pygrenade_vx.network.abstract.Neuron

class pygrenade_vx.network.abstract.Neuron

Bases: pybind11_builtins.pybind11_object

__init__(self: _pygrenade_vx_network_abstract.Neuron) → None

Methods

`__init__`(self)
`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, descriptor)	Return iterators to begin and end of adjacent compartments.
`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.
`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_max_degree_compartment`(self)	Return compartment with largest degree.
`is_chain`(self, compartment, marked_compartments)	Distinguishes chains from branches.
`is_connected`(self)	Check if neuron is fully connected
`isomorphism`(self, other)	Return mapping of compartments between this and other neuron.
`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.
`set`(args, *kwargs)	Overloaded function.
`source`(self, descriptor)	Return source of the given connection.
`target`(self, descriptor)	Return target of the given connection.
`valid`(self, parameter_space)	Check if the given paramter space is valid for the neuron.
`write_graphviz`(self, filename, name)	Writes neuron topology in graphviz format.

class ParameterSpace

Bases: pybind11_builtins.pybind11_object

class Parameterization

Bases: pybind11_builtins.pybind11_object

property compartments

property compartments

valid(self: _pygrenade_vx_network_abstract.Neuron.ParameterSpace, parameterization: _pygrenade_vx_network_abstract.Neuron.ParameterSpace.Parameterization) → bool: Check if the given parameterization is valid for the parameter space. This checks if the parameterization for each compartment is valid.

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, descriptor: _pygrenade_vx_network_abstract.CompartmentOnNeuron) → boost::iterator_range<boost::iterators::transform_iterator<grenade::common::detail::DescriptorTransform<grenade::vx::network::abstract::CompartmentOnNeuron, void*>, boost::adjacency_iterator<boost::adjacency_list<boost::setS, boost::listS, boost::undirectedS, boost::no_property, boost::no_property, boost::no_property, boost::listS>, void*, boost::detail::out_edge_iter<std::_Rb_tree_const_iterator<boost::detail::stored_edge_iter<void*, std::_List_iterator<boost::list_edge<void*, boost::no_property> >, boost::no_property> >, void*, boost::detail::edge_desc_impl<boost::undirected_tag, void*>, long>, long>, boost::use_default, boost::use_default> >: Return iterators to begin and end of adjacent compartments.

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) → boost::iterator_range<boost::iterators::transform_iterator<grenade::common::detail::DescriptorTransform<grenade::vx::network::abstract::CompartmentOnNeuron, void*>, std::_List_iterator<void*>, boost::use_default, boost::use_default> >

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.

get(*args, **kwargs)

Overloaded function.

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

Get a compartment via its descriptor.

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_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.

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

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.

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.

set(*args, **kwargs)

Overloaded function.

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.

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(self: _pygrenade_vx_network_abstract.Neuron, parameter_space: _pygrenade_vx_network_abstract.Neuron.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.

write_graphviz(self: _pygrenade_vx_network_abstract.Neuron, filename: str, name: str) → None: Writes neuron topology in graphviz format.