pygrenade_vx.network.abstract.Neuron

class pygrenade_vx.network.abstract.Neuron

Bases: pygrenade_common.Population.Cell

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: _pygrenade_vx_network_abstract.Neuron) -> None

2. __init__(self: _pygrenade_vx_network_abstract.Neuron, arg0: _pygrenade_vx_network_abstract.Neuron) -> None

Methods

__init__(*args, **kwargs)	Overloaded function.
add_compartment(self, compartment)	Adds a compartment to the neuron.
add_compartment_connection(self, source, …)	Add a compartment connection to the neuron.
adjacent_compartments(self, arg0)
branch_compartments(self, compartment, …)	Return ordered list of compartments inside a branch or chain.
branch_size(self, compartment, …)	Return the number of compartments on a branch starting from the given compartment.
classify_neighbours(self, compartment, …)	Classify neighbours into parts of branches, chains or as a leaf.
clear(self)	Clear the neuron.
compartment_connections(self)
compartments(self)
compartments_connected(self)	Check if all compartments are connected.
contains(self, descriptor)	Check if neuron contains a compartment.
copy(self)
get(*args, **kwargs)	Overloaded function.
get_compartment_degree(self, descriptor)	Return number of connections on a compartment.
get_compartment_index_map(self)	Return a map of each compartment-descriptor to an index.
get_input_ports(self)	Get input ports of neuron.
get_max_degree_compartment(self)	Return compartment with largest degree.
get_output_ports(self)	Get output ports of neuron.
has_equal_morphology(self, other)	Check whether compartment assignment and connectivity is the same for the given neuron.
is_chain(self, compartment, marked_compartments)	Distinguishes chains from branches.
is_connected(self)	Check if neuron is fully connected
is_partitionable(self)
isomorphism(self, other)	Return mapping of compartments between this and other neuron.
move(self)
neighbour(self, source, target)	Check if two compartments are neighbours.
num_compartment_connections(self)	Return number of connections on the neuron.
num_compartments(self)	Return number of compartments on the neuron.
remove_compartment(self, descriptor)	Removes a compartment from the neuron.
remove_compartment_connection(self, descriptor)	Remove a connection from the neuron.
requires_time_domain(self)
set(*args, **kwargs)	Overloaded function.
source(self, descriptor)	Return source of the given connection.
target(self, descriptor)	Return target of the given connection.
valid(*args, **kwargs)	Overloaded function.
write_graphviz(self, filename, name)	Writes neuron topology in graphviz format.

class ParameterSpace

Bases: pygrenade_common.Population.Cell.ParameterSpace

CompartmentConnections

alias of _pygrenade_vx_network_abstract.Map_grenade_vx_network_abstract_CompartmentConnectionOnNeuron_grenade_vx_network_abstract_CompartmentConnection_ParameterSpace_

class Parameterization

Bases: pygrenade_common.Population.Cell.ParameterSpace.Parameterization

CompartmentConnections

alias of _pygrenade_vx_network_abstract.Map_grenade_vx_network_abstract_CompartmentConnectionOnNeuron_grenade_vx_network_abstract_CompartmentConnection_ParameterSpace_Parameterization_

property compartment_connections

property compartments

copy(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace.Parameterization) → pygrenade_common.PortData

get_section(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace.Parameterization, sequence: pygrenade_common.MultiIndexSequence) → pygrenade_common.Population.Cell.ParameterSpace.Parameterization

move(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace.Parameterization) → pygrenade_common.PortData

size(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace.Parameterization) → int

property compartment_connections

property compartments

copy(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace) → pygrenade_common.Population.Cell.ParameterSpace

get_section(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace, sequence: pygrenade_common.MultiIndexSequence) → pygrenade_common.Population.Cell.ParameterSpace

move(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace) → pygrenade_common.Population.Cell.ParameterSpace

size(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace) → int

valid(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace, input_port_on_cell: int, parameterization: pygrenade_common.Population.Cell.ParameterSpace.Parameterization) → bool

class ParameterizationPortType

Bases: pygrenade_common.VertexPortType

copy(self: _pygrenade_vx_network_abstract.Neuron.ParameterizationPortType) → pygrenade_common.VertexPortType

move(self: _pygrenade_vx_network_abstract.Neuron.ParameterizationPortType) → pygrenade_common.VertexPortType

add_compartment(self: _pygrenade_vx_network_abstract.Neuron, compartment: _pygrenade_vx_network_abstract.Compartment) → _pygrenade_vx_network_abstract.CompartmentOnNeuron

Adds a compartment to the neuron.

add_compartment_connection(self: _pygrenade_vx_network_abstract.Neuron, source: _pygrenade_vx_network_abstract.CompartmentOnNeuron, target: _pygrenade_vx_network_abstract.CompartmentOnNeuron, edge: _pygrenade_vx_network_abstract.CompartmentConnection) → _pygrenade_vx_network_abstract.CompartmentConnectionOnNeuron

Add a compartment connection to the neuron.

adjacent_compartments(self: _pygrenade_vx_network_abstract.Neuron, arg0: _pygrenade_vx_network_abstract.CompartmentOnNeuron) → list[_pygrenade_vx_network_abstract.CompartmentOnNeuron]

branch_compartments(self: _pygrenade_vx_network_abstract.Neuron, compartment: _pygrenade_vx_network_abstract.CompartmentOnNeuron, blacklist_compartment: _pygrenade_vx_network_abstract.CompartmentOnNeuron = CompartmentOnNeuron(0)) → list[_pygrenade_vx_network_abstract.CompartmentOnNeuron]

Return ordered list of compartments inside a branch or chain.

branch_size(self: _pygrenade_vx_network_abstract.Neuron, compartment: _pygrenade_vx_network_abstract.CompartmentOnNeuron, marked_compartments: set[_pygrenade_vx_network_abstract.CompartmentOnNeuron]) → int

Return the number of compartments on a branch starting from the given compartment.

classify_neighbours(self: _pygrenade_vx_network_abstract.Neuron, compartment: _pygrenade_vx_network_abstract.CompartmentOnNeuron, neighbours_whitelist: set[_pygrenade_vx_network_abstract.CompartmentOnNeuron] = set()) → grenade::vx::network::abstract::CompartmentNeighbours

Classify neighbours into parts of branches, chains or as a leaf.

clear(self: _pygrenade_vx_network_abstract.Neuron) → None

Clear the neuron. Remove all compartments and connections.

compartment_connections(self: _pygrenade_vx_network_abstract.Neuron) → boost::iterator_range<boost::iterators::transform_iterator<grenade::common::detail::DescriptorTransform<grenade::vx::network::abstract::CompartmentConnectionOnNeuron, boost::detail::edge_desc_impl<boost::undirected_tag, void*> >, boost::detail::undirected_edge_iter<std::_List_iterator<boost::list_edge<void*, boost::no_property> >, boost::detail::edge_desc_impl<boost::undirected_tag, void*>, long>, boost::use_default, boost::use_default> >

compartments(self: _pygrenade_vx_network_abstract.Neuron) → list[pygrenade_common.CompartmentOnNeuron]

compartments_connected(self: _pygrenade_vx_network_abstract.Neuron) → bool

Check if all compartments are connected.

contains(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentOnNeuron) → bool

Check if neuron contains a compartment.

copy(self: _pygrenade_vx_network_abstract.Neuron) → pygrenade_common.Population.Cell

get(*args, **kwargs)

Overloaded function.

1. get(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentOnNeuron) -> _pygrenade_vx_network_abstract.Compartment

Get a compartment via its descriptor.

2. get(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentConnectionOnNeuron) -> _pygrenade_vx_network_abstract.CompartmentConnection

Get a compartment connection via its descriptor.

get_compartment_degree(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentOnNeuron) → int

Return number of connections on a compartment. Since the neuron has a undirected graph representation the ingoing and outgoing degree is equal.

get_compartment_index_map(self: _pygrenade_vx_network_abstract.Neuron) → dict[int, int]

Return a map of each compartment-descriptor to an index.

get_input_ports(self: _pygrenade_vx_network_abstract.Neuron) → list[pygrenade_common.Vertex.Port]

Get input ports of neuron. Ports are aggregated over compartments and input ports of the mechanisms on the compartments. If a port with equal properties (except channels) already exists, its channels are extended instead of creating a new port. To distinglish the different channels, they can be accessed with a three dimensional index of the form: (compartment_on_neuron, mechanism_on_compartment, mechanism_port_channels). The last port is the parameterization.

get_max_degree_compartment(self: _pygrenade_vx_network_abstract.Neuron) → _pygrenade_vx_network_abstract.CompartmentOnNeuron

Return compartment with largest degree. Since the neuron has a undirected graph representation the ingoing and outgoing degree is equal.

get_output_ports(self: _pygrenade_vx_network_abstract.Neuron) → list[pygrenade_common.Vertex.Port]

Get output ports of neuron. Ports are aggregated over compartments and output ports of the mechanisms on the compartments. If a port with equal properties (except channels) already exists, its channels are extended instead of creating a new port. To distinglish the different channels, they can be accessed with a three dimensional index of the form: (compartment_on_neuron, mechanism_on_compartment, mechanism_port_channels).

has_equal_morphology(self: _pygrenade_vx_network_abstract.Neuron, other: _pygrenade_vx_network_abstract.Neuron) → bool

Check whether compartment assignment and connectivity is the same for the given neuron.

is_chain(self: _pygrenade_vx_network_abstract.Neuron, compartment: _pygrenade_vx_network_abstract.CompartmentOnNeuron, marked_compartments: set[_pygrenade_vx_network_abstract.CompartmentOnNeuron]) → bool

Distinguishes chains from branches.

is_connected(self: _pygrenade_vx_network_abstract.Neuron) → bool

Check if neuron is fully connected

is_partitionable(self: _pygrenade_vx_network_abstract.Neuron) → bool

isomorphism(self: _pygrenade_vx_network_abstract.Neuron, other: _pygrenade_vx_network_abstract.Neuron) → dict[_pygrenade_vx_network_abstract.CompartmentOnNeuron, _pygrenade_vx_network_abstract.CompartmentOnNeuron]

Return mapping of compartments between this and other neuron. If no mapping between all the neurons compartments is possible an map with the possible compartment mappings is returned.

move(self: _pygrenade_vx_network_abstract.Neuron) → pygrenade_common.Population.Cell

neighbour(self: _pygrenade_vx_network_abstract.Neuron, source: _pygrenade_vx_network_abstract.CompartmentOnNeuron, target: _pygrenade_vx_network_abstract.CompartmentOnNeuron) → bool

Check if two compartments are neighbours.

num_compartment_connections(self: _pygrenade_vx_network_abstract.Neuron) → int

Return number of connections on the neuron.

num_compartments(self: _pygrenade_vx_network_abstract.Neuron) → int

Return number of compartments on the neuron.

remove_compartment(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentOnNeuron) → None

Removes a compartment from the neuron.

remove_compartment_connection(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentConnectionOnNeuron) → None

Remove a connection from the neuron.

requires_time_domain(self: _pygrenade_vx_network_abstract.Neuron) → bool

set(*args, **kwargs)

Overloaded function.

1. set(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentOnNeuron, compartment: _pygrenade_vx_network_abstract.Compartment) -> None

Set a compartment via a descriptor.

2. set(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentConnectionOnNeuron, connection: _pygrenade_vx_network_abstract.CompartmentConnection) -> None

Set a compartment connection via a descriptor.

source(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentConnectionOnNeuron) → _pygrenade_vx_network_abstract.CompartmentOnNeuron

Return source of the given connection.

target(self: _pygrenade_vx_network_abstract.Neuron, descriptor: _pygrenade_vx_network_abstract.CompartmentConnectionOnNeuron) → _pygrenade_vx_network_abstract.CompartmentOnNeuron

Return target of the given connection.

valid(*args, **kwargs)

Overloaded function.

1. valid(self: _pygrenade_vx_network_abstract.Neuron, parameter_space: pygrenade_common.Population.Cell.ParameterSpace) -> bool

Check if the given paramter space is valid for the neuron. This checks if the parameter space for each compartment of the neuron is valid.

2. valid(self: _pygrenade_vx_network_abstract.Neuron, input_port_on_cell: int, dynamics: pygrenade_common.Population.Cell.Dynamics) -> bool

3. valid(self: _pygrenade_vx_network_abstract.Neuron, time_domain_runtimes: pygrenade_common.TimeDomainRuntimes) -> bool

write_graphviz(self: _pygrenade_vx_network_abstract.Neuron, filename: str, name: str) → None

Writes neuron topology in graphviz format.