Contours from a csv file

#!/usr/user/local/bin/python2.7
import os
from scipy.interpolate import griddata
from numpy import genfromtxt
import matplotlib.pyplot as plt
import numpy as np
from shapely.geometry import mapping, Polygon, LineString, MultiLineString
import fiona

path = os.getcwd()

my_data = genfromtxt( path + '/WaterTable.csv', delimiter=',')

z = my_data[1:,2:3]
x = my_data[1:,0]
y = my_data[1:,1]

xmax = max(x)
xmin = min(x)
ymax = max(y)
ymin = min(y)

xi = np.linspace(xmin, xmax, 70)

yi = np.linspace(ymin, ymax, 70)

# grid the data.

zi = griddata((x, y), z.ravel(), (xi[None,:], yi[:,None]), method='cubic')

print(zi)

print(zi.shape)
print(xi.shape)
print(yi.shape)

# contour the gridded data

cs = plt.contour(xi,yi,zi,20) #,linewidths=2,colors='k')
#cs = plt.contourf(xi,yi,zi,20) #,cmap=plt.cm.jet)
plt.colorbar() # draw colorbar
# plot data points.
plt.scatter(x,y,marker='o',c='b',s=5)
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
#plt.title('griddata test (%d points)') # % npts)
plt.show()

#def get_contour_verts(cn):
#   contours = []
#   # for each contour line
#   for cc in cs.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

lenvar = (len(cs.collections))   #number of contours

print(lenvar)
print(cs.collections)

lines = []  # Empty list for contour sections

for i in range(lenvar):
    n = i
    p = cs.collections[i].get_paths()[0]
    v = p.vertices # getting the individual verticies as a numpy.ndarray
    x = v[:,0] #takes first column
    y = v[:,1] #takes second column
    line = LineString([(i[0], i[1]) for i in zip(x,y)])  #Defines Linestring
    #varnam = ("contour_%d" %n)
    lines.append(line) #appends to list

schema = {'geometry': 'LineString','properties': {'id': 'int'}}  # sets up parameter for shapefile

with fiona.open('ConShp.shp', 'w', 'ESRI Shapefile', schema) as c:  # creates new file to be written to
    for j in range(len(lines)):
        l = (lines[j])   # creates variable
        print(l)
        print(type(l))
        c.write({'geometry': mapping(l),'properties': {'id': j},})

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