def run_custom():
num_points = 10
resolution = 96
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
# k == Diffusion rate.
mesh_wrapper.k = 6.0
run_simulation(num_points, mesh_wrapper, num_steps=500, print_frequency=20)
def run_custom():
num_points = 10
resolution = 96
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
# k == Diffusion rate.
mesh_wrapper.k = 6.0
run_simulation(num_points, mesh_wrapper, num_steps=500,
print_frequency=20)
def plot_custom():
X_CENTER1 = 0.0
X_CENTER2 = 100.0
X_CENTER3 = 200.0
X_CENTER4 = 300.0
MAX_RADIUS = 15.0
def in_box(value, center):
delta = value - center
if np.allclose(delta, MAX_RADIUS) or np.allclose(delta, -MAX_RADIUS):
return True
return -MAX_RADIUS <= delta <= MAX_RADIUS
def in_x_y_box(point, x_center):
return in_box(point.x, x_center) and in_box(point.y, 0.0)
def custom_color_function(point):
if np.allclose(point.z, 50.0):
return 'b'
if np.allclose(point.z, 0) or point.z >= 0:
if in_x_y_box(point, X_CENTER1) or in_x_y_box(point, X_CENTER3):
return 'r'
elif in_x_y_box(point, X_CENTER2) or in_x_y_box(point, X_CENTER4):
return 'y'
return 'g'
resolution = 96
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
mesh_wrapper.k = 6.0
x = mesh_wrapper.all_vertices[:, 0]
y = mesh_wrapper.all_vertices[:, 1]
z = mesh_wrapper.all_vertices[:, 2]
# Consider putting this into `plot_simulation`.
plot_boundary = PlotBoundary(np.min(x), np.max(x), np.min(y), np.max(y),
np.min(z), np.max(z))
plot_simulation(10,
mesh_wrapper,
plot_boundary,
color_function=custom_color_function,
num_frames=500,
print_frequency=20,
show_mesh=True,
filename='plots/10points_500steps_bigger_k.gif')
def test_accuracy_on_face(mesh_wrapper=None, num_steps=1000):
if mesh_wrapper is None:
resolution = 96
serialized_mesh_filename = ('data/serialized_mesh_res_%d.npz' %
(resolution,))
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
point = Point(mesh_wrapper)
for i in xrange(num_steps):
point.move()
errors = [error_off_plane(mesh_wrapper.faces[face_id], pt)
for face_id, pt in point.values]
print 'Max Error after %d steps' % num_steps
print np.max(np.abs(errors))
def plot_custom():
X_CENTER1 = 0.0
X_CENTER2 = 100.0
X_CENTER3 = 200.0
X_CENTER4 = 300.0
MAX_RADIUS = 15.0
def in_box(value, center):
delta = value - center
if np.allclose(delta, MAX_RADIUS) or np.allclose(delta, - MAX_RADIUS):
return True
return -MAX_RADIUS <= delta <= MAX_RADIUS
def in_x_y_box(point, x_center):
return in_box(point.x, x_center) and in_box(point.y, 0.0)
def custom_color_function(point):
if np.allclose(point.z, 50.0):
return 'b'
if np.allclose(point.z, 0) or point.z >= 0:
if in_x_y_box(point, X_CENTER1) or in_x_y_box(point, X_CENTER3):
return 'r'
elif in_x_y_box(point, X_CENTER2) or in_x_y_box(point, X_CENTER4):
return 'y'
return 'g'
resolution = 96
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
mesh_wrapper.k = 6.0
x = mesh_wrapper.all_vertices[:, 0]
y = mesh_wrapper.all_vertices[:, 1]
z = mesh_wrapper.all_vertices[:, 2]
# Consider putting this into `plot_simulation`.
plot_boundary = PlotBoundary(np.min(x), np.max(x),
np.min(y), np.max(y),
np.min(z), np.max(z))
plot_simulation(10, mesh_wrapper, plot_boundary,
color_function=custom_color_function,
num_frames=500, print_frequency=20, show_mesh=True,
filename='plots/10points_500steps_bigger_k.gif')
def test_accuracy_on_face(mesh_wrapper=None, num_steps=1000):
if mesh_wrapper is None:
resolution = 96
serialized_mesh_filename = ('data/serialized_mesh_res_%d.npz' %
(resolution, ))
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
point = Point(mesh_wrapper)
for i in xrange(num_steps):
point.move()
errors = [
error_off_plane(mesh_wrapper.faces[face_id], pt)
for face_id, pt in point.values
]
print 'Max Error after %d steps' % num_steps
print np.max(np.abs(errors))
def save_serialized_mesh():
print 'Importing dolfin, takes a bit of time...'
import dolfin
print 'Done importing dolfin.'
resolution = 96
mesh_full_filename = 'data/mesh_res_%d_full.xml' % resolution
mesh_3d = dolfin.Mesh(mesh_full_filename)
# NOTE: This is temporary. These are parameters of the mesh (when it was
# created in full_dendrite_mesh.py) and we should package them in a
# different way.
SCALE_FACTOR = 50.0
STARTING_X = SCALE_FACTOR * 0.0
STARTING_Y = SCALE_FACTOR * 0.0
STARTING_Z = SCALE_FACTOR * 1.0
STARTING_K = SCALE_FACTOR * 0.01
initial_point = np.array((STARTING_X, STARTING_Y, STARTING_Z))
mesh_wrapper = Mesh.from_mesh(mesh_3d, initial_point, STARTING_K)
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper.serialize_mesh(serialized_mesh_filename)
def save_serialized_mesh():
print 'Importing dolfin, takes a bit of time...'
import dolfin
print 'Done importing dolfin.'
resolution = 96
mesh_full_filename = 'data/mesh_res_%d_full.xml' % resolution
mesh_3d = dolfin.Mesh(mesh_full_filename)
# NOTE: This is temporary. These are parameters of the mesh (when it was
# created in full_dendrite_mesh.py) and we should package them in a
# different way.
SCALE_FACTOR = 50.0
STARTING_X = SCALE_FACTOR * 0.0
STARTING_Y = SCALE_FACTOR * 0.0
STARTING_Z = SCALE_FACTOR * 1.0
STARTING_K = SCALE_FACTOR * 0.01
initial_point = np.array((STARTING_X, STARTING_Y, STARTING_Z))
mesh_wrapper = Mesh.from_mesh(mesh_3d, initial_point, STARTING_K)
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper.serialize_mesh(serialized_mesh_filename)
from mpl_toolkits.mplot3d import Axes3D # Needs to be imported for 3D
from matplotlib import cm
import matplotlib.pyplot as plt
import numpy as np
from particle_diffusion_on_mesh import Mesh
resolution = 96
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
x = mesh_wrapper.all_vertices[:, 0]
y = mesh_wrapper.all_vertices[:, 1]
z = mesh_wrapper.all_vertices[:, 2]
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.plot_trisurf(x,
y,
z,
triangles=mesh_wrapper.triangles,
color=(0, 0, 0, 0),
edgecolor='Gray',
linewidth=0.05)
plt.show()
# http://stackoverflow.com/questions/7965743/
# python-matplotlib-setting-aspect-ratio
from mpl_toolkits.mplot3d import Axes3D # Needs to be imported for 3D
from matplotlib import cm
import matplotlib.pyplot as plt
import numpy as np
from particle_diffusion_on_mesh import Mesh
resolution = 96
serialized_mesh_filename = 'data/serialized_mesh_res_%d.npz' % resolution
mesh_wrapper = Mesh.from_file(serialized_mesh_filename)
x = mesh_wrapper.all_vertices[:, 0]
y = mesh_wrapper.all_vertices[:, 1]
z = mesh_wrapper.all_vertices[:, 2]
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.plot_trisurf(x, y, z, triangles=mesh_wrapper.triangles,
color=(0, 0, 0, 0), edgecolor='Gray', linewidth=0.05)
plt.show()
# http://stackoverflow.com/questions/7965743/
# python-matplotlib-setting-aspect-ratio