arborize package#

Subpackages#

Submodules#

arborize.definitions module#

class arborize.definitions.Assert[source]#

Bases: object

assert_()[source]#
class arborize.definitions.CableProperties(Ra: float = None, cm: float = None)[source]#

Bases: Copy, Merge, Assert

Ra: float = None#
cm: float = None#

Axial resistivity in ohm/cm

copy()[source]#
class arborize.definitions.CableType[source]#

Bases: object

add_ion(key: str, ion: Ion)[source]#
add_mech(mech_id: str | tuple[str] | tuple[str, str] | tuple[str, str, str], mech: Mechanism)[source]#
add_synapse(label: str | tuple[str] | tuple[str, str] | tuple[str, str, str], synapse: Synapse)[source]#
static anchor(defs: Iterable[CableType], synapses: dict[str, arborize.definitions.Synapse] | None = None, use_defaults: bool = False) → CableType[source]#
assert_()[source]#
cable: CableProperties#
copy()[source]#
classmethod default()[source]#
ions: dict[str, arborize.definitions.Ion]#
mechs: dict[Union[str, tuple[str], tuple[str, str], tuple[str, str, str]], arborize.definitions.Mechanism]#
merge(def_right: CableType)[source]#
set(param: Parameter)[source]#
synapses: dict[str, arborize.definitions.Synapse]#
class arborize.definitions.Copy[source]#

Bases: object

copy()[source]#
class arborize.definitions.Ion(rev_pot: float = None, int_con: float = None, ext_con: float = None)[source]#

Bases: Copy, Merge, Assert

ext_con: float = None#
int_con: float = None#
rev_pot: float = None#
class arborize.definitions.Mechanism(parameters)[source]#

Bases: object

copy()[source]#
merge(other)[source]#
parameters: dict[str, float]#
class arborize.definitions.Merge[source]#

Bases: object

merge(other)[source]#
class arborize.definitions.ModelDefinition(use_defaults=False)[source]#

Bases: object

add_cable_type(label: str, def_: CableType)[source]#
add_synapse_type(label: str | tuple[str] | tuple[str, str] | tuple[str, str, str], synapse: Synapse)[source]#
copy()[source]#
get_cable_types()[source]#
get_synapse_types()[source]#
class arborize.definitions.Synapse(parameters, mech_id: str | tuple[str] | tuple[str, str] | tuple[str, str, str])[source]#

Bases: Mechanism

copy()[source]#
mech_id: tuple[str] | tuple[str, str] | tuple[str, str, str]#
class arborize.definitions.default_ions_dict[source]#

Bases: dict

arborize.definitions.define_model(templ_or_def, def_dict=None, /, use_defaults=False)[source]#
arborize.definitions.is_mech_id(mech_id)[source]#
class arborize.definitions.mechdict[source]#

Bases: dict

arborize.definitions.to_mech_id(mech_id: str | tuple[str] | tuple[str, str] | tuple[str, str, str]) → tuple[str] | tuple[str, str] | tuple[str, str, str][source]#

arborize.exceptions module#

exception arborize.exceptions.ArborizeError(*args, **kwargs)#

Bases: DetailedException

ArborizeError exception

exception arborize.exceptions.ConstructionError(*args, **kwargs)#

Bases: SchematicError

ConstructionError exception

exception arborize.exceptions.FrozenError(*args, **kwargs)#

Bases: SchematicError

FrozenError exception

exception arborize.exceptions.ModelDefinitionError(*args, **kwargs)#

Bases: ArborizeError

ModelDefinitionError exception

exception arborize.exceptions.ModelError(*args, **kwargs)#

Bases: ArborizeError

ModelError exception

exception arborize.exceptions.SchematicError(*args, **kwargs)#

Bases: ArborizeError

SchematicError exception

exception arborize.exceptions.TransmitterError(*args, **kwargs)#

Bases: ModelError

TransmitterError exception

exception arborize.exceptions.UnknownLocationError(*args, **kwargs)#

Bases: ModelError

UnknownLocationError exception

exception arborize.exceptions.UnknownSynapseError(*args, **kwargs)#

Bases: ModelError

UnknownSynapseError exception

arborize.parameter module#

class arborize.parameter.CableParameter(prop: str, value: float)[source]#

Bases: Parameter

set_cable_params(cable)[source]#
class arborize.parameter.IonParameter(ion: str, prop: str, value: float)[source]#

Bases: Parameter

class arborize.parameter.MechParameter[source]#

Bases: Parameter

class arborize.parameter.Parameter[source]#

Bases: object

arborize.schematic module#

class arborize.schematic.Branch[source]#

Bases: object

append(point)[source]#
points: list[arborize.schematic.Point]#
class arborize.schematic.CableBranch[source]#

Bases: Branch

append(loc, coords, radius, labels)[source]#
points: list[arborize.schematic.Point]#
class arborize.schematic.Point(loc, branch, coords, radius)[source]#

Bases: object

branch: UnitBranch#
class arborize.schematic.Schematic(name=None)[source]#

Bases: object

create_empty()[source]#
create_location(location, coords, radii, labels, endpoint=None)[source]#
create_name()[source]#
property definition#
freeze()[source]#
get_cable_types()[source]#
get_synapse_types()[source]#
property name#
set_param(location: tuple[int, int] | tuple[tuple[int, int], tuple[int, int]] | str, param: Parameter)[source]#
class arborize.schematic.UnitBranch[source]#

Bases: Branch

children: list['UnitBranch']#
definition: CableType#
labels: list[str]#
parent: UnitBranch | None#
arborize.schematic.throw_frozen()[source]#

arborize.synapse module#

class arborize.synapse.Synapse(cell, section, point_process_name, attributes={}, variant=None, type=None, source=None)[source]#

Bases: object

presynaptic(section, x=0.5, **kwargs)[source]#
record()[source]#
stimulate(*args, **kwargs)[source]#

Module contents#