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|
from math import pi
import pytest
from testutils import compare_data, tol
@pytest.fixture
def ecs_example(neuron_instance):
"""A model where something is created in one cell and diffuses to another.
This model makes use of parameters, multicompartment reactions, an NMODL
and the extracellular space. A substance is created in an organelle in cell1
and leaks into the cytosol. It then enters the ECS using an NMODL mechanism,
where it diffuses to cell 2 and enters via the same NMODL mechanism.
"""
h, rxd, data, save_path = neuron_instance
def make_model(alpha, lambd):
# create cell1 where `x` will be created and leak out
cell1 = h.Section(name="cell1")
cell1.pt3dclear()
cell1.pt3dadd(-2, 0, 0, 1)
cell1.pt3dadd(-1, 0, 0, 1)
cell1.nseg = 11
cell1.insert("pump")
# create cell2 where `x` will be pumped in and accumulate
cell2 = h.Section(name="cell2")
cell2.pt3dclear()
cell2.pt3dadd(1, 0, 0, 1)
cell2.pt3dadd(2, 0, 0, 1)
cell2.nseg = 11
cell2.insert("pump")
# Where?
# the intracellular spaces
cyt = rxd.Region(
h.allsec(),
name="cyt",
nrn_region="i",
geometry=rxd.FractionalVolume(0.9, surface_fraction=1.0),
)
org = rxd.Region(h.allsec(), name="org", geometry=rxd.FractionalVolume(0.1))
cyt_org_membrane = rxd.Region(
h.allsec(),
name="mem",
geometry=rxd.ScalableBorder(pi / 2.0, on_cell_surface=False),
)
# the extracellular space
ecs = rxd.Extracellular(
-55, -55, -55, 55, 55, 55, dx=33, volume_fraction=alpha, tortuosity=lambd
)
# Who?
x = rxd.Species(
[cyt, org, cyt_org_membrane, ecs], name="x", d=1.0, charge=1, initial=0
)
Xcyt = x[cyt]
Xorg = x[org]
# What? - produce X in cell 1
# parameter to limit production to cell 1
cell1_param = rxd.Parameter(
org, initial=lambda node: 1.0 if node.segment.sec == cell1 else 0
)
# production with a rate following Michaels Menton kinetics
createX = rxd.Rate(Xorg, cell1_param[org] * 1.0 / (10.0 + Xorg))
# leak between organelles and cytosol
cyt_org_leak = rxd.MultiCompartmentReaction(
Xcyt, Xorg, 1e4, 1e4, membrane=cyt_org_membrane
)
model = (
cell1,
cell2,
cyt,
org,
cyt_org_membrane,
ecs,
x,
Xcyt,
Xorg,
createX,
cell1_param,
createX,
cyt_org_leak,
)
return model
yield (neuron_instance, make_model)
def test_ecs_example(ecs_example):
"""Test ecs_example with fixed step methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(0.2, 1.6)
h.finitialize(-65)
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_example_cvode(ecs_example):
"""Test ecs_example with variable step methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(0.2, 1.6)
h.CVode().active(True)
h.CVode().atol(1e-5)
h.finitialize(-65)
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_example_alpha(ecs_example):
"""Test ecs_example with fixed step and inhomogeneous volume fraction methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(lambda x, y, z: 0.2, 1.6)
h.finitialize(-65)
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_example_cvode_alpha(ecs_example):
"""Test ecs_example with variable step and inhomogeneous volume fraction
methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(lambda x, y, z: 0.2, 1.6)
h.CVode().active(True)
h.CVode().atol(1e-5)
h.finitialize(-65)
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_example_tort(ecs_example):
"""Test ecs_example with fixed step and inhomogeneous tortuosity methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(lambda x, y, z: 0.2, 1.6)
h.finitialize(-65)
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_example_cvode_tort(ecs_example):
"""Test ecs_example with variable step and inhomogeneous tortuosity methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(lambda x, y, z: 0.2, 1.6)
h.CVode().active(True)
h.CVode().atol(1e-5)
h.finitialize(-65)
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_nodelists(ecs_example):
"""Test accessing species nodes with both Node1D and NodeExtracellular"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(0.2, 1.6)
ecs, x = model[5], model[6]
# test accessing NodeExtracellular from species with both 1D and ECS
assert len(x.nodes(ecs)) == 64
assert all([nd.region == ecs for nd in x.nodes(ecs)])
# test accessing specific node by location
nd = x[ecs].nodes((-38, 27, 27))[0]
assert (nd.x3d, nd.y3d, nd.z3d) == (-38.5, 27.5, 27.5)
def test_ecs_example_dynamic_tort(ecs_example):
"""Test ecs_example with dynamic tortuosity"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(lambda x, y, z: 1.0, 1)
h.finitialize(-65)
(
cell1,
cell2,
cyt,
org,
cyt_org_membrane,
ecs,
x,
Xcyt,
Xorg,
createX,
cell1_param,
createX,
cyt_org_leak,
) = model
perm = rxd.Species(ecs, name="perm", initial=1.0 / 1.6**2)
ecs.permeability = perm
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ecs_example_dynamic_alpha(ecs_example):
"""Test ecs_example with fixed step and inhomogeneous tortuosity methods"""
(h, rxd, data, save_path), make_model = ecs_example
model = make_model(lambda x, y, z: 1.0, 1.6)
h.finitialize(-65)
(
cell1,
cell2,
cyt,
org,
cyt_org_membrane,
ecs,
x,
Xcyt,
Xorg,
createX,
cell1_param,
createX,
cyt_org_leak,
) = model
alpha = rxd.Species(ecs, name="alpha", initial=0.2)
ecs.alpha = alpha
h.continuerun(1000)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
|
