import tubetk
from tubetk.numpy import tubes_from_file

import os
filepath = os.path.join(os.path.dirname(tubetk.__file__),
                        '..', '..', '..',
                        'MIDAS_Data', 'VascularNetwork.tre')

tubes = tubes_from_file(filepath)

print(type(tubes))
print(tubes.dtype)

print(len(tubes))
print(tubes.shape)

print('Entire points 0, 2:')
print(tubes[:4:2])

print('\nPosition of points 0, 2')
print(tubes['Position'][:4:2])

%pylab inline
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt

fig = plt.figure(figsize=(16, 6))

ax = fig.add_subplot(1, 2, 1)
ax.hist(tubes['Radius'], bins=100)
ax.set_xlabel('Radius')
ax.set_ylabel('Count')

ax = fig.add_subplot(1, 2, 2, projection='3d')
subsample = 100
position = tubes['Position'][::subsample]
radius = tubes['Radius'][::subsample]
ax.scatter(position[:,0], position[:,1], position[:,2], s=(2*radius)**2)
ax.set_title('Point Positions')
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z');