- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-03-31 10:48:40+13:00
- Desc:
- Add open channel IV of HH models; Add simulation and plot python scripts
- Permanent Source URI:
- https://models.fieldml.org/workspace/64f/rawfile/ab2962b8796666ad9938a2577611c954f006b5fd/sed-ml/subthreshold_plot.py
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
# The prefix of the saved output file name
prefilename = 'simFig21'
V_initial = [-6, -5, -2, -7]
# Figure name
prefig = 'subthreshold'
figfile = '%s.png' % prefig
# Set figure dimension (width, height) in inches.
fw, fh = 12, 9
fig = plt.figure(figsize=(fw,fh))
# Set subplots
subpRow, subpCol = 5, 2
ax, lns = {}, {}
lfontsize, labelfontsize = 10, 12 # legend, label fontsize
# This gives list with the colors from the cycle, which you can use to iterate over.
cycle = plt.rcParams['axes.prop_cycle'].by_key()['color']
# Read data from the files
plotindex = [1, 3, 5, 7, 9, 2, 4, 6, 8, 10]
x_name = 'outputs/time'
y_names =['outputs/minus_V','outputs/m','outputs/h','outputs/gNa','outputs/INa',
'outputs/n','outputs/gK','outputs/IK','outputs/Ileak','outputs/Ii']
y_labels =['-V (mV)','m','h','$g_{Na}$','$I_{Na}$','n','$g_{K}$','$I_{K}$','$I_{l}$','$I_{i}$']
rol=int(10*100)
ylims=[[-2.5,8],[0.04,0.12],[0.52,0.60],[0,0.08],[0,8],[0.31,0.37],[0.3,0.7],[-10,-4],[0,5],[-6,4]]
for j, iV_initial in enumerate(V_initial):
filename ='%s_(%d)mV.csv' % (prefilename, iV_initial)
data = pd.read_csv(filename)
for i, y_name in enumerate(y_names):
x_data = data[x_name][0:rol]
y_data = data[y_name][0:rol]
if j ==0:
ax[i] = fig.add_subplot(subpRow, subpCol, plotindex[i])
ax[i].set_ylim(ylims[i][0],ylims[i][1])
else:
ax[i].grid(linestyle='-.')
ax[i].tick_params(direction='in', axis='both')
ax[i].set_ylabel (y_labels[i], fontsize= labelfontsize)
if plotindex[i] in [9,10]:
ax[i].set_xlabel ('time(ms)', fontsize= labelfontsize)
else:
ax[i].set_xticklabels([])
if j==3:
ax[i].plot(x_data, y_data, '-.', color=cycle[j],label='V_init=%d mV' % (iV_initial))
else:
ax[i].plot(x_data, y_data, color=cycle[j],label='V_init=%d mV' % (iV_initial))
ax[i].grid(True,linestyle='-.')
ax[0].legend(loc = 'best', fontsize=lfontsize, frameon=False)
plt.savefig(figfile)
plt.show()
