def test_pure_diffusion_3d(ics_pure_diffusion):
"""Test ics_pure_diffusion with fixed step methods"""
neuron_instance, model = ics_pure_diffusion
h, rxd, data = neuron_instance
dend, r, ca = model
h.dt *= 50
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_hybrid_cvode(ics_diffusion_hybrid):
"""Test ics_diffusion_hybrid with variable step methods"""
neuron_instance, model = ics_diffusion_hybrid
h, rxd, data = neuron_instance
dend, r, ca = model
h.CVode().active(True)
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_soma_outlines(cell_model):
"""Import a Neurolucida model and use the soma outline for voxelization."""
h, rxd, data, save_path, Cell = cell_model
c = Cell()
rxd.set_solve_type(c.all, dimension=3)
cyt = rxd.Region(c.all, name="cyt", nrn_region="i", dx=1.0)
ca = rxd.Species(
cyt, initial=lambda node: 1 if node in c.soma[0] else 0, d=0.5, charge=2
)
h.finitialize(-65)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_anisotropic_z(ics_pure_diffusion_anisotropic):
"""Test anisotropic without diffusion in the z direction with fixed step
methods"""
neuron_instance, make_test = ics_pure_diffusion_anisotropic
h, rxd, data = neuron_instance
dend, r, ca = make_test([0.1, 0.1, 0])
h.dt *= 50
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_anisotropic_z_inhom(ics_pure_diffusion_anisotropic):
"""Test inhomogeneous anisotropic diffusion without diffusion in the z
direction with fixed step methods"""
neuron_instance, make_test = ics_pure_diffusion_anisotropic
h, rxd, data, save_path = neuron_instance
dend, r, ca = make_test(lambda nd, dr: 0 if dr == 2 else 0.1)
h.dt *= 50
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
if not save_path: assert loss < tol
max_err = compare_data(data)
if not save_path: assert max_err < tol
def test_empty_region_multicompartment_reaction(empty_regions_model):
"""Test a reaction that should change the ECS with an empty region"""
neuron_instance, model = empty_regions_model
h, rxd, data = neuron_instance
sec, cyt, mem, ecs, k = model
kcyt, kecs = k[cyt], k[ecs]
react = rxd.MultiCompartmentReaction(kcyt,
kecs,
1e5,
0,
membrane=mem,
membrane_flux=False)
h.finitialize(-70)
h.continuerun(10)
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_anisotropic_x_cvode(ics_pure_diffusion_anisotropic):
"""Test anisotropic without diffusion in the x direction with variable step
methods"""
neuron_instance, make_test = ics_pure_diffusion_anisotropic
h, rxd, data, save_path = neuron_instance
dend, r, ca = make_test([0, 0.1, 0.1])
h.CVode().active(True)
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
if not save_path: assert loss < tol
max_err = compare_data(data)
if not save_path: assert max_err < tol
def test_soma_move(cell_model):
"""Import a Neurolucida model and move it."""
h, rxd, data, save_path, Cell = cell_model
c = Cell(shift=(20, 10, 20))
rxd.set_solve_type(c.all, dimension=3)
cyt = rxd.Region(c.all, name="cyt", nrn_region="i", dx=1.0)
ca = rxd.Species(
cyt, initial=lambda node: 1 if node in c.soma[0] else 0, d=0.5, charge=2
)
h.finitialize(-65)
h.continuerun(10)
assert min([nd.x3d for nd in ca.nodes(c.soma[0])]) > 29
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_cvode(ics_pure_diffusion):
"""Test ics_pure_diffusion with variable step methods"""
neuron_instance, model = ics_pure_diffusion
h, rxd, data, save_path = neuron_instance
dend, r, ca = model
h.CVode().active(True)
vec = h.Vector()
h.CVode().states(vec)
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
if not save_path: assert loss < tol
max_err = compare_data(data)
if not save_path: assert max_err < tol
def test_pure_diffusion_3d_anisotropic_y_inhom_cvode(
ics_pure_diffusion_anisotropic):
"""Test inhomogeneous anisotropic diffusion without diffusion in the y
direction with variable step methods"""
neuron_instance, make_test = ics_pure_diffusion_anisotropic
h, rxd, data = neuron_instance
dend, r, ca = make_test(lambda nd, dr: 0 if dr == 1 else 0.1)
h.CVode().active(True)
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_inhom_cvode(ics_pure_diffusion):
"""Test ics_pure_diffusion with variable step methods and inhomogeneous
diffusion coefficients.
"""
neuron_instance, model = ics_pure_diffusion
h, rxd, data = neuron_instance
dend, r, ca = model
h.CVode().active(True)
for nd in ca.nodes:
if nd.x >= 0.5:
nd.d = 0
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_cvode(ics_pure_diffusion):
"""Test ics_pure_diffusion with variable step methods"""
neuron_instance, model = ics_pure_diffusion
h, rxd, data = neuron_instance
dend, r, ca = model
h.CVode().active(True)
vec = h.Vector()
h.CVode().states(vec)
print(vec.size())
h.finitialize(-65)
print(vec.size(), vec.min(), vec.max(), vec.mean())
print(list(ca._intracellular_instances.values())[0]._grid_id)
loss = -(numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_hybrid_small_grid(ics_diffusion_hybrid):
"""Test ics_diffusion_hybrid with fixed step methods where 1D sections are
outside the 3D grid
"""
neuron_instance, model = ics_diffusion_hybrid
h, rxd, data, save_path = neuron_instance
dend, r, ca = model
dend[1].diam = 0.75
h.dt *= 50
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
if not save_path:
assert loss < tol
max_err = compare_data(data)
assert max_err < tol
def test_ecs_diffusion_3d_tort_state(ecs_diffusion):
neuron_instance, make_model = ecs_diffusion
ecs, k = make_model(11,
11,
11,
0.2,
None,
perm={
"name": "permeability",
"initial": 0
})
h, rxd, data, save_path = neuron_instance
for nd in ecs.permeability.nodes:
nd.value = 100 / (10 + (nd.x3d + nd.y3d + nd.z3d)**2)
h.finitialize(1000)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_multiple_soma(cell_model):
"""Create two Neurolucida models."""
h, rxd, data, save_path, Cell = cell_model
c = Cell()
c2 = Cell(shift=(20, 10, 20))
rxd.set_solve_type(c.all, dimension=3)
cyt = rxd.Region(c.all, name="cyt", nrn_region="i", dx=1.0)
ca = rxd.Species(
cyt,
initial=lambda node: 1 if node in c.soma[0] or node in c2.soma[0] else 0,
d=0.5,
charge=2,
)
h.finitialize(-65)
h.continuerun(10)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_3d_inhom(ics_pure_diffusion):
"""Test ics_pure_diffusion with fixed step methods and inhomogeneous
diffusion coefficients.
"""
neuron_instance, model = ics_pure_diffusion
h, rxd, data, save_path = neuron_instance
dend, r, ca = model
h.dt *= 50
for nd in ca.nodes:
if nd.x >= 0.5:
nd.d = 0
h.finitialize(-65)
loss = -(numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
h.continuerun(125)
loss += (numpy.array(ca.nodes.concentration) *
numpy.array(ca.nodes.volume)).sum()
if not save_path: assert loss < tol
max_err = compare_data(data)
if not save_path: assert max_err < tol
def test_multicompartment_reactions(neuron_instance):
"""A tests of mulicompartment reactions using an intracellular Ca model.
Test based on example copied from the RxD tutorial;
http://www.neuron.yale.edu/neuron/static/docs/rxd/index.html
Where 1D intracellular space is divided into cytsol and endoplasmic
reticulum. Calcium is transported between the regions by multicompartment
reactions for a leak, SERCA pump and IP3 receptor.
"""
h, rxd, data = neuron_instance
sec = h.Section()
sec.L = 100
sec.diam = 1
sec.nseg = 100
h.CVode().active(1)
h.CVode().atol(1e-4)
caDiff = 0.016
ip3Diff = 0.283
cac_init = 1.0e-4
ip3_init = 0.1
gip3r = 12040
gserca = 0.3913
gleak = 6.020
kserca = 0.1
kip3 = 0.15
kact = 0.4
ip3rtau = 2000.0
# These parameters where missing in the tutorial so arbitrary values were chosen
# any resemblance to experimental values is purely coincidental.
fc = 0.7
fe = 0.3
caCYT_init = 0.1
cyt = rxd.Region(
h.allsec(),
name='cyt',
nrn_region='i',
geometry=rxd.FractionalVolume(fc, surface_fraction=1),
)
er = rxd.Region(h.allsec(),
name='er',
geometry=rxd.FractionalVolume(fe / 2.0))
cyt_er_membrane = rxd.Region(h.allsec(),
name='mem',
geometry=rxd.ScalableBorder(
1, on_cell_surface=False))
ca = rxd.Species([cyt, er],
d=caDiff,
name="ca",
charge=2,
initial=caCYT_init)
ip3 = rxd.Species(cyt, d=ip3Diff, name="ip3", initial=ip3_init)
ip3r_gate_state = rxd.Species(cyt_er_membrane, name="gate", initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
minf = ip3[cyt] * 1000.0 * ca[cyt] / (ip3[cyt] +
kip3) / (1000.0 * ca[cyt] + kact)
k = gip3r * (minf * h_gate)**3
ip3r = rxd.MultiCompartmentReaction(ca[er],
ca[cyt],
k,
k,
membrane=cyt_er_membrane)
serca = rxd.MultiCompartmentReaction(
ca[cyt],
ca[er],
gserca / ((kserca / (1000.0 * ca[cyt]))**2 + 1),
membrane=cyt_er_membrane,
custom_dynamics=True,
)
leak = rxd.MultiCompartmentReaction(ca[er],
ca[cyt],
gleak,
gleak,
membrane=cyt_er_membrane)
ip3rg = rxd.Rate(h_gate,
(1.0 / (1 + 1000.0 * ca[cyt] / (0.3)) - h_gate) / ip3rtau)
h.finitialize(-65)
cae_init = (0.0017 - cac_init * fc) / fe
ca[er].concentration = cae_init
for node in ip3.nodes:
if node.x < 0.2:
node.concentration = 2
h.CVode().re_init()
h.continuerun(1000)
max_err = compare_data(data)
assert max_err < tol
def test_multicompartment_reactions_aligment(neuron_instance):
""" A test for multicompartment reactions where one regions has more
sections than the other.
"""
h, rxd, data, save_path = neuron_instance
#Dendrite and spine
dend = h.Section(name='dend')
dend.nseg = 101
dend.pt3dclear()
dend.pt3dadd(-10, 0, 0, 1)
dend.pt3dadd(10, 0, 0, 1)
spine = h.Section(name='spine')
spine.nseg = 11
spine.pt3dclear()
spine.pt3dadd(0, 0, 0, 0.2)
spine.pt3dadd(0, 1, 0, 0.2)
spine.connect(dend(0.5))
# Where -- define the shells and borders
N = 5 # number of shells -- must be >= 2
# Where -- shells and border between them
shells = []
border = []
for i in range(N - 1):
shells.append(
rxd.Region([dend],
name='shell%i' % i,
geometry=rxd.Shell(float(i) / N, (1.0 + i) / N)))
border.append(
rxd.Region([dend],
name='border%i' % i,
geometry=rxd.FixedPerimeter(2.0 * h.PI * (1.0 + i))))
shells.append(
rxd.Region([dend, spine],
nrn_region='i',
name='shell%i' % (N - 1),
geometry=rxd.MultipleGeometry(
secs=[dend, spine],
geos=[rxd.Shell((N - 1.0) / N, 1), rxd.inside])))
# Who -- calcium with an inhomogeneous initial condition
Dca = 0.6 #um^2/ms
# scale factor so the flux (Dca/dr)*Ca has units molecules/um^2/ms (where dr is the thickness of the shell)
mM_to_mol_per_um = 6.0221409e+23 * 1e-18
ca = rxd.Species(shells,
d=Dca,
name='ca',
charge=2,
initial=lambda nd: 1000e-6
if nd.segment in spine else 100e-6)
# What -- use reactions to setup diffusion between the shells
cas = [] # calcium on the shells
for reg in shells:
cas.append(ca[reg])
# create the multi-compartment reactions between the pairs of shells
diffusions = []
for i in range(N - 1):
diffusions.append(
rxd.MultiCompartmentReaction(cas[i],
cas[i + 1],
mM_to_mol_per_um * Dca,
mM_to_mol_per_um * Dca,
border=border[i]))
h.finitialize(-65)
h.continuerun(2.5)
if not save_path:
max_err = compare_data(data)
assert max_err < tol