- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2022-02-03 22:14:50+13:00
- Desc:
- updated overview.srt
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/702/rawfile/a0bf492b6e68947d32caf1e4f2d77efa59ce1bb4/fig8.py
import os
import matplotlib
matplotlib.use('agg')
import numpy as np
import matplotlib.pyplot as plt
import opencor as opencor
import timeit
start = timeit.default_timer()
def load_sedml(filename):
return opencor.open_simulation(filename)
def get_data(filename):
data = filename.data()
data.set_ending_point(100)
data.set_point_interval(1)
return data
def run_sim(data, filename, Ki):
ik1_list = []
voltage = np.arange(-150, 51, 1)
var1_list = [0.0229, 0.0841, 0.1338, 0.3745, 0.185]
var2_list = [0.0012, 0.0861, 0.4780, 0.1815, 1.6433]
var3_list = [1.2173, 93.9391, 27.2428, 10.5111, 0.3036]
var4_list = [8.5590, 9.5527, 4.9250, 0.0448, 1.5436]
var5_list = [0.1162, 23.0096, 8.7222, 0.0203, 0.1132]
var6_list = [77.5571, 5.8902, 56.6362, 89.1151, 53.9824]
key_ids = ["one", "two", "three", "four", "five"]
results1 = {}
file = load_sedml(filename)
for var1, var2, var3, var4, var5, var6, index in zip(var1_list, var2_list, var3_list, var4_list, var5_list, var6_list, key_ids):
file.reset(True)
file.clear_results()
data.constants()["Current_Ik1/var_1"] = var1
data.constants()["Current_Ik1/var_2"] = var2
data.constants()["Current_Ik1/var_3"] = var3
data.constants()["Current_Ik1/var_4"] = var4
data.constants()["Current_Ik1/var_5"] = var5
data.constants()["Current_Ik1/var_6"] = var6
results1[index] = []
for v in voltage:
data.constants()["Current_Ik1/Ki"] = Ki
data.constants()["Current_Ik1/v"] = v
file.run()
ds = file.results().data_store()
value1 = ds.voi_and_variables()["Current_Ik1/i_k1"].values()[-1]
results1[index].append(value1)
return results1
if __name__ == '__main__':
Channel_file = "Current_Ik1.sedml"
Channel = load_sedml(Channel_file)
data = get_data(Channel)
Ik1_kurokawa_list = run_sim(data, Channel_file, 125)
Ik1_ma_list = run_sim(data, Channel_file, 150)
Ik1_baseline_list = run_sim(data, Channel_file, 148)
Jalife_Mature_IK1_list = run_sim(data, Channel_file, 148)
Jalife_Immature_IK1_list = run_sim(data, Channel_file, 148)
voltage = np.arange(-150, 51, 1)
plt.figure(figsize=(7, 6))
plt.plot(voltage, Jalife_Mature_IK1_list["four"], color='green', linewidth=3, label='Jalife Mature')
plt.plot(voltage, Jalife_Immature_IK1_list["five"], color='purple', linewidth=3, label='Jalife Immature')
plt.plot(voltage, Ik1_ma_list['two'], color='blue', linewidth=3, label='Ma et al.')
plt.plot(voltage, Ik1_kurokawa_list['one'], color='orangered', linewidth=3, label='Kurokawa Lab')
plt.plot(voltage, Ik1_baseline_list["three"], color='black', linewidth=3, label='Baseline Model')
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('I$_{K1}$ (pA/pF)', fontsize=18)
plt.xticks(np.arange(-150, 51, 50))
plt.yticks((np.arange(-20, 5.1, 5)))
plt.xlim(-150, 50)
plt.ylim(-20, 5)
plt.tick_params(axis='both', labelsize='18')
plt.legend(fontsize='14')
plt.tick_params(axis='both', labelsize='18')
plt.xlabel('Voltage (mV)', size='18')
plt.ylabel('I$_{k1}$ (pA/pF)', size='18')
plt.subplots_adjust(left=0.2,
bottom=0.2,
right=0.9,
top=0.9,
wspace=0.4,
hspace=0.4)
plt.savefig('Figure08.png')
stop = timeit.default_timer()
print('Time: ', stop - start)
