How to fit result of matplotlib.pyplot.contourf into circle?

Question

Here is my code to plot some data:

from scipy.interpolate import griddata
from numpy import linspace
import matplotlib.pyplot as plt
meanR = [9.95184937,   9.87947708,   9.87628496,   9.78414422,
         9.79365258,   9.96168969,   9.87537519,   9.74536093,
        10.16686878,  10.04425475,  10.10444126,  10.2917172 ,
        10.16745917,  10.0235203 ,   9.89914   ,  10.11263505,
         9.99756449,  10.17861254,  10.04704248]
koord = [[1,4],[3,4],[1,3],[3,3],[2,3],[1,2],[3,2],[2,2],[1,1],[3,1],[2,1],[1,0],[3,0],[0,3],[4,3],[0,2],[4,2],[0,1],[4,1]]
x,y=[],[]
for i in koord:
    x.append(i[0])
    y.append(i[1])
z = meanR
xi = linspace(-2,6,300);
yi = linspace(-2,6,300);
zi = griddata((x, y), z, (xi[None,:], yi[:,None]), method='cubic')
CS = plt.contourf(xi,yi,zi,15,cmap=plt.cm.jet)
plt.scatter(x,y,marker='o',c='b',s=15)
plt.xlim(min(x),max(x))
plt.ylim(min(y),max(y))
plt.show()

In result we have:

enter image description here

How can I inscribe it in a circle? something like this enter image description here

you can try using polar coordinates. [This](http://stackoverflow.com/a/10838501/1860757) can give you some hint — Francesco Montesano, Mar 12 '13 at 12:42
can you give some context for your problem? what do you mean to inscribe it in a circle? you have polar data or you need to cut the plot image outside the cirle area? — EnricoGiampieri, Mar 14 '13 at 20:04
I need to plot topography of EEG. So it is projection of sphere on plane. But plot it inside the circle without lost any information will be great — sviter, Mar 15 '13 at 05:58

Robbert · Accepted Answer · 2013-03-15T13:13:06.503

Because you don't seem to need any axes you can also use a normal projection, remove the axes and draw a circle. I had some fun and added some bonus ears, a nose and a color bar. I annotated the code, I hope it is clear.

EEG

from __future__ import print_function
from __future__ import division
from __future__ import absolute_import

import scipy.interpolate
import numpy
import matplotlib 
import matplotlib.pyplot as plt

# close old plots
plt.close("all")

# some parameters
N = 300             # number of points for interpolation
xy_center = [2,2]   # center of the plot
radius = 2          # radius

# mostly original code
meanR = [9.95184937,   9.87947708,   9.87628496,   9.78414422,
         9.79365258,   9.96168969,   9.87537519,   9.74536093,
        10.16686878,  10.04425475,  10.10444126,  10.2917172 ,
        10.16745917,  10.0235203 ,   9.89914   ,  10.11263505,
         9.99756449,  10.17861254,  10.04704248]

koord = [[1,4],[3,4],[1,3],[3,3],[2,3],[1,2],[3,2],[2,2],[1,1],[3,1],[2,1],[1,0],[3,0],[0,3],[4,3],[0,2],[4,2],[0,1],[4,1]]

x,y = [],[]
for i in koord:
    x.append(i[0])
    y.append(i[1])

z = meanR

xi = numpy.linspace(-2, 6, N)
yi = numpy.linspace(-2, 6, N)
zi = scipy.interpolate.griddata((x, y), z, (xi[None,:], yi[:,None]), method='cubic')

# set points > radius to not-a-number. They will not be plotted.
# the dr/2 makes the edges a bit smoother
dr = xi[1] - xi[0]
for i in range(N):
    for j in range(N):
        r = numpy.sqrt((xi[i] - xy_center[0])**2 + (yi[j] - xy_center[1])**2)
        if (r - dr/2) > radius:
            zi[j,i] = "nan"

# make figure
fig = plt.figure()

# set aspect = 1 to make it a circle
ax = fig.add_subplot(111, aspect = 1)

# use different number of levels for the fill and the lines
CS = ax.contourf(xi, yi, zi, 60, cmap = plt.cm.jet, zorder = 1)
ax.contour(xi, yi, zi, 15, colors = "grey", zorder = 2)

# make a color bar
cbar = fig.colorbar(CS, ax=ax)

# add the data points
# I guess there are no data points outside the head...
ax.scatter(x, y, marker = 'o', c = 'b', s = 15, zorder = 3)

# draw a circle
# change the linewidth to hide the 
circle = matplotlib.patches.Circle(xy = xy_center, radius = radius, edgecolor = "k", facecolor = "none")
ax.add_patch(circle)

# make the axis invisible 
for loc, spine in ax.spines.iteritems():
    # use ax.spines.items() in Python 3
    spine.set_linewidth(0)

# remove the ticks
ax.set_xticks([])
ax.set_yticks([])

# Add some body parts. Hide unwanted parts by setting the zorder low
# add two ears
circle = matplotlib.patches.Ellipse(xy = [0,2], width = 0.5, height = 1.0, angle = 0, edgecolor = "k", facecolor = "w", zorder = 0)
ax.add_patch(circle)
circle = matplotlib.patches.Ellipse(xy = [4,2], width = 0.5, height = 1.0, angle = 0, edgecolor = "k", facecolor = "w", zorder = 0)
ax.add_patch(circle)
# add a nose
xy = [[1.5,3], [2,4.5],[2.5,3]]
polygon = matplotlib.patches.Polygon(xy = xy, facecolor = "w", zorder = 0)
ax.add_patch(polygon) 

# set axes limits
ax.set_xlim(-0.5, 4.5)
ax.set_ylim(-0.5, 4.5)

plt.show()

Francesco Montesano · Answer 2 · 2013-03-12T13:33:51.787

If you replace the part where you do the plotting with:

fig = plt.figure()
ax = fig.add_subplot(111, polar=True)
CS = ax.contourf(xi,yi,zi,15,cmap=plt.cm.jet)
ax.scatter(x,y,marker='o',c='b',s=15)
ax.set_xlim(min(x),max(x))
ax.set_ylim(min(y),max(y))

you get this enter image description here

To get what you want, you have to rescale the x, y, xi, yi such that the image is centered in zero. You might also need to convert to polar coordinates. Now I don't have time to provide more info, but I hope that this helps you in getting started

How to fit result of matplotlib.pyplot.contourf into circle?

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