fiji.plugin.trackmate

Class TrackModel

java.lang.Object

fiji.plugin.trackmate.TrackModel

public class TrackModel
extends Object

A component of Model specialized for tracks.

Author:

Jean-Yves Tinevez

Method Summary

Modifier and Type	Method and Description
boolean	containsEdge(Spot source, Spot target) Returns true if this model contains the specified edge.
<V> org.jgrapht.graph.SimpleDirectedWeightedGraph<V,org.jgrapht.graph.DefaultWeightedEdge>	copy(Supplier<V> factory, Function1<Spot,V> function, Map<Spot,V> mappings) Returns a new graph with the same structure as the one wrapped here, and with vertices generated by the given Function1.
List<org.jgrapht.graph.DefaultWeightedEdge>	dijkstraShortestPath(Spot source, Spot target) Returns the shortest path between two connected spot, using Dijkstra's algorithm.
String	echo()
Set<org.jgrapht.graph.DefaultWeightedEdge>	edgeSet() Returns a set of the edges contained in this model.
Set<org.jgrapht.graph.DefaultWeightedEdge>	edgesOf(Spot spot) Returns the set of edges of a spot.
void	from(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> lGraph, Map<Integer,Set<Spot>> trackSpots, Map<Integer,Set<org.jgrapht.graph.DefaultWeightedEdge>> trackEdges, Map<Integer,Boolean> trackVisibility, Map<Integer,String> trackNames) This method is meant to help building a model from a serialized source, such as a saved file.
org.jgrapht.traverse.GraphIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge>	getDepthFirstIterator(Spot start, boolean directed) Returns a new depth first iterator over the spots connected by links in this model.
TimeDirectedNeighborIndex	getDirectedNeighborIndex()
org.jgrapht.graph.DefaultWeightedEdge	getEdge(Spot source, Spot target) Returns the specified edge.
Spot	getEdgeSource(org.jgrapht.graph.DefaultWeightedEdge e) Returns the source spot of the specified edge.
Spot	getEdgeTarget(org.jgrapht.graph.DefaultWeightedEdge e) Returns the target spot of the specified edge.
double	getEdgeWeight(org.jgrapht.graph.DefaultWeightedEdge edge) Returns the weight assigned to the specified edge.
SortedDepthFirstIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge>	getSortedDepthFirstIterator(Spot start, Comparator<Spot> comparator, boolean directed) Returns a new depth first iterator over the spots connected by links in this model.
boolean	isVisible(Integer ID) Returns true if the track with the specified ID is marked as visible, false otherwise.
String	name(Integer id) Returns the name of the track with the specified ID.
int	nTracks(boolean visibleOnly)
void	setName(Integer id, String name) Sets the name of the track with the specified ID.
Set<org.jgrapht.graph.DefaultWeightedEdge>	trackEdges(Integer trackID) Returns the edges of the track with the specified ID.
Integer	trackIDOf(org.jgrapht.graph.DefaultWeightedEdge edge) Returns the track ID the specified edge belong to, or null if the specified edge cannot be found in this model.
Integer	trackIDOf(Spot spot) Returns the track ID the specified spot belong to, or null if the specified spot cannot be found in this model.
Set<Integer>	trackIDs(boolean visibleOnly) Returns the set of track IDs managed by this model, ordered by track names (alpha-numerically sorted).
Set<Spot>	trackSpots(Integer trackID) Returns the spots of the track with the specified ID.
Set<Integer>	unsortedTrackIDs(boolean visibleOnly) Returns the set of track IDs managed by this model, unsorted.
Set<Spot>	vertexSet() Returns a set of the vertices contained in this graph.

Methods inherited from class java.lang.Object

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

Method Detail

from

public void from(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> lGraph,
                 Map<Integer,Set<Spot>> trackSpots,
                 Map<Integer,Set<org.jgrapht.graph.DefaultWeightedEdge>> trackEdges,
                 Map<Integer,Boolean> trackVisibility,
                 Map<Integer,String> trackNames)

This method is meant to help building a model from a serialized source, such as a saved file. It allows specifying the exact mapping of track IDs to the connected sets. The model content is completely replaced by the specified parameters, including the global graph, its connected components (both in spots and edges), visibility and naming.

It is the caller responsibility to ensure that the graph and provided component are coherent. Unexpected behavior might result otherwise.

Parameters:

lGraph - the mother graph for the model.

trackSpots - the mapping of track IDs vs the connected components as sets of spots.

trackEdges - the mapping of track IDs vs the connected components as sets of edges.

trackVisibility - the track visibility.

trackNames - the track names.

copy

public <V> org.jgrapht.graph.SimpleDirectedWeightedGraph<V,org.jgrapht.graph.DefaultWeightedEdge> copy(Supplier<V> factory,
                                                                                                       Function1<Spot,V> function,
                                                                                                       Map<Spot,V> mappings)

Returns a new graph with the same structure as the one wrapped here, and with vertices generated by the given Function1. Edges are copied in direction and weight.

Type Parameters:

V - the type of the vertices.

Parameters:

factory - the vertex factory used to instantiate new vertices in the new graph

function - the function used to set values of a new vertex in the new graph, from the matching spot

mappings - a map that will receive mappings from Spot to the new vertices. Can be null if you do not want to get the mappings

Returns:

a new SimpleDirectedWeightedGraph.

containsEdge

public boolean containsEdge(Spot source,
                            Spot target)

Returns true if this model contains the specified edge.

Parameters:

source - the edge source vertex.

target - the edge target vertex.

Returns:

true if this model contains the specified edge.

See Also:

Graph.containsEdge(Object, Object)

getEdge

public org.jgrapht.graph.DefaultWeightedEdge getEdge(Spot source,
                                                     Spot target)

Returns the specified edge.

Parameters:

source - the edge source vertex.

target - the edge target vertex.

Returns:

the specified edge, or null if it does not exist.

See Also:

Graph.getEdge(Object, Object)

edgesOf

public Set<org.jgrapht.graph.DefaultWeightedEdge> edgesOf(Spot spot)

Returns the set of edges of a spot.

Parameters:

spot - the spot.

Returns:

the set of edges connected to this spot. Can be empty if the spot does not have any edge.

See Also:

Graph.edgesOf(Object)

edgeSet

public Set<org.jgrapht.graph.DefaultWeightedEdge> edgeSet()

Returns a set of the edges contained in this model. The set is backed by the graph, so changes to the graph are reflected in the set. If the graph is modified while an iteration over the set is in progress, the results of the iteration are undefined.

Returns:

the edges of this model.

See Also:

Graph.edgeSet()

vertexSet

public Set<Spot> vertexSet()

Returns a set of the vertices contained in this graph. The set is backed by the graph, so changes to the graph are reflected in the set. If the graph is modified while an iteration over the set is in progress, the results of the iteration are undefined.

Returns:

the vertices of this model.

See Also:

Graph.vertexSet()

getEdgeSource

public Spot getEdgeSource(org.jgrapht.graph.DefaultWeightedEdge e)

Returns the source spot of the specified edge.

Parameters:

e - the edge.

Returns:

the source spot of this edge.

See Also:

Graph.getEdgeSource(Object)

getEdgeTarget

public Spot getEdgeTarget(org.jgrapht.graph.DefaultWeightedEdge e)

Returns the target spot of the specified edge.

Parameters:

e - the edge.

Returns:

the target spot of this edge.

See Also:

Graph.getEdgeTarget(Object)

getEdgeWeight

public double getEdgeWeight(org.jgrapht.graph.DefaultWeightedEdge edge)

Returns the weight assigned to the specified edge. Its physical meaning depend on the particle-linking algorithm used to generate the edge.

Parameters:

edge - the edge.

Returns:

the edge weight.

See Also:

Graph.getEdgeWeight(Object)

isVisible

public boolean isVisible(Integer ID)

Returns true if the track with the specified ID is marked as visible, false otherwise. Throws a NullPointerException if the track ID is unknown to this model.

Parameters:

ID - the track ID.

Returns:

the track visibility.

trackIDs

public Set<Integer> trackIDs(boolean visibleOnly)

Returns the set of track IDs managed by this model, ordered by track names (alpha-numerically sorted).

Parameters:

visibleOnly - if true, only visible track IDs will be returned.

Returns:

a new set of track IDs.

unsortedTrackIDs

public Set<Integer> unsortedTrackIDs(boolean visibleOnly)

Returns the set of track IDs managed by this model, unsorted. This method exists to provide better performance for callers that do not need the IDs to be sorted.

Parameters:

visibleOnly - if true, only visible track IDs will be returned.

Returns:

the set of track IDs.

name

public String name(Integer id)

Returns the name of the track with the specified ID.

Parameters:

id - the track ID.

Returns:

the track name.

setName

public void setName(Integer id,
                    String name)

Sets the name of the track with the specified ID.

Parameters:

id - the track ID.

name - the name for the track.

trackEdges

public Set<org.jgrapht.graph.DefaultWeightedEdge> trackEdges(Integer trackID)

Returns the edges of the track with the specified ID.

Parameters:

trackID - the track ID.

Returns:

the set of edges.

trackSpots

public Set<Spot> trackSpots(Integer trackID)

Returns the spots of the track with the specified ID.

Parameters:

trackID - the track ID.

Returns:

the set of spots.

nTracks

public int nTracks(boolean visibleOnly)

trackIDOf

public Integer trackIDOf(org.jgrapht.graph.DefaultWeightedEdge edge)

Returns the track ID the specified edge belong to, or null if the specified edge cannot be found in this model.

Parameters:

edge - the edge to search for.

Returns:

the track ID it belongs to.

trackIDOf

public Integer trackIDOf(Spot spot)

Returns the track ID the specified spot belong to, or null if the specified spot cannot be found in this model.

Parameters:

spot - the spot to search for.

Returns:

the track ID it belongs to.

echo

public String echo()

getDepthFirstIterator

public org.jgrapht.traverse.GraphIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> getDepthFirstIterator(Spot start,
                                                                                                            boolean directed)

Returns a new depth first iterator over the spots connected by links in this model. A boolean flag allow to set whether the returned iterator does take into account the edge direction. If true, the iterator will not be able to iterate backward in time.

Parameters:

start - the spot to start iteration with. Can be null, then the start will be taken randomly and will traverse all the links.

directed - if true returns a directed iterator, undirected if false.

Returns:

a new depth-first iterator.

getSortedDepthFirstIterator

public SortedDepthFirstIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> getSortedDepthFirstIterator(Spot start,
                                                                                                        Comparator<Spot> comparator,
                                                                                                        boolean directed)

Returns a new depth first iterator over the spots connected by links in this model. This iterator is sorted: when branching, it chooses the next vertex according to a specified comparator. A boolean flag allow to set whether the returned iterator does take into account the edge direction. If true, the iterator will not be able to iterate backward in time.

Parameters:

start - the spot to start iteration with. Can be null, then the start will be taken randomly and will traverse all the links.

directed - if true returns a directed iterator, undirected if false.

comparator - the comparator to use to pick children in order when branching.

Returns:

a new depth-first iterator.

getDirectedNeighborIndex

public TimeDirectedNeighborIndex getDirectedNeighborIndex()

dijkstraShortestPath

public List<org.jgrapht.graph.DefaultWeightedEdge> dijkstraShortestPath(Spot source,
                                                                        Spot target)

Returns the shortest path between two connected spot, using Dijkstra's algorithm. The edge weights, if any, are ignored here, meaning that the returned path is the shortest in terms of number of edges.

Returns null if the two spots are not connected by a track, or if one of the spot do not belong to the graph, or if the graph field is null.

Parameters:

source - the spot to start the path with

target - the spot to stop the path with

Returns:

the shortest path, as a list of edges.