Package sc.fiji.snt.analysis.graph

Class GraphColorMapper<V,E extends org.jgrapht.graph.DefaultWeightedEdge>

java.lang.Object

sc.fiji.snt.analysis.ColorMapper

sc.fiji.snt.analysis.graph.GraphColorMapper<V,E>

Type Parameters:

V - the vertex type

E - the edge type, must extend DefaultWeightedEdge

public class GraphColorMapper<V,E extends org.jgrapht.graph.DefaultWeightedEdge>
extends ColorMapper

A color mapping utility for graph visualization that assigns colors to vertices and edges based on various graph metrics. This class supports multiple mapping strategies and color schemes for graph visualization.

The mapper supports the following metrics:

• BETWEENNESS_CENTRALITY - Colors vertices based on their betweenness centrality
• ECCENTRICITY - Maps colors based on vertex eccentricity
• CONNECTIVITY - Colors components based on connectivity
• EDGE_WEIGHT - Maps colors based on edge weights
• PAGE_RANK - Colors vertices based on PageRank algorithm
• IN_DEGREE - Maps colors based on vertex in-degree
• OUT_DEGREE - Maps colors based on vertex out-degree
• INCOMING_WEIGHT - Colors based on sum of incoming edge weights
• OUTGOING_WEIGHT - Colors based on sum of outgoing edge weights
• HEAVY_PATH_DECOMPOSITION - Colors edges based on heavy path decomposition

The mapping can be applied to:

• Vertices only (VERTICES)
• Edges only (EDGES)
• Both vertices and edges (VERTICES_AND_EDGES)

See Also:

• ColorMapper
• SNTGraph

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BETWEENNESS_CENTRALITY	Flag for "Betweenness centrality" mapping.
static final String	CONNECTIVITY	Flag for "Connected components" mapping.
static final String	ECCENTRICITY	Flag for "Eccentricity" mapping.
static final String	EDGE_WEIGHT	Flag for "Edge weight" mapping.
static final int	EDGES
protected SNTGraph<V,E>	graph
static final String	HEAVY_PATH_DECOMPOSITION	Flag for "Heavy path decomposition" mapping.
static final String	IN_DEGREE	Flag for "In degree" mapping.
static final String	INCOMING_WEIGHT	Flag for "Incoming weight" mapping.
static final String	OUT_DEGREE	Flag for "Out degree" mapping.
static final String	OUTGOING_WEIGHT	Flag for "Outgoing weight" mapping.
static final String	PAGE_RANK	Flag for "Page rank" mapping.
protected org.jgrapht.graph.AsSubgraph<V,E>	subgraph
static final int	VERTICES
static final int	VERTICES_AND_EDGES

Fields inherited from class sc.fiji.snt.analysis.ColorMapper

colorTable, integerScale, luts, lutService, max, min

Constructor Summary

Constructors

Constructor	Description
GraphColorMapper()
GraphColorMapper(org.scijava.Context context)

Method Summary

Modifier and Type	Method	Description
Set<String>	getAvailableLuts()	Gets the available LUTs.
net.imglib2.display.ColorTable	getColorTable(String lut)
static List<String>	getMetrics()	Gets the list of supported mapping metrics.
int	map(SNTGraph<V,E> graph, String measurement, String lut)
int	map(SNTGraph<V,E> graph, String measurement, net.imglib2.display.ColorTable colorTable)
int	map(SNTGraph<V,E> graph, org.jgrapht.graph.AsSubgraph<V,E> subgraph, String measurement, net.imglib2.display.ColorTable colorTable)
protected void	mapToBetweennessCentrality(net.imglib2.display.ColorTable colorTable)
protected void	mapToConnectivity(net.imglib2.display.ColorTable colorTable)
protected void	mapToEccentricity(net.imglib2.display.ColorTable colorTable)
protected void	mapToEdgeWeight(net.imglib2.display.ColorTable colorTable)
protected void	mapToHeavyPathDecomposition(net.imglib2.display.ColorTable colorTable)
protected void	mapToIncomingWeight(net.imglib2.display.ColorTable colorTable)
protected void	mapToInDegree(net.imglib2.display.ColorTable colorTable)
protected void	mapToOutDegree(net.imglib2.display.ColorTable colorTable)
protected void	mapToOutgoingWeight(net.imglib2.display.ColorTable colorTable)
protected void	mapToPageRank(net.imglib2.display.ColorTable colorTable)
protected void	mapToProperty(String measurement, net.imglib2.display.ColorTable colorTable)
void	resetMinMax()
void	setLegend(GraphEditor editor)
void	setMinMax(double min, double max)	Sets the LUT mapping bounds.

Methods inherited from class sc.fiji.snt.analysis.ColorMapper

getColor, getColorRGB, getColorTable, getMinMax, getNaNColor, initLuts, isIntegerScale, map, setNaNColor, unMap, unMap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

BETWEENNESS_CENTRALITY

public static final String BETWEENNESS_CENTRALITY

Flag for "Betweenness centrality" mapping.

See Also:

• Constant Field Values

ECCENTRICITY

public static final String ECCENTRICITY

Flag for "Eccentricity" mapping.

See Also:

• Constant Field Values

CONNECTIVITY

public static final String CONNECTIVITY

Flag for "Connected components" mapping.

See Also:

• Constant Field Values

EDGE_WEIGHT

public static final String EDGE_WEIGHT

Flag for "Edge weight" mapping.

See Also:

• Constant Field Values

PAGE_RANK

public static final String PAGE_RANK

Flag for "Page rank" mapping.

See Also:

• Constant Field Values

IN_DEGREE

public static final String IN_DEGREE

Flag for "In degree" mapping.

See Also:

• Constant Field Values

OUT_DEGREE

public static final String OUT_DEGREE

Flag for "Out degree" mapping.

See Also:

• Constant Field Values

INCOMING_WEIGHT

public static final String INCOMING_WEIGHT

Flag for "Incoming weight" mapping.

See Also:

• Constant Field Values

OUTGOING_WEIGHT

public static final String OUTGOING_WEIGHT

Flag for "Outgoing weight" mapping.

See Also:

• Constant Field Values

HEAVY_PATH_DECOMPOSITION

public static final String HEAVY_PATH_DECOMPOSITION

Flag for "Heavy path decomposition" mapping.

See Also:

• Constant Field Values

VERTICES

public static final int VERTICES

See Also:

• Constant Field Values

EDGES

public static final int EDGES

See Also:

• Constant Field Values

VERTICES_AND_EDGES

public static final int VERTICES_AND_EDGES

See Also:

• Constant Field Values

graph

protected SNTGraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> graph

subgraph

protected org.jgrapht.graph.AsSubgraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> subgraph

Constructor Details

GraphColorMapper

public GraphColorMapper(org.scijava.Context context)

GraphColorMapper

public GraphColorMapper()

Method Details

getMetrics

public static List<String> getMetrics()

Gets the list of supported mapping metrics.

Returns:

the list of mapping metrics.

getAvailableLuts

public Set<String> getAvailableLuts()

Gets the available LUTs.

Returns:

the set of keys, corresponding to the set of LUTs available

getColorTable

public net.imglib2.display.ColorTable getColorTable(String lut)

map

public int map(SNTGraph<V,E> graph,
 String measurement,
 String lut)

map

public int map(SNTGraph<V,E> graph,
 String measurement,
 net.imglib2.display.ColorTable colorTable)

map

public int map(SNTGraph<V,E> graph,
 org.jgrapht.graph.AsSubgraph<V,E> subgraph,
 String measurement,
 net.imglib2.display.ColorTable colorTable)

mapToProperty

protected void mapToProperty(String measurement,
 net.imglib2.display.ColorTable colorTable)

mapToConnectivity

protected void mapToConnectivity(net.imglib2.display.ColorTable colorTable)

mapToEdgeWeight

protected void mapToEdgeWeight(net.imglib2.display.ColorTable colorTable)

mapToBetweennessCentrality

protected void mapToBetweennessCentrality(net.imglib2.display.ColorTable colorTable)

mapToEccentricity

protected void mapToEccentricity(net.imglib2.display.ColorTable colorTable)

mapToPageRank

protected void mapToPageRank(net.imglib2.display.ColorTable colorTable)

mapToInDegree

protected void mapToInDegree(net.imglib2.display.ColorTable colorTable)

mapToOutDegree

protected void mapToOutDegree(net.imglib2.display.ColorTable colorTable)

mapToIncomingWeight

protected void mapToIncomingWeight(net.imglib2.display.ColorTable colorTable)

mapToOutgoingWeight

protected void mapToOutgoingWeight(net.imglib2.display.ColorTable colorTable)

mapToHeavyPathDecomposition

protected void mapToHeavyPathDecomposition(net.imglib2.display.ColorTable colorTable)

setMinMax

public void setMinMax(double min,
 double max)

Description copied from class: ColorMapper

Sets the LUT mapping bounds.

Overrides:

setMinMax in class ColorMapper

Parameters:

min - the mapping lower bound (i.e., the highest measurement value for the LUT scale). It is automatically calculated (the default) when set to Double.NaN

max - the mapping upper bound (i.e., the highest measurement value for the LUT scale).It is automatically calculated (the default) when set to Double.NaN.

resetMinMax

public void resetMinMax()

setLegend

public void setLegend(GraphEditor editor)