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Merge pull request #6 from Poirazi-Lab/development
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@mpgl
mpgl authored Oct 15, 2022
2 parents d3cd41e + 98e2f59 commit 8ab4eb5
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4 changes: 2 additions & 2 deletions dendrify/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
from .compartment import Compartment, Dendrite, Soma
from .ephysproperties import EphysProperties
from .equations import library
from .compartment import Compartment, Soma, Dendrite
from .neuronmodel import NeuronModel
from .ephysproperties import EphysProperties
111 changes: 55 additions & 56 deletions dendrify/compartment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
import sys
from typing import Optional, Union

import brian2
import numpy as np
from brian2.units import Quantity, ms, pA

Expand All @@ -30,16 +29,16 @@ class Compartment:
name : str
A unique name used to tag compartment-specific equations and parameters.
It is also used to distinguish the various compartments belonging to the
same :class:`~dendrify.neuronmodel.NeuronModel`.
same :class:`.NeuronModel`.
model : str, optional
A keyword for accessing Dendrify's library models. Custom models can
also be provided but they should be in the same formattable structure as
the library models. Available options: ``'passive'`` (default),
``'adaptiveIF'``, ``'leakyIF'``, ``'adex'``.
kwargs : brian2.units.fundamentalunits.Quantity, optional
kwargs : :class:`~brian2.units.fundamentalunits.Quantity`, optional
Kwargs are used to specify important electrophysiological properties,
such as the specific capacitance or resistance. For more information
see: :class:`~dendrify.ephysproperties.EphysProperties`.
see: :class:`.EphysProperties`.
Examples
--------
Expand Down Expand Up @@ -101,14 +100,14 @@ def connect(self, other: Compartment,
----------
other : Compartment
Another compartment.
g : str | brian2.units.fundamentalunits.Quantity, optional
g : str or :class:`~brian2.units.fundamentalunits.Quantity`, optional
The coupling conductance. It can be set explicitly or calculated
automatically (provided all necessary parameters exist).
Available options: ``'half_cylinders'`` (default),
``'cylinder_<compartment name>'``.
Note
----
Warning
-------
The automatic approaches require that both compartments to be connected
have specified **length**, **diameter** and **axial resistance**.
Expand Down Expand Up @@ -202,11 +201,11 @@ def synapse(self, channel: Optional[str] = None,
pre : str
A unique name to distinguish synapses of the same type coming from
different input sources, by default ``None``
g : brian2.units.fundamentalunits.Quantity
g : :class:`~brian2.units.fundamentalunits.Quantity`
Maximum synaptic conductance, by default ``None``
t_rise : brian2.units.fundamentalunits.Quantity
t_rise : :class:`~brian2.units.fundamentalunits.Quantity`
Rise time constant, by default ``None``
t_decay : brian2.units.fundamentalunits.Quantity
t_decay : :class:`~brian2.units.fundamentalunits.Quantity`
Decay time constant, by default ``None``
scale_g : bool, optional
Option to add a normalization factor to scale the maximum
Expand Down Expand Up @@ -270,12 +269,12 @@ def noise(self, tau: Quantity = 20*ms, sigma: Quantity = 3*pA,
Parameters
----------
tau : brian2.units.fundamentalunits.Quantity, optional
Time constant of the Gaussian noise, by default 20*ms
sigma : brian2.units.fundamentalunits.Quantity, optional
Standard deviation of the Gaussian noise, by default 3*pA
mean : brian2.units.fundamentalunits.Quantity, optional
Mean of the Gaussian noise, by default 0*pA
tau : :class:`~brian2.units.fundamentalunits.Quantity`, optional
Time constant of the Gaussian noise, by default ``20*ms``
sigma : :class:`~brian2.units.fundamentalunits.Quantity`, optional
Standard deviation of the Gaussian noise, by default ``3*pA``
mean : :class:`~brian2.units.fundamentalunits.Quantity`, optional
Mean of the Gaussian noise, by default ``0*pA``
"""
I_noise_name = f'I_noise_{self.name}'
noise_eqs = library['noise'].format(self.name)
Expand Down Expand Up @@ -312,11 +311,11 @@ def parameters(self) -> dict:
def area(self) -> Quantity:
"""
A compartment's surface area (open cylinder) based on its length
and its diameter.
and diameter.
Returns
-------
brian2.units.fundamentalunits.Quantity
:class:`~brian2.units.fundamentalunits.Quantity`
"""
try:
return self._ephys_object.area
Expand All @@ -329,11 +328,11 @@ def area(self) -> Quantity:
def capacitance(self) -> Quantity:
"""
A compartment's absolute capacitance based on its specific capacitance
(cm) and its surface area.
(cm) and surface area.
Returns
-------
brian2.units.fundamentalunits.Quantity
:class:`~brian2.units.fundamentalunits.Quantity`
"""
try:
return self._ephys_object.capacitance
Expand All @@ -345,12 +344,12 @@ def capacitance(self) -> Quantity:
@property
def g_leakage(self) -> Quantity:
"""
A compartment's leakage conductance based on its specific leakage
conductance (gl) and its surface area.
A compartment's absolute leakage conductance based on its specific
leakage conductance (gl) and surface area.
Returns
-------
brian2.units.fundamentalunits.Quantity
:class:`~brian2.units.fundamentalunits.Quantity`
"""
try:
return self._ephys_object.g_leakage
Expand Down Expand Up @@ -413,27 +412,27 @@ class Soma(Compartment):
and parameters needed to describe a somatic compartment and any currents
(synaptic, dendritic, noise) passing through it.
Note
----
Soma acts as a wrapper for Compartment with slight changes to account for
certain somatic properties. For a full list of its methods and attributes,
please see: :class:`~dendrify.compartment.Compartment`.
.. seealso::
Soma acts as a wrapper for Compartment with slight changes to account for
certain somatic properties. For a full list of its methods and attributes,
please see: :class:`.Compartment`.
Parameters
----------
name : str
A unique name used to tag compartment-specific equations and parameters.
It is also used to distinguish the various compartments belonging to the
same :class:`~dendrify.neuronmodel.NeuronModel`.
same :class:`.NeuronModel`.
model : str, optional
A keyword for accessing Dendrify's library models. Custom models can
also be provided but they should be in the same formattable structure as
the library models. Available options: ``'leakyIF'`` (default),
``'adaptiveIF'``, ``'adex'``.
kwargs : brian2.units.fundamentalunits.Quantity, optional
kwargs : :class:`~brian2.units.fundamentalunits.Quantity`, optional
Kwargs are used to specify important electrophysiological properties,
such as the specific capacitance or resistance. For more information
see: :class:`~dendrify.ephysproperties.EphysProperties`.
see: :class:`.EphysProperties`.
Examples
--------
Expand Down Expand Up @@ -478,18 +477,17 @@ class Dendrite(Compartment):
mechanisms, and any currents (synaptic, dendritic, ionic, noise) passing
through it.
Note
----
Dendrite inherits all the methods and attributes of its parent class
:class:`~dendrify.compartment.Compartment`. For a complete list, please refer
to the documentation of the latter.
.. seealso::
Dendrite inherits all the methods and attributes of its parent class
:class:`.Compartment`. For a complete list, please
refer to the documentation of the latter.
Parameters
----------
name : str
A unique name used to tag compartment-specific equations and parameters.
It is also used to distinguish the various compartments belonging to the
same :class:`~dendrify.neuronmodel.NeuronModel`.
same :class:`.NeuronModel`.
model : str, optional
A keyword for accessing Dendrify's library models. Dendritic compartments
are by default set to ``'passive'``.
Expand Down Expand Up @@ -534,37 +532,38 @@ def dspikes(self, channel: str,
negative current (potassium-like current) when a specified dSpike
threshold is crossed.
Note
----
The dendritic spiking mechanism as implemented here has three distinct
phases.
.. hint::
The dendritic spiking mechanism as implemented here has three
distinct phases.
**INACTIVE PHASE:**\n
When the dendritic voltage is subthreshold OR the simulation step is
within the refractory period. dSpikes cannot be generated during this
phase.
**INACTIVE PHASE:**\n
When the dendritic voltage is subthreshold OR the simulation step is
within the refractory period. dSpikes cannot be generated during this
phase.
**DEPOLARIZATION PHASE:**\n
When the dendritic voltage crosses the dSpike threshold AND the
refractory period has elapsed. This triggers the instant activation of a
positive current that enters the dendrite and then decays exponentially.
**DEPOLARIZATION PHASE:**\n
When the dendritic voltage crosses the dSpike threshold AND the
refractory period has elapsed. This triggers the instant activation
of a positive current that enters the dendrite and then decays
exponentially.
**REPOLARIZATION PHASE:**\n
This phase starts automatically after a specified delay from the
initiation of the dSpike. A negative current is activated instantly and
then decays exponentially. Also a new refractory period begins.
**REPOLARIZATION PHASE:**\n
This phase starts automatically after a specified delay from the
initiation of the dSpike. A negative current is activated instantly
and then decays exponentially. Also a new refractory period begins.
Parameters
----------
channel : str
Ion channel type. Available options: ``'Na'``, ``'Ca'`` (coming soon).
threshold : brian2.units.fundamentalunits.Quantity
threshold : :class:`~brian2.units.fundamentalunits.Quantity`
The membrane voltage threshold for dendritic spiking, by default
``None``.
g_rise : brian2.units.fundamentalunits.Quantity
g_rise : :class:`~brian2.units.fundamentalunits.Quantity`
The conductance of the current that is activated during the
depolarization phase, by default ``None``.
g_fall : brian2.units.fundamentalunits.Quantity
g_fall : :class:`~brian2.units.fundamentalunits.Quantity`
The conductance of the current that is activated during the
repolarization phase, by default ``None``.
"""
Expand Down
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