python KDE get contours and paths into specific json format leaflet-friendly

Question

I am doing a Kernel Density Estimation in Python and getting the contours and paths as shown below. (here is my sample data: https://pastebin.com/193PUhQf).

from numpy import *
from math import *
import numpy as np
import matplotlib.pyplot as plt
from scipy import stats

x_2d = []
y_2d = []
data = {}
data['nodes'] = []

# here is the sample data:
# https://pastebin.com/193PUhQf
X =  [.....]

for Picker in xrange(0, len(X)):
    x_2d.append(X[Picker][0])
    y_2d.append(X[Picker][1])

# convert to arrays
m1 = np.array([x_2d])
m2 = np.array([y_2d])

x_min = m1.min() - 30
x_max = m1.max() + 30
y_min = m2.min() - 30
y_max = m2.max() + 30

x, y = np.mgrid[x_min:x_max:200j, y_min:y_max:200j]
positions = np.vstack([x.ravel(), y.ravel()])
values = np.vstack([m1, m2])

kde = stats.gaussian_kde(values)

z = np.reshape(kde(positions).T, x.shape)

fig = plt.figure(2, dpi=200)
ax = fig.add_subplot(111)

pc = ax.pcolor(x, y, z)
cb = plt.colorbar(pc)
cb.ax.set_ylabel('Probability density')

c_s = plt.contour(x, y, z, 20, linewidths=1, colors='k')
ax.plot(m1, m2, 'o', mfc='w', mec='k')
ax.set_title("My Title", fontsize='medium')
plt.savefig("kde.png", dpi=200)
plt.show()

There is a similar way to get the contours using R, which is described here: http://bl.ocks.org/diegovalle/5166482

Question: how can I achieve the same output using my python script or as a start point? the desired output should be like contours_tj.json which can be used by leaflet.js lib.

UPDATE:

My input data structure is composed of three columns, comma separated:

1. first one is the X value
2. second one is the Y value
3. third one is the ID of my data, it has no numerical value, it is simply an identifier of the data point.

Update 2:

Question, if simply put, is that I want the same output as in the above link using my input file which is in numpy array format.

update 3:

my input data structure is of list type:

print type(X)

<type 'list'>

and here are the first few lines:

print X[0:5]

[[10.800584, 11.446064, 4478597], [10.576840,11.020229, 4644503], [11.434276,10.790881, 5570870], [11.156718,11.034633, 6500333], [11.054956,11.100243, 6513301]]

Answer 1

geojsoncontour is a python library to convert matplotlib contours to geojson

geojsoncontour.contour_to_geojson requires a contour_levels argument. The levels in pyplot.contour are chosen automatically, but you can access them with c_s._levels

So, for your example you could do:

import geojsoncontour
# your code here

c_s = plt.contour(x, y, z, 20, linewidths=1, colors='k')

# Convert matplotlib contour to geojson
geojsoncontour.contour_to_geojson(
    contour=c_s,
    geojson_filepath='out.geojson',
    contour_levels=c_s._levels,
    ndigits=3,
    unit='m'
)