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Commit 197127e8 authored by Lars Hubatsch's avatar Lars Hubatsch
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Adding radial average for simulations.

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%% Cell type:markdown id: tags:
### FRAP geometries
%% Cell type:code id: tags:
``` python
from fem_sol import frap_solver
import matplotlib.pyplot as plt
import numpy as np
```
%% Cell type:code id: tags:
``` python
font = {'family' : 'normal',
'weight' : 'normal',
'size' : 12}
import matplotlib
matplotlib.rc('font', **font)
def make_graph_pretty(xlab, ylab, loc=0, markerfirst=True, handlelength=None):
color1 = 'black'#'darkorange'
color2 = (0, 0, 0)
color2 = (1, 1, 1)
ax = plt.gca()
ax.tick_params(axis='x', colors=color1, which='both')
ax.tick_params(axis='y', colors=color1, which='both')
plt.xlabel(xlab, color=color1)
plt.ylabel(ylab, color=color1)
ax.spines['left'].set_color(color1)
ax.spines['bottom'].set_color(color1)
# Hide the right and top spines
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.set_facecolor(color2)
plt.gcf().subplots_adjust(bottom=0.17, left=0.15)
plt.legend(frameon=False, loc=loc, labelspacing=0.1,
markerfirst=markerfirst, handlelength=handlelength)
```
%% Cell type:code id: tags:
``` python
m = ['Meshes/multi_drop_gauss.xml', 'Meshes/multi_drop_gauss_med.xml',
'Meshes/multi_drop_gauss_far.xml']
point_lists = [[[4, 4.5, 0.5], [4, 3.5, 0.5], [3.5, 4, 0.5], [4.5, 4, 0.5]],
[[4, 5, 0.5], [4, 3, 0.5], [3, 4, 0.5], [5, 4, 0.5]],
[[4, 5.5, 0.5], [4, 2.5, 0.5], [2.5, 4, 0.5], [5.5, 4, 0.5]]]
f_i = []
for j in range(len(m)):
f = frap_solver([4, 4, 0.5], m[j], name=str(j), point_list=point_lists[j],
T=50, phi_tot_int=0.99, phi_tot_ext=0.01)
f.solve_frap()
f_i.append(f)
```
%% Cell type:code id: tags:
``` python
import fem_utils
alphas = np.linspace(0,2*np.pi, 100)
ns = np.c_[np.cos(alphas), np.sin(alphas), np.zeros(len(alphas))]
eps = np.linspace(0, 0.25, 100)
profs = []
for i in range(5):
values=[]
fs = fem_utils.load_time_point(f_i[0].name+'t_p_'+str(i)+'.h5',
f_i[0].mesh)
for n in ns:
# values.append([f_i[0].fs[i]([4, 4, 0.5]+e*n) for e in eps])
values.append([fs([4, 4, 0.5]+e*n) for e in eps])
profs.append(np.mean(np.transpose(values), 1))
```
%% Cell type:code id: tags:
``` python
plt.plot(np.transpose(profs))
```
%% Cell type:code id: tags:
``` python
for i in range(len(cs[0])):
plt.plot([np.mean(x[1:49])/0.8 for x in cs[0][0:i]], label='dist=0.5')
plt.plot([np.mean(x[1:49])/0.8 for x in cs[1][0:i]], label='dist=1')
plt.plot([np.mean(x[1:49])/0.8 for x in cs[2][0:i]], label='dist=1.5')
plt.plot(range(0, 100), np.ones(100), linestyle='--', color='k')
plt.ylim((0, 1.1))
plt.xlim((0, 100))
make_graph_pretty('t (a.u.)', 'intensity (a.u)', loc=4)
# plt.savefig('img_'+str(i)+'.png', dpi=300)
plt.show()
```
%% Cell type:code id: tags:
``` python
f_0 = frap_solver([4, 4, 0.5], 'Meshes/single_drop_coverslip.xml',
name='FRAP_coverslip', T=50, phi_tot_int=0.99,
phi_tot_ext=0.01)
f_0.solve_frap()
f_1 = frap_solver([4, 4, 1.5], 'Meshes/single_drop_1_5.xml',
name='FRAP_symmetric', T=50, phi_tot_int=0.99,
phi_tot_ext=0.01)
f_1.solve_frap()
f_2 = frap_solver([4, 4, 4], 'Meshes/single_drop_symmetric.xml',
name='FRAP_symmetric', T=50, phi_tot_int=0.99,
phi_tot_ext=0.01)
f_2.solve_frap()
```
%% Cell type:code id: tags:
``` python
f_3 = frap_solver([4, 4, 0.5], 'Meshes/single_drop_coverslip.xml',
name='FRAP_symmetric', T=50, G_in=0.1, G_out=0.99/0.9,
phi_tot_int=0.9, phi_tot_ext=0.1)
f_3.solve_frap()
f_4 = frap_solver([4, 4, 1.5], 'Meshes/single_drop_1_5.xml',
name='FRAP_symmetric', T=50, G_in=0.1, G_out=0.99/0.9,
phi_tot_int=0.9, phi_tot_ext=0.1)
f_4.solve_frap()
f_5 = frap_solver([4, 4, 4], 'Meshes/single_drop_symmetric.xml',
name='FRAP_symmetric', T=50, G_in=0.1, G_out=0.99/0.9,
phi_tot_int=0.9, phi_tot_ext=0.1)
f_5.solve_frap()
```
%% Cell type:code id: tags:
``` python
plt.plot([np.mean(x[1:49])/0.99 for x in f_0.cs], label='dist=0.5')
plt.plot([np.mean(x[1:49])/0.99 for x in f_1.cs], label='dist=1.5')
plt.plot([np.mean(x[1:49])/0.99 for x in f_2.cs], label='dist=4')
plt.plot([np.mean(x[1:49])/0.9 for x in f_3.cs], label='dist=0.5, G_out=10')
plt.plot([np.mean(x[1:49])/0.9 for x in f_4.cs], label='dist=1.5, G_out=10')
plt.plot([np.mean(x[1:49])/0.9 for x in f_5.cs], label='dist=4, G_out=10')
plt.plot(range(0, 50), np.ones(50), linestyle='--', color='k')
plt.ylim((0, 1.1))
plt.xlim((0, 50))
make_graph_pretty('t (a.u.)', 'intensity (a.u)', loc=4)
```
%% Cell type:code id: tags:
``` python
plt.plot(np.transpose(f_3.cs))
```
%% Cell type:code id: tags:
``` python
```
......
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