Python: find contour lines from matplotlib.pyplot.contour()
You can get the vertices back by looping over collections and paths and using the iter_segments()
method of matplotlib.path.Path
.
Here's a function that returns the vertices as a set of nested lists of contour lines, contour sections and arrays of x,y vertices:
import numpy as np
def get_contour_verts(cn):
contours = []
# for each contour line
for cc in cn.collections:
paths = []
# for each separate section of the contour line
for pp in cc.get_paths():
xy = []
# for each segment of that section
for vv in pp.iter_segments():
xy.append(vv[0])
paths.append(np.vstack(xy))
contours.append(paths)
return contours
Edit:
It's also possible to compute the contours without plotting anything using the undocumented matplotlib._cntr
C module:
from matplotlib import pyplot as plt
from matplotlib import _cntr as cntr
z = np.array([[0.350087, 0.0590954, 0.002165],
[0.144522, 0.885409, 0.378515],
[0.027956, 0.777996, 0.602663],
[0.138367, 0.182499, 0.460879],
[0.357434, 0.297271, 0.587715]])
x, y = np.mgrid[:z.shape[0], :z.shape[1]]
c = cntr.Cntr(x, y, z)
# trace a contour at z == 0.5
res = c.trace(0.5)
# result is a list of arrays of vertices and path codes
# (see docs for matplotlib.path.Path)
nseg = len(res) // 2
segments, codes = res[:nseg], res[nseg:]
fig, ax = plt.subplots(1, 1)
img = ax.imshow(z.T, origin='lower')
plt.colorbar(img)
ax.hold(True)
p = plt.Polygon(segments[0], fill=False, color='w')
ax.add_artist(p)
plt.show()
I would suggest to use scikit-image find_contours
It returns a list of contours for a given level.
matplotlib._cntr
has been removed from matplotlib since v2.2 (see here).