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import os
import mayavi.mlab as mayavi
from brian2 import *
def find_max_coordinates(morpho, current_max):
max_x, max_y, max_z = np.max(np.abs(morpho.coordinates), axis=0)
new_max = (max([max_x, current_max[0]]),
max([max_y, current_max[1]]),
max([max_z, current_max[2]]))
for child in morpho.children:
new_max = find_max_coordinates(child, new_max)
return new_max
DARKRED = (0.5450980392156862, 0.0, 0.0)
DARKBLUE = (0.0, 0.0, 0.5450980392156862)
def plot_morphology3D(morpho, color_switch=False, show_compartments=False):
if isinstance(morpho, Soma):
mayavi.points3d(morpho.x/um, morpho.y/um, morpho.z/um, morpho.diameter/um,
color=DARKRED, scale_factor=1.0, resolution=16)
else:
coords = morpho.coordinates
if color_switch:
color = DARKBLUE
else:
color = DARKRED
mayavi.plot3d(coords[:, 0]/um, coords[:, 1]/um, coords[:, 2]/um, color=color,
tube_radius=1)
# dots at the center of the compartments
if show_compartments:
mayavi.points3d(coords[:, 0]/um, coords[:, 1]/um, coords[:, 2]/um,
np.ones(coords.shape[0]), color=color, scale_factor=1,
transparent=0.25)
for child in morpho.children:
plot_morphology3D(child, color_switch=not color_switch)
def plot_morphology2D(morpho, axis, color_switch=False):
if isinstance(morpho, Soma):
ax.plot(morpho.x/um, morpho.y/um, 'o', color='darkred',
ms=morpho.diameter/um, mec='none')
else:
coords = morpho.coordinates
if color_switch:
color = 'darkblue'
else:
color = 'darkred'
ax.plot(coords[:, 0]/um, coords[:, 1]/um, color='black',
lw=2)
# dots at the center of the compartments
ax.plot(morpho.x/um, morpho.y/um, 'o', color=color,
mec='none', alpha=0.75)
for child in morpho.children:
plot_morphology2D(child, axis=axis, color_switch=not color_switch)
if __name__ == '__main__':
dirname = os.path.dirname(__file__)
PATH = os.path.join(dirname, '..', '..', '..', 'docs_sphinx', 'user', 'images')
# Construct binary tree according to Rall's formula
diameter = 32*um
length = 80*um
morpho = Soma(diameter=diameter)
endpoints = {morpho}
for depth in range(1, 10):
diameter /= 2.**(1./3.)
length /= 2.**(2./3.)
new_endpoints = set()
for endpoint in endpoints:
new_L = Cylinder(n=max([1, int(length/(5*um))]), diameter=diameter,
length=length)
new_R = Cylinder(n=max([1, int(length/(5*um))]), diameter=diameter,
length=length)
new_endpoints.add(new_L)
new_endpoints.add(new_R)
endpoint.L = new_L
endpoint.R = new_R
endpoints = new_endpoints
print('total number of sections and compartments', morpho.n_sections, len(morpho))
morpho_with_coords = morpho.generate_coordinates()
ax = plt.subplot(111)
plot_morphology2D(morpho_with_coords, ax)
plt.axis('equal')
plt.xlabel('x ($\mu$ m)')
plt.ylabel('y ($\mu$ m)')
plt.savefig(os.path.join(PATH, 'morphology_deterministic_coords.png'))
print('be careful, this plotting takes a long time')
for title, noise_sec, noise_comp in [('section', 25, 0),
('section_compartment', 25, 15)]:
for idx in range(3):
fig = mayavi.figure(bgcolor=(0.95, 0.95, 0.95))
print(idx)
morpho_with_coords = morpho.generate_coordinates(section_randomness=noise_sec,
compartment_randomness=noise_comp)
plot_morphology3D(morpho_with_coords)
cam = fig.scene.camera
cam.zoom(1.1)
mayavi.draw()
mayavi.savefig(os.path.join(PATH, 'morphology_random_%s_%d.png' % (title, idx+1)))
mayavi.close()
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