Cosmetic changes.

9c0f4b3a · Lars Hubatsch · 82aa51be · 9c0f4b3a
Commit 9c0f4b3a authored 4 years ago by Lars Hubatsch
--- a/Half_Frap_Phi_u.ipynb
+++ b/Half_Frap_Phi_u.ipynb
 {
 "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### FRAP geometries"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": null,
@@ -108,6 +115,15 @@
    "make_graph_pretty('t (a.u.)', 'intensity (a.u)', loc=4)"
   ]
  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "f_coverslip.cs"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": null,

+%% 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=3)
    f.solve_frap()
    f_i.append(f)
 ```

 %% 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_coverslip = frap_solver([4, 4, 0.5], 'Meshes/single_drop_coverslip.xml',
                          name='FRAP_coverslip', T=300)
 f_coverslip.solve_frap()
 f_symmetric = frap_solver([4, 4, 4], 'Meshes/single_drop_symmetric.xml',
                          name='FRAP_symmetric', T=300)
 f_symmetric.solve_frap()
 ```

 %% Cell type:code id: tags:

 ``` python
 plt.plot([np.mean(x[1:49])/0.8 for x in f_coverslip.cs], label='coverslip')
 plt.plot([np.mean(x[1:49])/0.8 for x in f_symmetric.cs], label='symmetric')
 plt.plot(range(0, 300), np.ones(300), linestyle='--', color='k')
 plt.ylim((0, 1.1))
 plt.xlim((0, 300))
 make_graph_pretty('t (a.u.)', 'intensity (a.u)', loc=4)
 ```

 %% Cell type:code id: tags:

 ``` python
+f_coverslip.cs
+```
+
+%% Cell type:code id: tags:
+
+``` python
 ```