From 5d6f90ffa8b66839b68eb1cc8a9d20c22bf1b365 Mon Sep 17 00:00:00 2001
From: Sebastian Schmitt <sebastian.schmitt@kip.uni-heidelberg.de>
Date: Wed, 2 Jun 2021 18:17:26 +0200
Subject: [PATCH] Improve mechanism painting documentation (#1573)
---
doc/python/mechanisms.rst | 57 ++++++++++++++++++++-------------------
1 file changed, 29 insertions(+), 28 deletions(-)
diff --git a/doc/python/mechanisms.rst b/doc/python/mechanisms.rst
index abab8e53..8617021e 100644
--- a/doc/python/mechanisms.rst
+++ b/doc/python/mechanisms.rst
@@ -48,6 +48,34 @@ mechanism that is to be painted or placed on the cable cell.
# by comma-separated list of parameter after the base mechanism name.
rev = arbor.mechanism('nernst/F=96485,x=ca')
+ Mechanisms can be painted to a region. Different mechanisms can be painted on top of each other.
+
+ .. code-block:: Python
+
+ import arbor
+
+ # Create pas mechanism with default parameter values (set in NOMDL file).
+ m1 = arbor.mechanism('pas')
+
+ # Create default mechainsm with custom conductance (range).
+ m2 = arbor.mechanism('pas', {'g', 0.1})
+
+ # Create a new pas mechanism with that changes reversal potential (global).
+ m3 = arbor.mechanism('pas/e=-45')
+
+ # Create an instance of the same mechanism, that also sets conductance (range).
+ m4 = arbor.mechanism('pas/e=-45', {'g', 0.1})
+
+ # This is an equivalent to m4, using set method to specify range parameters.
+ m5 = arbor.mechanism('pas/e=-45')
+ m5.set('g', 0.1)
+
+ # Decorate the 'soma' with (multiple) mechanisms
+ decor.paint('"soma"', m1)
+ decor.paint('"soma"', m2) # Error: can't place the same mechanism on overlapping regions
+ decor.paint('"soma"', m3) # This is ok: m3 is a new, derived mechanism by virtue of
+ # having a different name, i.e. 'pas/e=-45' vs. 'pas'.
+
.. method:: mechanism(name, params)
constructor for mechanism with *name* and range parameter overrides *params*,
@@ -83,34 +111,7 @@ mechanism that is to be painted or placed on the cable cell.
.. py:attribute:: values
:type: dict
- A dictionary of key-value pairs for the parameters.
-
- .. code-block:: Python
-
- import arbor
-
- # Create pas mechanism with default parameter values (set in NOMDL file).
- m1 = arbor.mechanism('pas')
-
- # Create default mechainsm with custom conductance (range).
- m2 = arbor.mechanism('pas', {'g', 0.1})
-
- # Create a new pas mechanism with that changes reversal potential (global).
- m3 = arbor.mechanism('pas/e=-45')
-
- # Create an instance of the same mechanism, that also sets conductance (range).
- m4 = arbor.mechanism('pas/e=-45', {'g', 0.1})
-
- # This is an equivalent to m4, using set method to specify range parameters.
- m5 = arbor.mechanism('pas/e=-45')
- m5.set('g', 0.1)
-
- # Decorate the 'soma' on a cable_cell.
-
- cell.paint('"soma"', m1)
- cell.paint('"soma"', m2) # Error: can't place the same mechanism on overlapping regions
- cell.paint('"soma"', m3) # This would be ok: m3 is a new, derived mechanism by virtue of
- # having a different name, i.e. 'pas/e=-45' vs. 'pas'.
+ A dictionary of key-value pairs for the parameters.
.. py:class:: mechanism_info
--
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