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plot-validation-protocols.py
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#!/usr/bin/env python2
import sys
sys.path.append('../lib')
import os
import numpy as np
if '--show' not in sys.argv:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import glob
import protocols
import model_ikr as m
savepath = './figs'
if not os.path.isdir(savepath):
os.makedirs(savepath)
#
# Protocols
#
protocol_funcs = {
'staircaseramp': protocols.leak_staircase,
'pharma': protocols.pharma, # during drug application
'apab': 'protocol-apab.csv',
'apabv3': 'protocol-apabv3.csv',
'ap05hz': 'protocol-ap05hz.csv',
'ap1hz': 'protocol-ap1hz.csv',
'ap2hz': 'protocol-ap2hz.csv',
'sactiv': None,
'sinactiv': None,
}
protocol_dir = '../protocol-time-series'
protocol_list = [
'staircaseramp',
'pharma',
'apab',
'apabv3',
'ap1hz',
'ap2hz',
]
data_dir = '../data'
file_dir = './out'
file_list = [
'herg25oc1',
]
temperatures = np.array([25.0])
temperatures += 273.15 # in K
fit_seed = '542811797'
withfcap = False
#
# Get new parameters and traces
#
for i_temperature, (file_name, temperature) in enumerate(zip(file_list,
temperatures)):
print('Plotting %s' % file_name)
savedir = '%s/%s' % (savepath, file_name)
if not os.path.isdir(savedir):
os.makedirs(savedir)
# Get selected cells
files_dir = os.path.realpath(os.path.join(file_dir, file_name))
searchwfcap = '-fcap' if withfcap else ''
selectedfile = './manualselected-%s.txt' % (file_name)
selectedwell = []
with open(selectedfile, 'r') as f:
for l in f:
if not l.startswith('#'):
selectedwell.append(l.split()[0])
# Model
prt2model = {}
for prt in protocol_list:
protocol_def = protocol_funcs[prt]
if type(protocol_def) is str:
protocol_def = '%s/%s' % (protocol_dir, protocol_def)
prt2model[prt] = m.Model('../mmt-model-files/kylie-2017-IKr.mmt',
protocol_def=protocol_def,
temperature=temperature, # K
transform=None,
useFilterCap=False) # ignore capacitive spike
for cell in selectedwell[:]:
# Fitted parameters
param_file = '%s/%s-staircaseramp-%s-solution%s-%s.txt' % \
(files_dir, file_name, cell, searchwfcap, fit_seed)
obtained_parameters = np.loadtxt(param_file)
# Create figure
# Do a very very tailored version........ :(
fig = plt.figure(figsize=(16, 7))
grid = plt.GridSpec(28, 3, hspace=0.0, wspace=0.2)
axes = np.empty([4, len(protocol_list) // 2], dtype=object)
for i in range(3):
# First 'row'
if i != 2:
axes[0, i] = fig.add_subplot(grid[0:6, i]) # , sharex=axes[2, i])
axes[0, i].set_xticklabels([])
axes[1, i] = fig.add_subplot(grid[6:12, i]) # , sharex=axes[2, i])
else:
axes[0, i] = fig.add_subplot(grid[0:4, i]) # , sharex=axes[2, i])
axes[1, i] = fig.add_subplot(grid[7:12, i]) # , sharex=axes[2, i])
# Second 'row'
axes[2, i] = fig.add_subplot(grid[16:22, i]) # , sharex=axes[5, i])
axes[2, i].set_xticklabels([])
axes[3, i] = fig.add_subplot(grid[22:28, i]) # , sharex=axes[5, i])
# Set labels
axes[0, 0].set_ylabel('Voltage [mV]', fontsize=14)
axes[1, 0].set_ylabel('Current [pA]', fontsize=14)
axes[2, 0].set_ylabel('Voltage [mV]', fontsize=14)
axes[3, 0].set_ylabel('Current [pA]', fontsize=14)
axes[-1, len(protocol_list) // 2 // 2].set_xlabel('Time [s]',
fontsize=18)
for i_prt, prt in enumerate(protocol_list):
# Data
data = np.loadtxt('%s/%s-%s-%s.csv' % (data_dir, file_name, prt,
cell), delimiter=',', skiprows=1)
times = np.loadtxt('%s/%s-%s-times.csv' % (data_dir, file_name,
prt), delimiter=',', skiprows=1)
assert(data.shape == times.shape)
# Simulation
model = prt2model[prt]
simulation = model.simulate(obtained_parameters, times)
if False:
for _ in range(5):
assert(all(simulation ==
model.simulate(obtained_parameters, times)))
voltage = model.voltage(times)
# Plot
ai = (i_prt // (len(protocol_list) // 2)) * 2
aj = i_prt % (len(protocol_list) // 2)
amplitude = np.max(simulation) - np.min(simulation)
if prt == 'staircaseramp':
axes[ai, aj].set_title('Calibration', fontsize=16)
# Fix ylim using simulation
axes[ai + 1, aj].set_ylim([
np.min(simulation) - 0.05 * amplitude,
np.max(simulation) + 0.05 * amplitude])
else:
axes[ai, aj].set_title('Validation %s' % i_prt, fontsize=16)
# Fix ylim using simulation
axes[ai + 1, aj].set_ylim([
np.min(simulation) - 0.3 * amplitude,
np.max(simulation) + 0.3 * amplitude])
axes[ai, aj].plot(times, voltage)
axes[ai + 1, aj].plot(times, data, alpha=0.5, label='Data')
axes[ai + 1, aj].plot(times, simulation, label='Model')
axes[1, 0].legend()
grid.tight_layout(fig, pad=0.6)
grid.update(wspace=0.12, hspace=0.0)
if '--show' not in sys.argv:
plt.savefig('%s/%s.png' % (savedir, cell),
bbox_inches='tight', pad_inches=0)
else:
plt.show()
plt.close('all')
print('Done ' + file_name + cell)
del(prt2model)