Class Network2D

Object

AbstractCollection<Node2D>

AbstractList<Node2D>

Network<Node2D>

Network2D

All Implemented Interfaces:

Iterable<Node2D>, Collection<Node2D>, Iterator<Node2D>, List<Node2D>, SequencedCollection<Node2D>

Direct Known Subclasses:

Network2DGWT

public abstract class Network2D
extends Network<Node2D>

Graphical representation of generic population geometries in 2D. A network corresponds to a (possibly ephemeral) collection and configuration of nodes.

Author:

Christoph Hauert

Nested Class Summary

Nested classes/interfaces inherited from class Network

Network.LayoutListener, Network.Status

Field Summary

Fields

Modifier and Type	Field	Description
private final Vector2D	attraction	Helper variable to store intermediate results when considering the potential energy resulting from the attraction between neighbouring nodes.
private static final double	CONVERGENCE_ACCURACY_SCALE	Scale factor applied to the nominal 2D accuracy.
private static final double	FIBONACCI_RADIAL_EXPONENT	Radial growth exponent of the deterministic well-mixed phyllotactic seed.
protected static final double	IR	The inverse size of the baseline 2D universe.
protected static final double	IR2	The inverse squared size of the baseline 2D universe, 1/R<sup>2</sup>.
protected Path2D	links	The links in this network.
static final double	R	The baseline size of the 2D universe.
private final Vector2D	repulsion	Helper variable to store intermediate results when considering the potential energy resulting from the repulsion between nodes.
private final Vector2D	vec	Temporary storage for the directional vector connecting two nodes.

Fields inherited from class Network

accuracy, engine, fLinks, geometry, GOLDEN_ANGLE, HARD_CORE_STIFFNESS, initialAdjust, isRunning, layoutProgress, layoutTimeout, listener, MAX_LINK_COUNT, MIN_DISTANCE, MIN_SCALED_DISTANCE, nLinks, nNodes, nodes, norm, potential, prevAdjust, prevPotential, radius, rng, status, timestamp

Fields inherited from class AbstractList

modCount

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	Network2D(EvoLudo engine, AbstractGeometry geometry)	Create a new network in 2D for the given engine and geometry.

Method Summary

Modifier and Type	Method	Description
private void	addArc(int source, int target, Vector2D link, Vector2D tip, double arrowsize)	Add a directed arc, including its arrowhead, to the link path.
private void	addEdge(int source, int target)	Add an undirected edge to the link path.
protected double	attraction(int nodeidx)	Calculate the potential energy based on attraction to its neighbours for the node with index nodeidx.
boolean	equals(Object obj)
void	finishLayout()	Add the finishing touches to the graph layout: shift center of mass into origin rescale size of graph find number of links
Node2D	get(int index)
protected double	getConvergenceAccuracy()	Get the effective convergence threshold for the layouting process.
Path2D	getLinks()	Get the links in this network for the GUI to draw.
int	hashCode()
void	initNodes(double pnorm, double nnorm, double unitradius)	Generate the initial placement of all nodes.
void	linkNodes()	Generate the links for the current configuration of the network.
private double	pairDistance(Node2D from, Node2D to, int fromidx, int toidx)	Set vec to the directional vector from from to to and return the corresponding center-to-center distance.
double	relax(int nodeidx)	Relax the potential energy a single node with index nodeidx by adjusting its position.
double	relax(int nodeidx, double dt)	Relaxes the network node with index nodeidx.
protected double	repulsion(int nodeidx)	Calculate the potential energy based on repulsion for the node with index nodeidx.
Node2D[]	toArray()

Methods inherited from class Network

cancelLayout, clear, collectEdges, collectLinks, completeLayout, contains, doLayout, doLayoutPrep, getGeometry, getLayoutTimout, getNLinks, getRadius, getStatus, getTimestamp, getUnitRadius, hasNext, indexOf, isStatus, iterator, lastIndexOf, next, reset, sampleIndices, scaledNodeRadius, scaleRadiusTo, set, setLayoutListener, setLayoutTimout, setRadius, setStatus, shake, size, updateLayoutProgress

Methods inherited from class AbstractList

add, add, addAll, listIterator, listIterator, remove, removeRange, subList

Methods inherited from class AbstractCollection

addAll, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toString

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface Iterable

forEach

Methods inherited from interface Iterator

forEachRemaining, remove

Methods inherited from interface List

addAll, addFirst, addLast, containsAll, getFirst, getLast, isEmpty, remove, removeAll, removeFirst, removeLast, replaceAll, retainAll, reversed, sort, spliterator, toArray

Field Details

FIBONACCI_RADIAL_EXPONENT

private static final double FIBONACCI_RADIAL_EXPONENT

Radial growth exponent of the deterministic well-mixed phyllotactic seed. The value 0.5 reproduces Vogel's area-uniform law, while larger values move the layout towards an Archimedean-looking spiral with a denser center. Convenient values to compare are 0.5, 0.7, 0.8, and 1.0.

See Also:

• Constant Field Values

links

protected Path2D links

The links in this network.

attraction

private final Vector2D attraction

Helper variable to store intermediate results when considering the potential energy resulting from the attraction between neighbouring nodes.

repulsion

private final Vector2D repulsion

Helper variable to store intermediate results when considering the potential energy resulting from the repulsion between nodes.

vec

private final Vector2D vec

Temporary storage for the directional vector connecting two nodes.

R

public static final double R

The baseline size of the 2D universe.

See Also:

• Constant Field Values

IR

protected static final double IR

The inverse size of the baseline 2D universe. Convenience constant.

See Also:

• Constant Field Values

IR2

protected static final double IR2

The inverse squared size of the baseline 2D universe, 1/R<sup>2</sup>. Convenience constant.

See Also:

• Constant Field Values

CONVERGENCE_ACCURACY_SCALE

private static final double CONVERGENCE_ACCURACY_SCALE

Scale factor applied to the nominal 2D accuracy. The contact-based spring energy is smaller than the former center-distance energy, so 2D layouts use a tighter effective threshold to avoid terminating too early.

See Also:

• Constant Field Values

Constructor Details

Network2D

protected Network2D(EvoLudo engine,
 AbstractGeometry geometry)

Create a new network in 2D for the given engine and geometry.

Parameters:

engine - the pacemaker for running the model

geometry - the structure of the population

Method Details

getLinks

public Path2D getLinks()

Get the links in this network for the GUI to draw.

Returns:

the links in this network

initNodes

public void initNodes(double pnorm,
 double nnorm,
 double unitradius)

Description copied from class: Network

Generate the initial placement of all nodes. The size of nodes scales with their total number of incoming and outgoing links in heterogeneous networks.

Specified by:

initNodes in class Network<Node2D>

Parameters:

pnorm - the maximal radius of a node

nnorm - the minimal radius of a node

unitradius - the reference radius of a node

relax

public double relax(int nodeidx)

Description copied from class: Network

Relax the potential energy a single node with index nodeidx by adjusting its position. The potential energy increases proportional to D where D denotes the distance to its neighbours and decreases proportional to 1/D<sup>2</sup> where D refers to the distance from all other nodes.

Specified by:

relax in class Network<Node2D>

Parameters:

nodeidx - the index of the node to relax

Returns:

the change in potential energy

relax

public double relax(int nodeidx,
 double dt)

Description copied from class: Network

Relaxes the network node with index nodeidx. The attraction and repulsion forces act on the node for a time interval dt, which limits the changes in the position of the node.

Specified by:

relax in class Network<Node2D>

Parameters:

nodeidx - the index of the node to relax

dt - the time interval

Returns:

the change in potential energy

See Also:

• Network.relax(int)

getConvergenceAccuracy

protected double getConvergenceAccuracy()

Description copied from class: Network

Get the effective convergence threshold for the layouting process. The base implementation returns Network.accuracy, but subclasses may tighten or relax the criterion when their layout energies use a different natural scale.

Overrides:

getConvergenceAccuracy in class Network<Node2D>

Returns:

the effective convergence threshold

repulsion

protected double repulsion(int nodeidx)

Description copied from class: Network

Calculate the potential energy based on repulsion for the node with index nodeidx. Return the net repulsion (overall direction and magnitude) acting on it in Network.repulsion(int). Implementations may include additional short-range penalties here, for example to discourage overlap between nodes with finite size.

Note:

To prevent disjoint parts of a network (and unstructured populations, in particular) to continue to fly apart, the repulsion changes sign, i.e. turns into attraction, once the distance between nodes exceeds the radius of the universe.

Specified by:

repulsion in class Network<Node2D>

Parameters:

nodeidx - the index of the node to relax

Returns:

the potential energy of the node

attraction

protected double attraction(int nodeidx)

Description copied from class: Network

Calculate the potential energy based on attraction to its neighbours for the node with index nodeidx. Return the net attraction (overall direction and magnitude) acting on it in Network.attraction(int).

Specified by:

attraction in class Network<Node2D>

Parameters:

nodeidx - the index of the node to relax

Returns:

the potential energy of the node

pairDistance

private double pairDistance(Node2D from,
 Node2D to,
 int fromidx,
 int toidx)

Set vec to the directional vector from from to to and return the corresponding center-to-center distance. Coincident nodes are separated by a deterministic fallback direction to keep layouting stable and reproducible.

Parameters:

from - the source node

to - the target node

fromidx - the index of the source node

toidx - the index of the target node

Returns:

the center-to-center distance

finishLayout

public void finishLayout()

Description copied from class: Network

Add the finishing touches to the graph layout:

1. shift center of mass into origin
2. rescale size of graph
3. find number of links

Specified by:

finishLayout in class Network<Node2D>

linkNodes

public void linkNodes()

Description copied from class: Network

Generate the links for the current configuration of the network.

Specified by:

linkNodes in class Network<Node2D>

addEdge

private void addEdge(int source,
 int target)

Add an undirected edge to the link path.

Parameters:

source - the source node index

target - the target node index

addArc

private void addArc(int source,
 int target,
 Vector2D link,
 Vector2D tip,
 double arrowsize)

Add a directed arc, including its arrowhead, to the link path.

Parameters:

source - the source node index

target - the target node index

link - helper vector aligned with the arc

tip - helper vector storing the arrow tip position

arrowsize - the normalized arrow size

toArray

public Node2D[] toArray()

Specified by:

toArray in interface Collection<Node2D>

Specified by:

toArray in interface List<Node2D>

Overrides:

toArray in class AbstractCollection<Node2D>

get

public Node2D get(int index)

Specified by:

get in interface List<Node2D>

Specified by:

get in class AbstractList<Node2D>

equals

public boolean equals(Object obj)

Specified by:

equals in interface Collection<Node2D>

Specified by:

equals in interface List<Node2D>

Overrides:

equals in class Network<Node2D>

hashCode

public int hashCode()

Specified by:

hashCode in interface Collection<Node2D>

Specified by:

hashCode in interface List<Node2D>

Overrides:

hashCode in class Network<Node2D>