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Diffusion Example Improvements (and a bit of clean-up) #1914

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merged 5 commits into from
Jun 23, 2022
Merged

Diffusion Example Improvements (and a bit of clean-up) #1914

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16621d2
Example improvements and clean-up.
thorstenhater Jun 23, 2022
f46694f
Merge remote-tracking branch 'origin/master' into diffusion/better-py…
thorstenhater Jun 23, 2022
3a4207a
Example improvements and clean-up.
thorstenhater Jun 23, 2022
4ff3c8a
Add diffusion to example canon.
thorstenhater Jun 23, 2022
35f8da1
Undo ooops.
thorstenhater Jun 23, 2022
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7 changes: 5 additions & 2 deletions mechanisms/default/decay.mod
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
NEURON {
SUFFIX decay
USEION x WRITE xd, ix
USEION x WRITE xd
RANGE F, tau
}

PARAMETER { tau = 5 }

INITIAL { F = xd }

STATE { F }
Expand All @@ -14,5 +17,5 @@ BREAKPOINT {

DERIVATIVE dF {
F = xd
F' = -5*F
F' = -tau*F
}
2 changes: 1 addition & 1 deletion mechanisms/default/inject.mod
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
NEURON {
POINT_PROCESS inject
USEION x WRITE xd, ix
USEION x WRITE xd
RANGE alpha, beta
}

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28 changes: 19 additions & 9 deletions python/example/diffusion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,14 +28,18 @@ def probes(self, gid):
def global_properties(self, kind):
return self.the_props

def event_generators(self, gid):
return [A.event_generator("Zap", 0.005, A.explicit_schedule([0.0]))]


tree = A.segment_tree()
s = tree.append(A.mnpos, A.mpoint(-3, 0, 0, 3), A.mpoint(3, 0, 0, 3), tag=1)
_ = tree.append(s, A.mpoint(3, 0, 0, 1), A.mpoint(33, 0, 0, 1), tag=3)

dec = A.decor()
dec.set_property(Vm=-40)
# dec.paint('(tag 1)', A.density('hh'))
dec.set_ion("na", int_con=0.0, diff=0.005)
dec.place("(location 0 0.5)", A.synapse("inject/x=na", {"alpha": 200.0}), "Zap")
dec.paint("(all)", A.density("decay/x=na"))
dec.discretization(A.cv_policy("(max-extent 5)"))

# Set up ion diffusion
Expand All @@ -47,9 +51,7 @@ def global_properties(self, kind):
]
cel = A.cable_cell(tree, A.label_dict(), dec)
rec = recipe(cel, prb)
ctx = A.context()
dom = A.partition_load_balance(rec, ctx)
sim = A.simulation(rec, dom, ctx)
sim = A.simulation(rec)
hdl = (sim.sample((0, 0), A.regular_schedule(0.1)),)

sim.run(tfinal=0.5)
Expand All @@ -58,10 +60,18 @@ def global_properties(self, kind):
fg, ax = plt.subplots()
for h in hdl:
for d, m in sim.samples(h):
xs = d[:, 0]
# Plot
for lbl, ix in zip(m, range(1, d.shape[1])):
ys = d[:, ix]
print(lbl, ys.min(), ys.max())
ax.plot(xs, ys, label=lbl)
ax.plot(d[:, 0], d[:, ix], label=lbl)
# Table
print("Sodium concentration (NaD/mM)")
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Can we use pandas/sth else to pretty print the table?

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In theory yes, but the code is usually neither more comprehensible nor shorter. You would be looking for
DataFrame::to_string(buf=None, columns=None, col_space=None, header=True, index=True, na_rep='NaN', formatters=None, float_format=None, sparsify=None, index_names=True, justify=None, max_rows=None, max_cols=None, show_dimensions=False, decimal='.', line_width=None, min_rows=None, max_colwidth=None, encoding=None) .

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something else = pip install tabulate, but I am not going to add a dependency for that

print("|-" + "-+-".join("-" * 20 for _ in range(d.shape[1])) + "-|")
print(
"| Time (ms) | " + " | ".join(f"{str(l):<20}" for l in m) + " |"
)
print("|-" + "-+-".join("-" * 20 for _ in range(d.shape[1])) + "-|")
for ix in range(d.shape[0]):
print("| " + " | ".join(f"{v:>20.3f}" for v in d[ix, :]) + " |")
print("|-" + "-+-".join("-" * 20 for _ in range(d.shape[1])) + "-|")
ax.legend()
fg.savefig("results.pdf")
1 change: 1 addition & 0 deletions scripts/run_python_examples.sh
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Expand Up @@ -28,3 +28,4 @@ $PREFIX python python/example/single_cell_recipe.py
$PREFIX python python/example/single_cell_stdp.py
$PREFIX python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
$PREFIX python python/example/two_cell_gap_junctions.py
$PREFIX python python/example/diffusion.py