- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2022-02-03 22:14:50+13:00
- Desc:
- updated overview.srt
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/702/rawfile/a0bf492b6e68947d32caf1e4f2d77efa59ce1bb4/fig5.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)
start, stop, step = -100, 100, 5
Vm_plot = np.arange(start, stop + step, step)
Vm_plot = Vm_plot.reshape((1, Vm_plot.shape[0]))
file = load_sedml("Current_Ito.sedml")
def run_sim1(Vm_step, protocol, r_0, r_1, r_2, r_5, r_6, s_1, s_2, s_5, s_6, tau_r_const, tau_s_const):
if protocol == 1: #Ma
period = [500, 500, 1000, 50]
step1 = -50 #mV
step2 = -50 #mV
stepf = -50 #mV
elif protocol ==2: #cordiero
period = [1000, 10, 500, 50]
step1 = -80
step2 = -50
stepf = -50
else: #veerman
period = [1000, 5, 400, 50]
step1 = -80
step2 = -40
stepf = -50
col1 = step1 * np.ones(Vm_step.T.shape)
col2 = step2 * np.ones(Vm_step.T.shape)
col3 = Vm_step.T
col4 = stepf * np.ones(Vm_step.T.shape)
Vm_mat = np.hstack((col1, col2, col3, col4))
Y = np.array((-80, 0, 1)).reshape(3, 1)
Ito = 0.01 * np.ones((sum(period) * 100, len(Vm_step.T)))
Time = sum(period) * np.ones((sum(period) * 100, len(Vm_step.T)))
# sedml file
data = file.data()
Ito_IV = []
x_act = np.zeros(Vm_step.T.shape)
x_inact = np.zeros(Vm_step.T.shape)
tau_act = np.zeros(Vm_step.T.shape)
tau_inact = np.zeros(Vm_step.T.shape)
for j in range(len(Vm_step.T)):
print(j)
file.reset(True)
file.clear_results()
if protocol == 1:
data.constants()["Current_Ito/Ki"] = 150 # Ma
elif protocol == 2:
data.constants()["Current_Ito/Ki"] = 135 # Cordiero
else:
data.constants()["Current_Ito/Ki"] = 125 # veerman
data.constants()["Current_Ito/Ko"] = 5.4
data.constants()["Current_Ito/r_0"] = r_0
data.constants()["Current_Ito/r_1"] = r_1
data.constants()["Current_Ito/r_2"] = r_2
data.constants()["Current_Ito/r_5"] = r_5
data.constants()["Current_Ito/r_6"] = r_6
data.constants()["Current_Ito/s_1"] = s_1
data.constants()["Current_Ito/s_2"] = s_2
data.constants()["Current_Ito/s_5"] = s_5
data.constants()["Current_Ito/s_6"] = s_6
data.constants()["Current_Ito/tau_r_const"] = tau_r_const
data.constants()["Current_Ito/tau_s_const"] = tau_s_const
# for v in Vm_step:
data.states()["Current_Ito/v"] = Vm_step.T[j]
data.set_starting_point(0)
data.set_ending_point(10)
data.set_point_interval(10)
file.run()
ds = file.results().data_store()
x_to_inf_act = ds.voi_and_variables()["Current_Ito/x_to_inf_act"].values()
x_to_inf_inact = ds.voi_and_variables()["Current_Ito/x_to_inf_inact"].values()
tau_to_act = ds.voi_and_variables()["Current_Ito/tau_to_act"].values()
tau_to_inact = ds.voi_and_variables()["Current_Ito/tau_to_inact"].values()
x_act[j] = x_to_inf_act[-1]
x_inact[j] = x_to_inf_inact[-1]
tau_act[j] = tau_to_act[-1]
tau_inact[j] = tau_to_inact[-1]
Y_init = Y.flatten()
for i in range(len(period)):
Y_init[0] = Vm_mat[j, i].T
timespan = [sum(period[0:(i)]), sum(period[0:i+1])]
# file = load_sedml(filename)
file.reset(True)
file.clear_results()
if protocol == 1:
data.constants()["Current_Ito/Ki"] = 150 #Ma
elif protocol == 2:
data.constants()["Current_Ito/Ki"] = 135 #Cordiero
else:
data.constants()["Current_Ito/Ki"] = 125 #veerman
data.constants()["Current_Ito/Ko"] = 5.4
data.constants()["Current_Ito/r_0"] = r_0
data.constants()["Current_Ito/r_1"] = r_1
data.constants()["Current_Ito/r_2"] = r_2
data.constants()["Current_Ito/r_5"] = r_5
data.constants()["Current_Ito/r_6"] = r_6
data.constants()["Current_Ito/s_1"] = s_1
data.constants()["Current_Ito/s_2"] = s_2
data.constants()["Current_Ito/s_5"] = s_5
data.constants()["Current_Ito/s_6"] = s_6
data.constants()["Current_Ito/tau_r_const"] = tau_r_const
data.constants()["Current_Ito/tau_s_const"] = tau_s_const
data.states()["Current_Ito/X_to_act"] = Y_init[2]
data.states()["Current_Ito/X_to_inact"] = Y_init[1]
# data.constants()["main/k_new"] = k_new
data.states()["Current_Ito/v"] = Y_init[0]
data.set_starting_point(timespan[0])
data.set_ending_point(timespan[1])
data.set_point_interval(0.1)
file.run()
ds = file.results().data_store()
dX_to_act = ds.voi_and_variables()["Current_Ito/X_to_act"].values()
dX_to_inact = ds.voi_and_variables()["Current_Ito/X_to_inact"].values()
i_to = ds.voi_and_variables()["Current_Ito/i_to"].values()
dv = ds.voi_and_variables()["Current_Ito/v"].values()
x_to_inf_act = ds.voi_and_variables()["Current_Ito/x_to_inf_act"].values()
x_to_inf_inact = ds.voi_and_variables()["Current_Ito/x_to_inf_inact"].values()
Time_hold = (ds.voi_and_variables()["Current_Ito/t"].values()).T
Time_hold = Time_hold.reshape(Time_hold.shape[0], 1)
results = np.stack((dv, dX_to_inact, dX_to_act))
values_hold = results.T
Y_init = results.T[-1, :]
print()
Ito_hold = np.zeros(Time_hold.shape)
for k in range(0, 50):
timespan1 = [0, 50]
# file.reset(True)
# file.clear_results()
if protocol == 1:
data.constants()["Current_Ito/Ki"] = 150 # Ma
elif protocol == 2:
data.constants()["Current_Ito/Ki"] = 135 # Cordiero
else:
data.constants()["Current_Ito/Ki"] = 125 # veerman
data.constants()["Current_Ito/Ko"] = 5.4
data.constants()["Current_Ito/r_0"] = r_0
data.constants()["Current_Ito/r_1"] = r_1
data.constants()["Current_Ito/r_2"] = r_2
data.constants()["Current_Ito/r_5"] = r_5
data.constants()["Current_Ito/r_6"] = r_6
data.constants()["Current_Ito/s_1"] = s_1
data.constants()["Current_Ito/s_2"] = s_2
data.constants()["Current_Ito/s_5"] = s_5
data.constants()["Current_Ito/s_6"] = s_6
data.constants()["Current_Ito/tau_r_const"] = tau_r_const
data.constants()["Current_Ito/tau_s_const"] = tau_s_const
data.states()["Current_Ito/X_to_act"] = values_hold[k][2]
data.states()["Current_Ito/X_to_inact"] = values_hold[k][1]
# data.constants()["main/k_new"] = k_new
data.states()["Current_Ito/v"] = values_hold[k][0]
data.set_starting_point(timespan1[0])
data.set_ending_point(timespan1[1])
data.set_point_interval(10)
file.run()
ds = file.results().data_store()
dX_to_act = ds.voi_and_variables()["Current_Ito/X_to_act"].values()
dX_to_inact = ds.voi_and_variables()["Current_Ito/X_to_inact"].values()
i_to = ds.voi_and_variables()["Current_Ito/i_to"].values()
Ito_hold[k] = i_to[0]
if i == 0:
Time_j = Time_hold
Ito_j = Ito_hold
else:
Time_j = np.vstack((Time_j, Time_hold))
Ito_j = np.vstack((Ito_j, Ito_hold))
c = Time[0:len(Time_j), j].reshape((1, (Time[0:len(Time_j), j]).shape[-1]))
c = Time_j
d = Ito[0:len(Ito_j), j].reshape((1, (Ito[0:len(Ito_j), j]).shape[-1]))
d = Ito_j
Ito_IV.append(np.max(d))
Ito_IV = np.array(Ito_IV)
Ito_IV = (Ito_IV.reshape((1, Ito_IV.shape[0]))).T
return Ito_IV, x_act, x_inact, tau_act, tau_inact
if __name__ == '__main__':
r_0_list = [0.025, 0.15, 0.1785, 0.1178]
r_1_list = [0.0478, 0.0591, 0.0591, 0.0554]
r_2_list = [15.1653, 9.9437, 9.9436, 11.6842]
r_5_list = [5.2098, 3.3787, 3.3789, 3.9892]
r_6_list = [-14.6505, -9.2455, -9.2454, -11.0471]
s_1_list = [1.5665e-4, 3.9748e-4, 4.7856e-4, 3.4423e-4]
s_2_list = [-11.3965, -21.8363, -19.6705, -17.6345]
s_5_list = [235.6863, 247.8116, 76.7837, 186.7605]
s_6_list = [7.3083, 7.2455, 9.989, 8.1809]
tau_r_const_list = [0.3680, 0.8611, 0.8611, 0.6968]
tau_s_const_list = [9.1434, 15.3766, 9.1533, 11.2245]
#
plt.figure(figsize=(15, 13))
plt.subplot(2, 2, 1)
protocol = 1
Iks_IV1 = run_sim1(Vm_plot, protocol, r_0_list[0], r_1_list[0], r_2_list[0], r_5_list[0], r_6_list[0], s_1_list[0],
s_2_list[0], s_5_list[0], s_6_list[0], tau_r_const_list[0], tau_s_const_list[0])
plt.plot(Vm_plot.T, Iks_IV1[1], color='blue', label='Ma et al.', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV1[2], color='blue', linewidth=4)
protocol = 2
Iks_IV2 = run_sim1(Vm_plot, protocol, r_0_list[1], r_1_list[1], r_2_list[1], r_5_list[1], r_6_list[1], s_1_list[1],
s_2_list[1], s_5_list[1], s_6_list[1], tau_r_const_list[1], tau_s_const_list[1])
plt.plot(Vm_plot.T, Iks_IV2[1], color='green', label='Cordeiro et al.', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV2[2], color='green', linewidth=4)
# # #
# # #
protocol = 3
Iks_IV3 = run_sim1(Vm_plot, protocol, r_0_list[2], r_1_list[2], r_2_list[2], r_5_list[2], r_6_list[2], s_1_list[2],
s_2_list[2], s_5_list[2], s_6_list[2], tau_r_const_list[2], tau_s_const_list[2])
plt.plot(Vm_plot.T, Iks_IV3[1], color='orangered', label='Veerman et al.', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV3[2], color='orangered', linewidth=4)
#
protocol = 2
Iks_IV4 = run_sim1(Vm_plot, protocol, r_0_list[3], r_1_list[3], r_2_list[3], r_5_list[3], r_6_list[3], s_1_list[3],
s_2_list[3], s_5_list[3], s_6_list[3], tau_r_const_list[3], tau_s_const_list[3])
plt.plot(Vm_plot.T, Iks_IV4[1], color='black', label='Baseline Model', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV4[2], color='black', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Normalized I$_{to}$', fontsize=18)
plt.tick_params(axis='both', labelsize='18')
plt.xticks(np.arange(-100, 101, 50))
plt.yticks(np.arange(0, 1.1, 0.5))
plt.xlim(-100, 100, 50)
plt.ylim(0, 1, 0.5)
plt.title('A', fontsize=18)
plt.legend(fontsize='15', loc= 'best')
plt.subplot(2, 2, 3)
plt.plot(Vm_plot.T, Iks_IV1[3], color='blue', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV3[3], color='orangered', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV2[3], color='green', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV4[3], color='black', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Tau$_{act}$ (ms)', fontsize=18)
plt.tick_params(axis='both', labelsize='18')
plt.xticks(np.arange(-100, 101, 50))
plt.yticks(np.arange(0, 6.1, 2))
plt.xlim(-100, 100)
plt.ylim(0, 6)
plt.title('C', fontsize='18')
plt.subplot(2, 2, 4)
plt.plot(Vm_plot.T, Iks_IV1[4], color='blue', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV3[4], color='orangered', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV2[4], color='green', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV4[4], color='black', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Tau$_{inact}$ (ms)', fontsize=18)
plt.tick_params(axis='both', labelsize='18')
plt.xticks(np.arange(-100, 101, 50))
plt.yticks(np.arange(0, 301, 100))
plt.xlim(-100, 100)
plt.ylim(0, 300)
plt.title('D', fontsize=18)
plt.subplot(2, 2, 2)
plt.plot(Vm_plot.T, Iks_IV1[0], color='blue', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV2[0], color='green', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV3[0], color='orangered', linewidth=4)
plt.plot(Vm_plot.T, Iks_IV4[0], color='black', linewidth=4)
plt.xticks(np.arange(-100, 101, 50))
plt.yticks(np.arange(0, 21, 10))
plt.xlim(-100, 100)
plt.ylim(0, 20)
plt.xlabel('Voltage (mV)', size='18')
plt.ylabel('I$_{to}$ (pA/pF)', size='18')
plt.tick_params(axis='both', labelsize='18')
plt.title('B', fontsize=18)
plt.subplots_adjust(left=0.1,
bottom=0.1,
right=0.9,
top=0.9,
wspace=0.3,
hspace=0.3)
stop = timeit.default_timer()
print('Time: ', stop - start)
# plt.show()
plt.savefig('Figure05.png')
