Find contour lines from matplotlib.pyplot.contour()

contour, matplotlib, numpy, python, spatial

Solution

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()

Problem

I'm trying to find (but not draw!) contour lines for some data: ``` from pprint import pprint import matplotlib.pyplot z = [[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]] cn = matplotlib.pyplot.contour(z) ``` I know `cn` contains the contour lines I want, but I can't seem to get to them. I've tried several things: ``` print dir(cn) pprint(cn.collections[0]) print dir(cn.collections[0]) pprint(cn.collections[0].figure) print dir(cn.collections[0].figure) ``` to no avail. I know `cn` is a `ContourSet`, and `cn.collections` is an array of `LineCollection`s. I would think a `LineCollection` is an array of line segments, but I can't figure out how to extract those segments. My ultimate goal is to create a KML file that plots data on a world map, and the contours for that data as well. However, since some of my data points are close together, and others are far away, I need the actual polygons (linestrings) that make up the contours, not just a rasterized image of the contours. I'm somewhat surprised `qhull` doesn't do something like this. Using Mathematica's `ListContourPlot` and then exporting as SVG works, but I want to use something open source. I can't use the well-known CONREC algorithm because my data isn't on a mesh (there aren't always multiple y values for a given x value, and vice versa). The solution doesn't have to python, but does have to be open source and runnable on Linux.

Original source