diff --git a/doc/python/decor.rst b/doc/python/decor.rst index 0581f29fb64a6585aa29a8447a20a56a39c2de07..8573fc47c4b202b1570e86d7c01b8bfcb0af4d7f 100644 --- a/doc/python/decor.rst +++ b/doc/python/decor.rst @@ -7,7 +7,7 @@ Cable cell decoration .. py:class:: decor - A decor object contains a description of the cell dynamics, to be applied + A decor object contains a description of the cell dynamics to be applied to a morphology when used to instantiate a :py:class:`cable_cell` .. method:: __init__() @@ -35,9 +35,10 @@ Cable cell decoration .. code-block:: Python + import arbor as A # Set cell-wide values for properties for resistivity and capacitance - decor = arbor.decor() - decor.set_property(rL=100, cm=0.1) + decor = A.decor() + decor.set_property(rL=100 * U.Ohm * U.cm, cm=0.1 * U.F/ U.m2) .. method:: set_ion(ion, int_con=None, ext_con=None, rev_pot=None, method=None) @@ -60,13 +61,14 @@ Cable cell decoration .. code-block:: Python + import arbor as A # Set nernst reversal potential method for calcium. - ca_mech = arbor.mechanism('nernst/x=ca') + ca_mech = A.mechanism('nernst/x=ca') decor.set_ion('ca', method=ca_mech) # Set reversal potential and concentration for sodium. # The reversal potential is fixed, so we set the method to None. - decor.set_ion('na', int_con=5.0, rev_pot=70, method=None) + decor.set_ion('na', int_con=5.0 * U.mM, rev_pot=70 * U.mV, method=None) Various specialisations of the ``paint`` method are available for setting properties and density mechanisms that are applied to regions. @@ -74,7 +76,7 @@ Cable cell decoration .. method:: paint(region, Vm=None, cm=None, rL=None, tempK=None) Set cable properties on a region. A property ``v`` is given as a float - or a string. In the latter ``v`` will be interpreted as an inhomogeneous + or a string. In the latter, ``v`` will be interpreted as an inhomogeneous expression. :param str region: description of the region. @@ -90,10 +92,10 @@ Cable cell decoration .. code-block:: Python # Specialize resistivity on soma - decor.paint('"soma"', rL=100) + decor.paint('"soma"', rL=100 * U.Ohm * U.cm) # Specialize resistivity and capacitance on the axon, where # axon is defined using a region expression. - decor.paint('(tag 2)', cm=0.05, rL=80) + decor.paint('(tag 2)', cm=0.05 * U.F/U.m2, rL=80 * U.Ohm * U.cm) # Specialize resistivity on soma and set :math:`r_L(s) = 42.0 \cdot d(s)` # where `s` parametrises the cable segment(s) and :math:`d(s)` is the cable # diameter at `s`. @@ -103,7 +105,7 @@ Cable cell decoration :noindex: Set ion species properties initial conditions on a region. A property - ``v`` is given as a float or a string. In the latter ``v`` will be + ``v`` is given as a float or a string. In the latter, ``v`` will be interpreted as an inhomogeneous expression. :param str name: name of the ion species. @@ -141,7 +143,7 @@ Cable cell decoration Place one instance of the gap junction mechanism described by ``junction`` at each location in ``locations`` and label the group of gap junction sites with ``label``. The label can be used to form gap junction - connections to/from one of labeled sites in the :py:class:`arbor.recipe` by creating a + connections to/from one of the labeled sites in the :py:class:`arbor.recipe` by creating a :py:class:`arbor.gap_junction_connection`. :param str locations: description of the locset.