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plot_Ih_kinetics.py
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Thu, Oct 31, 19:18
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text/x-python
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R4670 PySONIC (old)
plot_Ih_kinetics.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2016-10-11 20:35:38
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-03-12 19:45:05
""" Plot the voltage-dependent kinetics of the hyperpolarization-activated
cationic current found in thalamo-cortical neurons. """
import
numpy
as
np
import
matplotlib.pyplot
as
plt
import
matplotlib.cm
as
cm
from
matplotlib.colors
import
LogNorm
# from PointNICE.solvers import SolverElec
from
PointNICE.neurons
import
ThalamoCortical
from
PointNICE.utils
import
rescale
# -------------- SIMULATION -----------------
# Create channels mechanism
neuron
=
ThalamoCortical
()
# Input vectors
nV
=
100
nC
=
10
CCa_min
=
0.01
# uM
CCa_max
=
10
# um
Vm
=
np
.
linspace
(
-
100
,
50
,
nV
)
# mV
CCa
=
np
.
logspace
(
np
.
log10
(
CCa_min
),
np
.
log10
(
CCa_max
),
nC
)
# uM
# Output matrix: relative activation (0-2)
BA
=
neuron
.
betao
(
Vm
)
/
neuron
.
alphao
(
Vm
)
P0
=
neuron
.
k2
/
(
neuron
.
k2
+
neuron
.
k1
*
(
CCa
*
1e-6
)
**
4
)
gH_rel
=
np
.
empty
((
nV
,
nC
))
for
i
in
range
(
nC
):
O_form
=
neuron
.
k4
/
(
neuron
.
k3
*
(
1
-
P0
[
i
])
+
neuron
.
k4
*
(
1
+
BA
))
OL_form
=
(
1
-
O_form
*
(
1
+
BA
))
gH_rel
[:,
i
]
=
O_form
+
2
*
OL_form
mymap
=
cm
.
get_cmap
(
'viridis'
)
sm
=
plt
.
cm
.
ScalarMappable
(
cmap
=
mymap
,
norm
=
LogNorm
(
CCa_min
,
CCa_max
))
sm
.
_A
=
[]
fs
=
18
fig
,
ax
=
plt
.
subplots
(
figsize
=
(
8
,
5
))
ax
.
set_title
(
'global activation'
,
fontsize
=
fs
)
ax
.
set_xlabel
(
'$V_m\ (mV)$'
,
fontsize
=
fs
)
ax
.
set_ylabel
(
'$(O + 2O_L)_{\infty}$'
,
fontsize
=
fs
)
ax
.
set_yticks
([
0
,
1
,
2
])
for
i
in
range
(
nC
):
ax
.
plot
(
Vm
,
gH_rel
[:,
i
],
linewidth
=
2
,
c
=
mymap
(
rescale
(
np
.
log10
(
CCa
[
i
]),
np
.
log10
(
CCa_min
),
np
.
log10
(
CCa_max
))))
fig
.
subplots_adjust
(
right
=
0.85
)
cbar_ax
=
fig
.
add_axes
([
0.87
,
0.1
,
0.02
,
0.8
])
fig
.
add_axes
()
fig
.
colorbar
(
sm
,
cax
=
cbar_ax
)
cbar_ax
.
set_ylabel
(
'$[Ca^{2+}_i]\ (uM)$'
,
fontsize
=
fs
)
plt
.
show
()
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