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Unverified Commit 6e1d0482 authored by Brent Huisman's avatar Brent Huisman Committed by GitHub
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Docs: minor plot tweaking (#1184)

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doc/gs_single_cell.rst
+ 5
− 4
View file @ 6e1d0482
......@@ -22,7 +22,7 @@ Single compartment cell with HH dynamics
The most trivial representation of a cell in Arbor is to model the entire cell as a
cylinder. The following example shows the steps required to construct a model of a
cylindrical cell with radius 3 μm, Hodgkin–Huxley dynamics and a current clamp stimulus,
then run the model for 100 ms.
then run the model for 30 ms.
The first step is to construct the cell. In Arbor, the abstract representation used to
define a cell with branching "cable" morphology is a ``cable_cell``, which holds a
......@@ -107,8 +107,8 @@ and provides an interface for recording potentials and running the simulation.
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
m.probe('voltage', '"center"', frequency=10000)
# (6) Run simulation for 100 ms of simulated activity.
m.run(tfinal=100)
# (6) Run simulation for 30 ms of simulated activity.
m.run(tfinal=30)
Step **(4)** instantiates the :class:`arbor.single_cell_model<arbor.single_cell_model>`
with our single-compartment cell.
......@@ -118,7 +118,7 @@ is used to record variables from the model. Three pieces of information are
provided: the type of quantity we want probed (voltage), the location where we want to
probe ('center'), and the frequency at which we want to sample (10kHz).
Finally, step **(6)** starts the actual simulation for a duration of 100 ms.
Finally, step **(6)** starts the actual simulation for a duration of 30 ms.
Results
----------------------------------------------------
......@@ -139,6 +139,7 @@ spike_detector and a voltage probe. Let's see what they have produced!
# (8) Plot the recorded voltages over time.
import pandas, seaborn # You may have to pip install these.
seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({'t/ms': m.traces[0].time, 'U/mV': m.traces[0].value})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV").savefig('single_cell_model_result.svg')
......
doc/images/single_cell_model_result.svg
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......@@ -2,7 +2,7 @@
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python/example/single_cell_model.py
+ 3
− 2
View file @ 6e1d0482
......@@ -21,8 +21,8 @@ m = arbor.single_cell_model(cell)
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
m.probe('voltage', '"center"', frequency=10000)
# (6) Run simulation for 100 ms of simulated activity.
m.run(tfinal=100)
# (6) Run simulation for 30 ms of simulated activity.
m.run(tfinal=30)
# (7) Print spike times, if any.
if len(m.spikes)>0:
......@@ -34,6 +34,7 @@ else:
# (8) Plot the recorded voltages over time.
import pandas, seaborn # You may have to pip install these.
seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({'t/ms': m.traces[0].time, 'U/mV': m.traces[0].value})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV").savefig('single_cell_model_result.svg')
......
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