( np.cos(th), ),)
datasets.append(( th,         ),)
datasets.append(( -th, dict(_with = 'points ps 0.5') ),)

plot_options = dict()
plot_options['with'] = 'lines'

gp.plot(*datasets, **plot_options)
#+END_SRC

#+RESULTS:

Finally, [[https://docs.scipy.org/doc/numpy/user/basics.broadcasting.html][broadcasting]] is fully supported here, and can be used to simplify the
=plot()= call. Previously we plotted two sinusoids together using a tuple for
each dataset. With broadcasting, we can avoid that:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
gp.plot( th,
         nps.cat(np.sin(th),
                 np.cos(th)),

         legend = np.array( ("sin", "cos"), ) )
#+END_SRC

#+RESULTS:
[[file:guide-13.svg]]

I passed in an aray of shape =(100,)= for the x, and an array of shape
=(2,100,)= for the y. The broadcasting logic kicks in, and we get a plot of two
separate datasets, one for each row of y. The curve options broadcast as well:
the =legend= is expecting a scalar, but I gave it an array of shape =(2,)=, so
it uses a different legend for each of the two plotted datasets.

** Specifying multiple plots
If we want multiple plot windows, the object-oriented =gnuplotlib= interface
provides this. Each =gnuplotlib= object represents a separate =gnuplot= process
and a separate plot window. All the one-call =plot()= commands shown so far
reuse a single global =gnuplotlib= object for convenience. So if we want
multiple simultaneous plot windows, we explicitly create and use separate
=gnuplotlib= objects. The general sequence is:

#+BEGIN_SRC python :results none :exports code
plot1 = gp.gnuplotlib(plot_options_and_default_curve_options)
plot1.plot(curves)

plot2 = gp.gnuplotlib(plot_options_and_default_curve_options)
plot2.plot(curves)

...
#+END_SRC

#+RESULTS:

A trivial example:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(-2.*np.pi, 2.*np.pi, 100)
plot1 = gp.gnuplotlib( title  = 'sinusoid',
                       xlabel = 'Angle (rad)')
plot1.plot(th, np.sin(th),
           _with  = 'lines',
           legend = 'sine')
#+END_SRC

#+RESULTS:
[[file:guide-15.svg]]

Or if we want /one plot window/ containing /multiple/ plots, we can use the
/multiplot/ interface. This extends the previous structure where

- a plot (configured with plot options) contains datasets (configured with curve
  options)

so that we instead have

- a process (configured with process options) contains plots (configured with
  plot options) contains datasets (configured with curve options)

In the usual non-multiplot case, process options are lumped into the larger set
of plot options. When making a multiplot, we still have a single =plot()=
command, but now each /plot/ lives in a separate tuple. We have similar
semantics as before: default plot options can be given together with the process
options. Plot options can be given as a =dict= in the last element of that
plot's tuple. Example. Two sinusoids together, in a multiplot:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(0, np.pi*2, 30)
gp.plot( (th, np.cos(th), dict(title="cos",
                               _xrange = [0,2.*np.pi],
                               _yrange = [-1,1],)),
         (th, np.sin(th), dict(title="sin",
                               _xrange = [0,2.*np.pi],
                               _yrange = [-1,1])),
         multiplot='title "multiplot sin,cos" layout 2,1',)
#+END_SRC

#+RESULTS:
[[file:guide-16.svg]]

We get a multiplot if we pass in a =multiplot= process option. The value of this
option is given directly to =gnuplot= in a =set multiplot= command. As before,
see the =gnuplot= documentation for all the details: run

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help multiplot'
#+END_SRC

* Recipes
This is a good overview of the syntax. Now let's demo some fancy plots to
serve as a cookbook.

Since the actual plotting is handled by =gnuplot=, its documentation and [[http://www.gnuplot.info/demo/][demos]]
are the primary reference on how to do stuff.

** Line, point sizes, thicknesses, styles
Most often, we're plotting lines or points. The most common styling keywords
are:

- =pt= (or equivalently =pointtype=)
- =ps= (or equivalently =pointsize=)
- =lt= (or equivalently =linetype=)
- =lw= (or equivalently =linewidth=)
- =lc= (or equivalently =linecolor=)
- =dt= (or equivalently =dashtype=)

For details about these and all other styles, see the =gnuplot= documentation.
For instance, the first little bit of the docs about the different line widths:

#+BEGIN_SRC shell :results output verbatim :exports both
gnuplot -e 'help linewidth' | head -n 20
#+END_SRC

#+RESULTS:
#+begin_example
 Each terminal has a default set of line and point types, which can be seen
 by using the command `test`.  `set style line` defines a set of line types
 and widths and point types and sizes so that you can refer to them later by
 an index instead of repeating all the information at each invocation.

 Syntax:
       set style line <index> default
       set style line <index> {{linetype  | lt} <line_type> | <colorspec>}
                              {{linecolor | lc} <colorspec>}
                              {{linewidth | lw} <line_width>}
                              {{pointtype | pt} <point_type>}
                              {{pointsize | ps} <point_size>}
                              {{pointinterval | pi} <interval>}
                              {{pointnumber | pn} <max_symbols>}
                              {{dashtype | dt} <dashtype>}
                              {palette}
       unset style line
       show style line

 `default` sets all line style parameters to those of the linetype with
#+end_example

gnuplot has a =test= command, which produces a demo of the various available
styles. This documentation uses the =svg= terminal (what gnuplot calls a
"backend"). So for the =svg= terminal, the various styles look like this:

#+begin_src gnuplot :results file link :session gnuplotlib-guide-gnuplot :exports both :file gnuplot-terminal-test.svg
test
#+end_src

#+RESULTS:
[[file:gnuplot-terminal-test.svg]]

So for instance if you plot something with =linespoints pt 4 dt 2 lc 7= you'll
get a red dashed line with square points. By default you'd be using one of the
interactive graphical terminals (=x11= or =qt=), which would have largely
similar styling.

Let's make a plot with some variable colors and point sizes:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

x = np.arange(21) - 10
gp.plot( ( x**2, np.abs(x)/2, x*50,
           dict(_with     = 'points pointtype 7 pointsize variable palette',
                tuplesize = 4) ),
         ( 3*x + 30,
           dict(_with = 'lines lw 3 lc "red" dashtype 2')),
         cbrange = '-600:600',)
#+END_SRC

#+RESULTS:
[[file:guide-17.svg]]

Let's now plot two datasets, one with variable color, the other with variable
size. We have =tuplesize=3= for both, but I'm passing in /one/ array. So the xy
domain is a regular grid of the appropriate size.

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

y,x = np.mgrid[-10:11, -8:2]
r   = np.sqrt(x*x + y*y)

gp.plot( nps.cat(x,r / 5.),
         tuplesize = 3,
         _with     = np.array(('points palette pt 7',
                               'points ps variable pt 6')),
         square = True)
#+END_SRC

#+RESULTS:
[[file:guide-18.svg]]

To see a sampling of all the availble line and point styles, run the =test=
command in =gnuplot=.

** Error bars
As before, the =gnuplot= documentation has the styling details:

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help xerrorbars'
gnuplot -e 'help yerrorbars'
gnuplot -e 'help xyerrorbars'
#+END_SRC

For brevity, I'm not including the contents of those help pages here. These tell
us how to specify errorbars: how many columns to pass in, what they mean, etc.
Example:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

x = np.arange(21) - 10
y = x**2 * 10 + 20
gp.plot( ( x + 1,
           y + 20,
           dict(_with = 'lines') ),

         ( x + 1,
           y + 20,
           x**2/80,
           x**2/4,
           dict(legend    = "using the 'x y xdelta ydelta' style",
                _with     = 'xyerrorbars',
                tuplesize = 4) ),
         ( x,
           y,
           x - x**2/80,
           x + x**2/40,
           y - x**2/4,
           y + x**2/4 / 2,
           dict(legend    = "using the 'x y xlow xhigh ylow yhigh' style",
                _with     = 'xyerrorbars',
                tuplesize = 6)),

         ( x, x*20 + 500., np.ones(x.shape) * 40,
           dict(legend    = "using the 'x y ydelta' style; constant ydelta",
                _with     = 'yerrorbars',
                tuplesize = 3)),

         xmin  = 1 + x[0],
         xmax  = 1 + x[-1],
         set = 'key box opaque')
#+END_SRC

#+RESULTS:
[[file:guide-19.svg]]

** Polar coordinates
See

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help polar'
#+END_SRC

Let's plot the [[https://en.wikipedia.org/wiki/Conchoid_of_de_Sluze][Conchoids of de Sluze]] using broadcasting:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

rho = np.linspace(0, 2*np.pi, 1000)  # dim=(  1000,)
a   = np.arange(-4,3)[:, np.newaxis] # dim=(7,1)

gp.plot( rho,
         1./np.cos(rho) + a*np.cos(rho), # broadcasted. dim=(7,1000)

         _with  = 'lines',
         set    = 'polar',
         square = True,
         yrange = [-5,5],
         legend = np.array(["a = {}".format(_) for _ in a.ravel()]) )
#+END_SRC

#+RESULTS:
[[file:guide-20.svg]]

** Labels
Docs:

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help labels'
gnuplot -e 'help set label'
#+END_SRC

Basic example:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

x = np.arange(5)
y = x+1
gp.plot(x, y,
        np.array( ['At x={}'.format(_) for _ in x], dtype=str),
        _with     = 'labels',
        tuplesize = 3,
        unset     = 'grid')
#+END_SRC

#+RESULTS:
[[file:guide-21.svg]]

More complex example:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

x = np.arange(5, dtype=float)
y = x+1
gp.plot(x, y,
        np.array( ['At x={}'.format(_) for _ in x], dtype=str),
        x / 4 * 90, # Angles, in degrees
        x,          # Mapped to colors
        _with     = 'labels rotate variable textcolor palette',
        tuplesize = 5,
        unset     = 'grid')
#+END_SRC

#+RESULTS:
[[file:guide-22.svg]]

** 3D plots
We can plot in 3D by passing in the plot option =_3d = True= or by calling
=plot3d()= instead of =plot()=. The latter is simply a convenience function to
set the =_3d= plot option. When plotting interactively, you can use the mouse to
rotate the plot, and look at it from different directions. Otherwise, the
viewing angle can be set with the =view= setting. See

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help set view'
#+END_SRC

In general there're lots of ways to plot images, meshes, contours, and so on.
Please see the =gnuplot= docs.

Let's plot a sphere:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

th = np.linspace(0,        np.pi*2, 30)
ph = np.linspace(-np.pi/2, np.pi*2, 30)[:,np.newaxis]
x  = (np.cos(ph) * np.cos(th))          .ravel()
y  = (np.cos(ph) * np.sin(th))          .ravel()
z  = (np.sin(ph) * np.ones( th.shape )) .ravel()

gp.plot3d( x, y, z,
           _with  = 'points',
           title  = 'sphere',
           square = True)
#+END_SRC

#+RESULTS:
[[file:guide-23.svg]]

A double-helix with variable color and variable pointsize

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

th    = np.linspace(0, 6*np.pi, 200)
z     = np.linspace(0, 5,       200)
size  = 0.5 + np.abs(np.cos(th))
color = np.sin(2*th)

gp.plot3d( np.cos(th) * nps.transpose(np.array((1,-1))),
           np.sin(th) * nps.transpose(np.array((1,-1))),
           z,
           size,
           color,
           legend = np.array(('spiral 1', 'spiral 2')),
           tuplesize = 5,
           _with = 'points pointsize variable pointtype 7 palette',
           title    = 'Double helix',
           squarexy = True)
#+END_SRC

#+RESULTS:
[[file:guide-24.svg]]

** 3D plots: meshes and contours
Both of these are plots of discrete 3D points. If we pass in exactly
=tuplesize-2= arrays, then we will use an implicit grid as our xy domain. Let's
create a mesh, and plot it:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot3d(z,
          squarexy = True)
#+END_SRC

#+RESULTS:
[[file:guide-25.svg]]

By default we plot with lines (meaning "wireframe" here) and points. Probably
just the wireframe would be nicer. And let's use variable colors to encode z.
And let's rotate it

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot3d(z, z,
          _with = 'lines palette',
          tuplesize = 4,
          set = ('view 50,30', 'view equal xy')
)
#+END_SRC

#+RESULTS:
[[file:guide-26.svg]]

Let's add some contours beneath

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot3d(z,
          _with = 'lines',
          set = ('view 60,30', 'view equal xy',
                 'contour base')
)
#+END_SRC

#+RESULTS:
[[file:guide-27.svg]]

When looking at contour plots I generally find them to be much more legible as a
top-down view, without the 3D component. So I usually do something like this
instead:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot3d(z,
          _with = np.array(('image', 'lines lw 2 nosurface')),
          legend = np.array(('surface', '')),
          set = ('key outside',
                 'view 0,0',
                 'view equal xy',
                 'contour base',
                 'cntrparam bspline',
                 'cntrparam levels 15'),
          unset=('grid', 'colorbox') )
#+END_SRC

#+RESULTS:
[[file:guide-28.svg]]

This is technically a 3D plot, but we're looking at it straight down, from the
top. The 3D plot processing is required to make contours. If we just want to
draw a colormapped grid, we can do this as a 2D plot. Let's do that, and also
use a grayscale colormap

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot(z,
        _with     = 'image pixels',
        tuplesize = 3,
        set       = 'palette grey',
        unset     = 'grid',
        square    = True)
#+END_SRC

#+RESULTS:
[[file:guide-29.svg]]

This is very useful for annotating images. Note that above I used the =image
pixels= instead of =image=. This is a compabilitity mode that is required to
work around a bug in github's .svg display. Usually you'd use the normal =image=
style.

Finally, in these few examples we used an implicit 2D grid as our domain. This
implicit grid is regular, and uses integers 0, 1, 2, ... in each dimension. What
if this grid isn't exactly what we want?

One method is to set up a transformation in the =using= directive. Here the
=image= style works properly only when a linear transformation is involved. With
a nonlinear transformation, the =pm3d= style is needed. It resamples the input
in a grid, so it's able to handle this.

Linear transformation:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot3d(z,
          _with = np.array(('image', 'lines nosurface')),
          set = ('view 0,0',
                 'view equal xy',
                 'contour base',
                 'cntrparam bspline',
                 'cntrparam levels 15'),
          using = '(100+$1+$2):($1-$2):3',
          ascii = True,
          unset = 'grid' )
#+END_SRC

#+RESULTS:
[[file:guide-30.svg]]

Nonlinear transformation:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 60
# shape (N+1,N+1,2). Linear values from -1 to 1
xy = nps.mv(np.mgrid[0:N+1,0:N+1], 0, -1)/(N/2.) - 1.
# shape (N+1,N+1)
r = nps.mag(xy)
z = np.exp(-r * 2.) * np.sin(xy[...,0]*6) * np.sin(xy[...,1]*6)

gp.plot3d(z,
          _with = 'pm3d',
          set = ('view 0,0',
                 'contour base',
                 'cntrparam bspline',
                 'cntrparam levels 15'),
          using = '($1*$1):2:3',
          ascii = True,
          unset = 'grid' )
#+END_SRC

#+RESULTS:
[[file:guide-31.svg]]

Some other techniques are possible using linked axes or passing in discrete
points, but I'm not going into those here.

What if we want multiple sets of contours in one plot? =gnuplot= doesn't
directly allow that. But you can use =multiplot= to draw the multiple contours
on top of one another, resulting in the plot we want:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import gnuplotlib as gp

x,y = np.meshgrid(np.linspace(-5,5,100),
                  np.linspace(-5,5,100))
z0 = np.sin(x) + y*y/8.
z1 = np.sin(x) + y*y/10.
z2 = np.sin(x) + y*y/12.

commonset = ( 'origin 0,0',
              'size 1,1',
              'view 60,20,1,1',
              'xrange [0:100]',
              'yrange [0:100]',
              'zrange [0:150]',
              'contour base' )
gp.plot3d( (z0, dict(_set = commonset + ('xyplane at 10',))),
           (z1, dict(_set = commonset + ('xyplane at 80',  'border 15'), unset=('ztics',))),
           (z2, dict(_set = commonset + ('xyplane at 150', 'border 15'), unset=('ztics',))),

           tuplesize=3,
           _with = np.array(('lines nosurface',
                             'labels boxed nosurface')),
           square=1,
           multiplot=True)
#+END_SRC

#+RESULTS:
[[file:guide-32.svg]]

** Histograms
=gnuplot= (and =gnuplotlib=) has support for histograms. So we can give it data,
and have it bin it for us. Or we can compute the histogram with =numpy=, and
just use =gnuplotlib= to plot the resulting bars. Let's sample a normal
distribution, and do it both ways. And let's compute the expected and observed
probability-density-functions, and plot those on top (as equations, evaluated by
=gnuplot=). With =gnuplotlib=:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp
 
from scipy.special import erf

N = 500
x = np.random.randn(N)
binwidth = 0.5

def equation_gaussian(N = 0, mean = 0, sigma = 0, title = ''):
    k = N * np.sqrt(2.*np.pi) * sigma * erf(binwidth/(2.*np.sqrt(2)*sigma))
    return '{k}*exp(-(x-{mean})*(x-{mean})/(2.*{sigma}*{sigma})) / sqrt(2.*pi*{sigma}*{sigma}) title "{title}" with lines lw 2'. \
        format(k     = k,
               mean  = mean,
               sigma = sigma,
               title = title)

gp.plot(x,
        histogram       = True,
        binwidth        = binwidth,
        equation_above  = \
          ( equation_gaussian( mean  = 0,
                               sigma = 1.0,
                               N     = N,
                               title = 'Expected PDF',),
            equation_gaussian( mean  = np.mean(x),
                               sigma = np.std(x),
                               N     = N,
                               title = 'Observed PDF',)))
#+END_SRC

#+RESULTS:
[[file:guide-33.svg]]

With =numpy=:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp
 
from scipy.special import erf

N = 500
x = np.random.randn(N)

hist, bin_edges = np.histogram(x, bins = 10)
binwidth = bin_edges[1] - bin_edges[0]

bin_centers = bin_edges[1:] - binwidth/2.

def equation_gaussian(N = 0, mean = 0, sigma = 0, title = ''):
    k = N * np.sqrt(2.*np.pi) * sigma * erf(binwidth/(2.*np.sqrt(2)*sigma))
    return '{k}*exp(-(x-{mean})*(x-{mean})/(2.*{sigma}*{sigma})) / sqrt(2.*pi*{sigma}*{sigma}) title "{title}" with lines lw 2'. \
        format(k     = k,
               mean  = mean,
               sigma = sigma,
               title = title)

gp.plot(bin_centers, hist,
        _with = 'boxes fill solid 1 border lt -1',
        _set  = 'boxwidth {}'.format(binwidth),
        equation_above  = \
          ( equation_gaussian( mean  = 0,
                               sigma = 1.0,
                               N     = N,
                               title = 'Expected PDF',),
            equation_gaussian( mean  = np.mean(x),
                               sigma = np.std(x),
                               N     = N,
                               title = 'Observed PDF',)))
#+END_SRC

#+RESULTS:
[[file:guide-34.svg]]

If we want multiple histograms drawn on top of one another, the styling should
be adjusted so that they both remain visible. For instance:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp
 
x1 = np.random.randn(1000)
x2 = np.random.randn(1000) / 2.0
binwidth = 0.2

gp.plot( nps.cat(x1,x2),
         histogram = True,
         binwidth  = binwidth,
         _with     = \
           np.array(('boxes fill transparent solid 0.3 border lt -1',
                     'boxes fill transparent pattern 1 border lt -1')))
#+END_SRC
#+RESULTS:
[[file:guide-35.svg]]

** Vector fields
Documentation in gnuplot available like this:

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help vectors'
#+END_SRC

The docs say that in 2D we want 4 columns: =x, y, xdelta, ydelta= and in 3D we
want 6 columns: =x, y, z, xdelta, ydelta, zdelta=. And we can have a variable
arrowstyle. A vectorfield in 2D:

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

# shape (2, 100)
xy = nps.clump( nps.cat( *np.meshgrid(np.linspace(-5,5,10),
                          np.linspace(-5,5,10)) ),
                n = -2 )
# each one has shape (100,)
x,y = xy

# shape (100,)
r = nps.mag( nps.transpose(xy) )


gp.plot( x, y, y/np.sqrt(r+0.1)*0.5, -x/np.sqrt(r+0.1)*0.5,
         tuplesize = 4,
         _with = 'vectors filled head',
         square=1)
#+END_SRC

#+RESULTS:
[[file:guide-36.svg]]

** Ellipses
Let's say we have a bunch of points with covariance matrices associated with
each one. We can plot each point and its 1-sigma ellipses. Let's do it two ways:

- with ellipses (possible only in 2D)
- with points sampled around the edge of the ellipse (possible in 2D and 3D)

The documentation for ellipses is available with

#+BEGIN_SRC shell :results none :exports code
gnuplot -e 'help ellipses'
#+END_SRC

The docs say that our options are

#+begin_example
      2 columns: x y
      3 columns: x y major_diam
      4 columns: x y major_diam minor_diam
      5 columns: x y major_diam minor_diam angle
#+end_example

Let's do it by plotting ellipses

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 8

# The center of my ellipses
# shape (2, N*N)
xy = nps.clump( nps.cat( *np.meshgrid(np.linspace(-5,5,N),
                                      np.linspace(-5,5,N)) ),
                n = -2 )
# each one has shape (N*N,)
x,y = xy

# I want repeatable random numbers
np.random.seed(0)

# Let's make up some covariances

th = np.random.random((N*N,))
v0 = nps.transpose(nps.cat(np.sin(th),  np.cos(th)))
v1 = nps.transpose(nps.cat(np.cos(th), -np.sin(th)))
l  = (np.random.random((N*N,2)) + 0.2) / 4
# shape (N*N, 2,2)
C = \
  nps.outer(v0*l[:,(0,)], v0*l[:,(0,)]) + \
  nps.outer(v1*l[:,(1,)], v1*l[:,(1,)])

# Got covariances C (let's pretend I didn't make them up). For gnuplot I need to
# compute the major and minor axis lengths, and the angle off horizontal.
# np.linalg.eig and np.arctan2 support broadcasting, so I can use them directly
l,v = np.linalg.eig(C)
major_diam = np.sqrt(l[:,0]) * 2.0
minor_diam = np.sqrt(l[:,1]) * 2.0
v_major = v[:,:,0]
angle = np.arctan2(v_major[:,1], v_major[:,0]) * 180./np.pi

gp.plot( ( x, y, major_diam, minor_diam, angle,
          dict(tuplesize = 5,
               _with = 'ellipses')),
         ( x, y,
          dict(_with = 'points ps 0.5')),
          _set = ('xrange [-6:6]', 'yrange [-6:6]'),
         square = True)
#+END_SRC

#+RESULTS:
[[file:guide-37.svg]]

And again, by sampling the angles, and plotting points. This is more work, but
can work in 3D too (we can remap a sphere). I'm using the same data here, so the
points should trace the same shape as the ellipses I just computed

#+BEGIN_SRC python :python python3 :results file link :session gnuplotlib-guide :exports both
import numpy      as np
import numpysane  as nps
import gnuplotlib as gp

N = 8

# The center of my ellipses
# shape (2, N*N)
xy = nps.clump( nps.cat( *np.meshgrid(np.linspace(-5,5,N),
                                      np.linspace(-5,5,N)) ),
                n = -2 )
# each one has shape (N*N,)
x,y = xy

# I want repeatable random numbers
np.random.seed(0)

# Let's make up some covariances

th = np.random.random((N*N,))
v0 = nps.transpose(nps.cat(np.sin(th),  np.cos(th)))
v1 = nps.transpose(nps.cat(np.cos(th), -np.sin(th)))
l  = (np.random.random((N*N,2)) + 0.2) / 4
# shape (N*N, 2,2)
C = \
  nps.outer(v0*l[:,(0,)], v0*l[:,(0,)]) + \
  nps.outer(v1*l[:,(1,)], v1*l[:,(1,)])

# Got covariances C (let's pretend I didn't make them up). I use this matrix to
# remap a circle, and plot the resulting points
l,v = np.linalg.eig(C)

# A = V sqrt(diag(l)) Vt
# numpy diag() function is weird, so I'm doing that myself here
A = nps.matmult(v * nps.dummy(np.sqrt(l), -2), nps.transpose(v))

th = np.linspace(0, 2.*np.pi, 20)
# shape (Nangles, 2)
v = nps.transpose(nps.cat(np.cos(th), np.sin(th)))
# shape (Nangles, N*N, 1, 2)
v = nps.matmult(nps.mv(v, -2, -4), A)
# shape (Nangles, N*N, 2)
xy_1sigma = nps.transpose(xy) + v[..., 0, :]
# shape (Nangles*N*N, 2)
xy_1sigma = nps.clump(xy_1sigma, n=2)

gp.plot( ( xy_1sigma,
          dict(tuplesize = -2,
               _with = 'dots')),
         ( x, y,
          dict(_with = 'points ps 0.5')),
          _set = ('xrange [-6:6]', 'yrange [-6:6]'),
         square = True)
#+END_SRC

#+RESULTS:
[[file:guide-38.svg]]

