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paper-fitting-and-validation-recordings-all.py
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#!/usr/bin/env python2
from __future__ import print_function
import sys
sys.path.append('../lib')
import os
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from mpl_toolkits.axes_grid1.inset_locator import mark_inset
import string
import protocols
from protocols import est_g_staircase
import model_ikr as m
from releakcorrect import I_releak, score_leak, protocol_leak_check
from scipy.optimize import fmin
import seaborn as sns
# Set seed
np.random.seed(101)
savedir = './figs/paper'
if not os.path.isdir(savedir):
os.makedirs(savedir)
savedirlr = './figs/paper-low-res'
if not os.path.isdir(savedirlr):
os.makedirs(savedirlr)
#
# Protocol info
#
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': protocols.sactiv,
'sinactiv': protocols.sinactiv,
}
protocol_dir = '../protocol-time-series'
protocol_list = [
'staircaseramp',
'sactiv',
'sinactiv',
'pharma',
'apab',
'apabv3',
'ap05hz',
'ap1hz',
'ap2hz',
]
# IV protocol special treatment
protocol_iv = [
'sactiv',
'sinactiv',
]
protocol_iv_times = {
'sactiv': protocols.sactiv_times,
'sinactiv': protocols.sinactiv_times,
}
protocol_iv_convert = {
'sactiv': protocols.sactiv_convert,
'sinactiv': protocols.sinactiv_convert,
}
protocol_iv_args = {
'sactiv': protocols.sactiv_iv_arg,
'sinactiv': protocols.sinactiv_iv_arg,
}
protocol_iv_v = {
'sactiv': protocols.sactiv_v,
'sinactiv': protocols.sinactiv_v,
}
data_dir_staircase = '../data'
data_dir = '../data-autoLC'
file_dir = './out'
file_list = [
'herg25oc',
'herg27oc',
'herg30oc',
'herg33oc',
'herg37oc',
]
temperatures = np.array([25.0, 27.0, 30.0, 33.0, 37.0])
temperatures += 273.15 # in K
fit_seed = '542811797'
add_inset = { # prt: (figsize, (xmin, xmax), (ymin, ymax), inc_loc, mark_loc)
'apab': ((3.5, 0.5), (0.05, 0.6), (-25 / 1000., 120 / 1000.), 1, (2, 4)),
'apabv3': ((3.5, 0.5), (0.05, 0.7), (-25 / 1000., 70 / 1000.), 1, (2, 4)),
'ap05hz': ((2, 0.5), (1.9, 2.7), (-25 / 1000., 70 / 1000.), 1, (2, 4)),
'ap1hz': ((2, 0.5), (2.9, 3.7), (-25 / 1000., 120 / 1000.), 2, (3, 1)),
}
isNorm = True
norm_method = 1
#
# Do a very very tailored version........ :(
#
fig = plt.figure(figsize=(18, 18))
bigygap = 5
n_ygrid = 34
n_subpanels = 1 + len(temperatures)
grid = plt.GridSpec(3 * n_ygrid + 2 * bigygap, 3, hspace=0.0, wspace=0.2)
axes = np.empty([3 * n_subpanels, int(len(protocol_list) / 3)], dtype=object)
# long list here:
for i in range(int(len(protocol_list)/3)):
# First 'row'
if i == 0:
axes[0, i] = fig.add_subplot(grid[0:4, i])
axes[0, i].set_xticklabels([])
axes[1, i] = fig.add_subplot(grid[4:10, i])
axes[2, i] = fig.add_subplot(grid[10:16, i])
axes[3, i] = fig.add_subplot(grid[16:22, i])
axes[4, i] = fig.add_subplot(grid[22:28, i])
axes[5, i] = fig.add_subplot(grid[28:34, i])
else:
axes[0, i] = fig.add_subplot(grid[0:4, i])
axes[1, i] = fig.add_subplot(grid[7:12, i])
axes[2, i] = fig.add_subplot(grid[12:17, i])
axes[3, i] = fig.add_subplot(grid[17:22, i])
axes[4, i] = fig.add_subplot(grid[22:27, i])
axes[5, i] = fig.add_subplot(grid[27:32, i])
axes[1, i].set_xticklabels([])
axes[2, i].set_xticklabels([])
axes[3, i].set_xticklabels([])
axes[4, i].set_xticklabels([])
# Second 'row'
n_shift = n_ygrid + bigygap
n_panel = n_subpanels
axes[n_panel, i] = fig.add_subplot(grid[n_shift+0:n_shift+4, i])
axes[n_panel, i].set_xticklabels([])
axes[n_panel + 1, i] = fig.add_subplot(grid[n_shift+4:n_shift+10, i])
axes[n_panel + 2, i] = fig.add_subplot(grid[n_shift+10:n_shift+16, i])
axes[n_panel + 3, i] = fig.add_subplot(grid[n_shift+16:n_shift+22, i])
axes[n_panel + 4, i] = fig.add_subplot(grid[n_shift+22:n_shift+28, i])
axes[n_panel + 5, i] = fig.add_subplot(grid[n_shift+28:n_shift+34, i])
axes[n_panel + 1, i].set_xticklabels([])
axes[n_panel + 2, i].set_xticklabels([])
axes[n_panel + 3, i].set_xticklabels([])
axes[n_panel + 4, i].set_xticklabels([])
# Third 'row'
n_shift = 2 * (n_ygrid + bigygap)
n_panel = 2 * n_subpanels
axes[n_panel, i] = fig.add_subplot(grid[n_shift+0:n_shift+4, i])
axes[n_panel, i].set_xticklabels([])
axes[n_panel + 1, i] = fig.add_subplot(grid[n_shift+4:n_shift+10, i])
axes[n_panel + 2, i] = fig.add_subplot(grid[n_shift+10:n_shift+16, i])
axes[n_panel + 3, i] = fig.add_subplot(grid[n_shift+16:n_shift+22, i])
axes[n_panel + 4, i] = fig.add_subplot(grid[n_shift+22:n_shift+28, i])
axes[n_panel + 5, i] = fig.add_subplot(grid[n_shift+28:n_shift+34, i])
axes[n_panel + 1, i].set_xticklabels([])
axes[n_panel + 2, i].set_xticklabels([])
axes[n_panel + 3, i].set_xticklabels([])
axes[n_panel + 4, i].set_xticklabels([])
Ts_oC = temperatures - 273.15 # in oC
for i in range(3):
ii = i * n_subpanels
axes[ii, 0].set_ylabel('Voltage\n[mV]', fontsize=14)
for j, T_oC in enumerate(Ts_oC):
j = j + 1
axes[ii + j, 0].set_ylabel('$%s^\circ$C' % int(T_oC), fontsize=14)
axes[ii + 3, 0].text(-0.175, 0.5, 'Normalised currents', fontsize=18,
rotation=90, ha='center', va='center',
transform=axes[ii + 3, 0].transAxes)
axes[n_subpanels - 1, 0].set_xlabel('Time [s]', fontsize=14)
for i in range(int(len(protocol_list) / 3)):
axes[-(n_subpanels + 1), i].set_xlabel('Time [s]', fontsize=14)
axes[-1, i].set_xlabel('Time [s]', fontsize=18)
# Liudmila suggested common y-axis
for i in range(3):
ai = n_subpanels * i + 1
for j in range(3):
aj = j
if i == 0 and j == 0: # staircaseramp
for ii in range(len(Ts_oC)):
axes[ai + ii, aj].set_ylim((-1, 1.5))
else:
for ii in range(len(Ts_oC)):
axes[ai + ii, aj].set_ylim((-0.25, 1.5))
# Gary suggested, add inset
axins = np.empty(axes.shape, dtype=object)
for i_prt, prt in enumerate(protocol_list):
ai, aj = n_subpanels * int(i_prt / 3), i_prt % 3
if prt in add_inset.keys():
for ii in [1, 2]:
axins[ai + ii, aj] = inset_axes(axes[ai + ii, aj],
*add_inset[prt][0], loc=add_inset[prt][3])
axins[ai + ii, aj].set_facecolor("#f1f1f1")
axins[ai + ii, aj].set_xlim(add_inset[prt][1])
axins[ai + ii, aj].set_ylim(add_inset[prt][2])
axins[ai + ii, aj].set_xticks([])
axins[ai + ii, aj].set_yticks([])
mark_inset(axes[ai + ii, aj], axins[ai + ii, aj],
loc1=add_inset[prt][4][0], loc2=add_inset[prt][4][1],
fc="#f1f1f1", ec="0.5")
# Add special x,y-label for IV protocols
for aj in [1, 2]:
axes[5, aj].set_xlabel('Voltage [mV]', fontsize=14)
# change y-label to right
for aj in [1, 2]:
axes[0, aj].set_xlabel('Time [s]', fontsize=14)
for ai in [1, 2, 3, 4, 5]:
'''
axes[ai, 1].yaxis.tick_right()
axes[ai, 1].yaxis.set_label_position("right")
axes[ai, 2].yaxis.tick_right()
axes[ai, 2].yaxis.set_label_position("right")
'''
axes[ai, 1].set_ylim(-0.1, 1.1)
axes[ai, 1].set_xlim(-50, 40)
axes[ai, 2].set_ylim(-2, 1.1)
axes[ai, 2].set_xlim(-100, 40)
# axes[3, 2].text(1.115, 0.5, 'Normalised currents', fontsize=18, rotation=90,
# ha='center', va='center', transform=axes[3, 2].transAxes)
# Set y-ticklabels for protocols
# TODO
#
# Protocol
#
file_name = file_list[0] + '1'
temperature = temperatures[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=temperatures[0], # K
transform=None,
useFilterCap=False) # ignore capacitive spike
for i_prt, prt in enumerate(protocol_list):
# Calculate axis index
ai, aj = n_subpanels * int(i_prt / 3), i_prt % 3
# Title
if prt == 'staircaseramp':
axes[ai, aj].set_title('Calibration', fontsize=16, loc='left')
else:
axes[ai, aj].set_title('Validation %s' % i_prt, fontsize=16,
loc='left')
# Time point
times = np.loadtxt('%s/%s-%s-times.csv' % (data_dir, file_name,
prt), delimiter=',', skiprows=1)
# Protocol
model = prt2model[prt]
if prt not in protocol_iv:
times_sim = np.copy(times)
voltage = model.voltage(times_sim) * 1000
else:
times_sim = protocol_iv_times[prt](times[1] - times[0])
voltage = model.voltage(times_sim) * 1000
voltage, t = protocol_iv_convert[prt](voltage, times_sim)
assert(np.mean(np.abs(t - times)) < 1e-8)
axes[ai, aj].set_ylim((np.min(voltage) - 10, np.max(voltage) + 15))
# Plot raw data
# Add label!
axes[ai, aj].text(-0.1, 1.1, string.ascii_uppercase[i_prt],
transform=axes[ai, aj].transAxes, size=20,
weight='bold')
if prt not in protocol_iv:
# protocol
axes[ai, aj].plot(times, voltage, c='#696969')
else:
# protocol
for i in range(voltage.shape[1]):
axes[ai, aj].plot(times, voltage[:, i], c='#696969')
#
# All cells
#
norm_data_all = []
for i_prt, prt in enumerate(protocol_list):
# Time point
times = np.loadtxt('%s/%s-%s-times.csv' % (data_dir, file_name,
prt), delimiter=',', skiprows=1)
# Protocol
model = prt2model[prt] # only use for getting voltage!
if prt not in protocol_iv:
times_sim = np.copy(times)
voltage = model.voltage(times_sim) * 1000
else:
times_sim = protocol_iv_times[prt](times[1] - times[0])
voltage = model.voltage(times_sim) * 1000
voltage, t = protocol_iv_convert[prt](voltage, times_sim)
assert(np.mean(np.abs(t - times)) < 1e-8)
for i_T, (file_name, T) in enumerate(zip(file_list, temperatures)):
# Calculate axis index
ai, aj = n_subpanels * int(i_prt / 3) + 1 + i_T, i_prt % 3
# Get ranking
cell_ranking_file = './manualselection/paper-rank-%s.txt' % file_name
RANKED_CELLS = []
with open(cell_ranking_file, 'r') as f:
for l in f:
if not l.startswith('#'):
RANKED_CELLS.append(l.split()[0])
# colour_list = sns.cubehelix_palette(len(SORTED_CELLS))
colour_list = sns.color_palette('Blues_d', n_colors=len(RANKED_CELLS))
colour_list = colour_list.as_hex()[::-1]
for i_CELL, CELL in enumerate(RANKED_CELLS):
file_name, cell = CELL[:-3], CELL[-3:]
# Data
if prt == 'staircaseramp':
data = np.loadtxt('%s/%s-%s-%s.csv' % (data_dir_staircase,
file_name, prt, cell), delimiter=',', skiprows=1)
elif prt not in protocol_iv:
data = np.loadtxt('%s/%s-%s-%s.csv' % (data_dir, file_name,
prt, cell), delimiter=',', skiprows=1)
# Re-leak correct the leak corrected data...
g_releak = fmin(score_leak, [0.0], args=(data, voltage, times,
protocol_leak_check[prt]), disp=False)
data = I_releak(g_releak[0], data, voltage)
else:
data = np.loadtxt('%s/%s-%s-%s.csv' % (data_dir, file_name,
prt, cell), delimiter=',', skiprows=1)
for i in range(data.shape[1]):
g_releak = fmin(score_leak, [0.0], args=(data[:, i],
voltage[:, i], times,
protocol_leak_check[prt]), disp=False)
data[:, i] = I_releak(g_releak[0], data[:, i], voltage[:, i])
assert(len(data) == len(times))
# Normalisation
if prt == 'staircaseramp':
norm_data = est_g_staircase(data, times, p0=[800, 0.025],
debug=False) if isNorm else 1.
if i_CELL == 0:
norm_data_all.append([])
norm_data_all[-1].append(norm_data)
else:
norm_data = norm_data_all[i_T][i_CELL]
# Plot
if prt not in protocol_iv:
axes[ai, aj].plot(times, data / norm_data,
lw=0.2, alpha=0.1,
c=colour_list[i_CELL], rasterized=True)
else:
iv_i = protocols.get_corrected_iv(data, times,
*protocol_iv_args[prt]())
iv_v = protocol_iv_v[prt]() * 1000 # mV
axes[ai, aj].plot(iv_v, iv_i / np.max(iv_i), lw=0.5, alpha=0.5,
c=colour_list[i_CELL])
# Plot inset
if i_T in [0, 1]:
if prt in add_inset.keys(): # not in provtocol_iv
axins[ai, aj].plot(times, data / norm_data,
lw=0.2, alpha=0.1,
c=colour_list[i_CELL], rasterized=True)
#
# Final adjustment and save
#
grid.tight_layout(fig, pad=0.6, rect=[0.01175, 0, 1, 1])
grid.update(wspace=0.12, hspace=0.0)
plt.savefig('%s/fitting-and-validation-recordings-all.png' % savedirlr,
bbox_inch='tight', pad_inches=0, dpi=100)
plt.savefig('%s/fitting-and-validation-recordings-all.png' % savedir,
bbox_inch='tight', pad_inches=0, dpi=300)
plt.savefig('%s/fitting-and-validation-recordings-all.pdf' % savedir,
format='pdf', bbox_inch='tight', pad_inches=0, dpi=300)
print('Done')