diff --git a/doc/contrib/doc.rst b/doc/contrib/doc.rst
index a77def2bd420986de2e1e845577fb5c843a2085c..237e9059f2acf7d8cbc2430e4ab02bff61160ac1 100644
--- a/doc/contrib/doc.rst
+++ b/doc/contrib/doc.rst
@@ -45,7 +45,7 @@ Wherever possible, observe:
* file names: avoid underscores as much as possible. E.g. `cpp/cable_cell.rst` -> `cpp/cablecell.rst`.
* page-level labels in each file: the path concatenated without spaces. E.g. `cpp/cablecell.rst` -> `cppcablecell`.
* heading labels in a file: `pagelevel-sectionname`. Feel free to slugify long headings.
-E.g. the morphology section in the C++ cable cell docs could be `cppcablecell-morph`.
+ E.g. the morphology section in the C++ cable cell docs could be `cppcablecell-morph`.
.. _contribdoc-lang:
diff --git a/doc/tutorial/single_cell_cable.rst b/doc/tutorial/single_cell_cable.rst
index 2926652f759bf75d70a2bb1a4a2a8d58dcd798fb..391da857c56d80c1bfc39b2303b0487a70c87ff2 100644
--- a/doc/tutorial/single_cell_cable.rst
+++ b/doc/tutorial/single_cell_cable.rst
@@ -43,7 +43,7 @@ We parse the command line arguments, instantiate the recipe, run the simulation,
.. literalinclude:: ../../python/example/single_cell_cable.py
:language: python
- :lines: 147-210
+ :lines: 145-202
The output plot below shows how the current pulse is attenuated and
gets broader the further it travels along the dendrite from the current
@@ -57,7 +57,7 @@ The conduction velocity in simulation is calculated from the time of the maximum
.. literalinclude:: ../../python/example/single_cell_cable.py
:language: python
- :lines: 212-
+ :lines: 204-
Please have in mind that the calculated (idealized) conduction velocity is only correct for an infinite cable.
@@ -72,6 +72,8 @@ When we set the control volume policy to cover the full dendrite, all probes wil
./single_cell_cable.py --length 1000 --cv_policy_max_extent 1000
+Output:
+
.. figure:: single_cell_cable_result_cv_policy.svg
:width: 800
:align: center
diff --git a/doc/tutorial/single_cell_cable_result.svg b/doc/tutorial/single_cell_cable_result.svg
index daa686f49416fc5b078f518aeaaf55b98afeb1c8..5c7d483eb211cbcec93ee2be00ab52c447b41bf6 100644
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diff --git a/python/example/single_cell_cable.py b/python/example/single_cell_cable.py
index 5cb93c17ab1a43448d90c879039c00be46471e8d..b44c56628dda9f364a7445bc093cc1c7d48a84bb 100755
--- a/python/example/single_cell_cable.py
+++ b/python/example/single_cell_cable.py
@@ -95,9 +95,7 @@ class Cable(arbor.recipe):
policy = arbor.cv_policy_max_extent(self.cv_policy_max_extent)
decor.discretization(policy)
- cell = arbor.cable_cell(tree, labels, decor)
-
- return cell
+ return arbor.cable_cell(tree, labels, decor)
def probes(self, gid):
assert gid == 0
@@ -194,24 +192,17 @@ if __name__ == "__main__":
sim.run(tfinal=30, dt=dt)
# retrieve the sampled membrane voltages and convert to a pandas DataFrame
- data = [sim.samples(handle)[0][0] for handle in handles]
- data_dict = {str(i): d[:, 1] for i, d in enumerate(data)}
- data_dict["t"] = data[0][:, 0]
-
- df = pandas.DataFrame.from_dict(data_dict)
+ print("Plotting results ...")
+ df_list = []
+ for probe in range(len(handles)):
+ samples, meta = sim.samples(handles[probe])[0]
+ df_list.append(pandas.DataFrame({'t/ms': samples[:, 0], 'U/mV': samples[:, 1], 'Probe': f"{probe}"}))
- # plot all probes and save to file
- for i in range(len(probes)):
- plot = seaborn.lineplot(data=df, x="t", y=str(
- i), ci=None, legend="full", label=i)
-
- plot.set(xlabel="t/ms")
- plot.set(ylabel="U/mV")
- plot.set_xlim(9, 14)
-
- plot.figure.savefig("single_cell_cable_result.svg")
+ df = pandas.concat(df_list,ignore_index=True)
+ seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Probe",ci=None).set(xlim=(9,14)).savefig('single_cell_cable_result.svg')
# calculcate the idealized conduction velocity, cf. cable equation
+ data = [sim.samples(handle)[0][0] for handle in handles]
rm = get_rm(args.g*1/(0.01*0.01))
taum = get_taum(args.cm, rm)
lambdam = get_lambdam(args.radius*1e-6, rm, args.rL*0.01)