| Modifier and Type | Field and Description |
|---|---|
static Comparator<Spot> |
Spot.frameComparator
A comparator used to sort spots by ascending frame.
|
static Comparator<Spot> |
Spot.nameComparator
A comparator used to sort spots by name.
|
protected Map<Spot,Boolean> |
SelectionChangeEvent.spots
Changes in
Spot selection this event represents. |
static Comparator<Spot> |
Spot.timeComparator
A comparator used to sort spots by ascending time feature.
|
| Modifier and Type | Method and Description |
|---|---|
Spot |
Model.addSpotTo(Spot spotToAdd,
Integer toFrame)
Adds a single spot to the collections managed by this model, mark it as
visible, then update its features.
|
static Spot |
SpotRoi.createSpot(double[] x,
double[] y,
double quality) |
Spot |
SpotCollection.getClosestSpot(Spot location,
int frame,
boolean visibleSpotsOnly)
Returns the closest
Spot to the given location (encoded as a
Spot), contained in the frame frame. |
Spot |
TrackModel.getEdgeSource(org.jgrapht.graph.DefaultWeightedEdge e)
Returns the source spot of the specified edge.
|
Spot |
TrackModel.getEdgeTarget(org.jgrapht.graph.DefaultWeightedEdge e)
Returns the target spot of the specified edge.
|
Spot |
SpotCollection.getSpotAt(Spot location,
int frame,
boolean visibleSpotsOnly)
Returns the
Spot at the given location (encoded as a Spot),
contained in the frame frame. |
Spot |
Model.moveSpotFrom(Spot spotToMove,
Integer fromFrame,
Integer toFrame)
Moves a single spot from a frame to another, make it visible if it was
not, then mark it for feature update.
|
Spot |
Model.removeSpot(Spot spotToRemove)
Removes a single spot from the collections managed by this model.
|
Spot |
SpotCollection.search(int ID)
Retrieves and returns the
Spot object in this collection with the
specified ID. |
| Modifier and Type | Method and Description |
|---|---|
static Comparator<Spot> |
Spot.featureComparator(String feature)
A comparator used to sort spots by ascending feature values.
|
org.jgrapht.traverse.GraphIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.getDepthFirstIterator(Spot start,
boolean directed)
Returns a new depth first iterator over the spots connected by links in
this model.
|
SortedDepthFirstIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.getSortedDepthFirstIterator(Spot start,
Comparator<Spot> comparator,
boolean directed)
Returns a new depth first iterator over the spots connected by links in
this model.
|
Map<Spot,Boolean> |
SelectionChangeEvent.getSpots()
Returns the spots that have been added or removed from the selection.
|
Set<Spot> |
ModelChangeEvent.getSpots() |
Set<Spot> |
SelectionModel.getSpotSelection() |
Iterable<Spot> |
SpotCollection.iterable(boolean visibleSpotsOnly)
A convenience methods that returns an
Iterable wrapper for this
collection as a whole. |
Iterable<Spot> |
SpotCollection.iterable(int frame,
boolean visibleSpotsOnly)
A convenience methods that returns an
Iterable wrapper for a
specific frame of this spot collection. |
Iterator<Spot> |
SpotCollection.iterator(boolean visibleSpotsOnly)
Return an iterator that iterates over all the spots contained in this
collection.
|
Iterator<Spot> |
SpotCollection.iterator(Integer frame,
boolean visibleSpotsOnly)
Return an iterator that iterates over the spots in the specified frame.
|
Set<Spot> |
TrackModel.trackSpots(Integer trackID)
Returns the spots of the track with the specified ID.
|
Set<Spot> |
TrackModel.vertexSet()
Returns a set of the vertices contained in this graph.
|
| Modifier and Type | Method and Description |
|---|---|
void |
SpotCollection.add(Spot spot,
Integer frame)
Adds the given spot to this collection, at the specified frame, and mark
it as visible.
|
org.jgrapht.graph.DefaultWeightedEdge |
Model.addEdge(Spot source,
Spot target,
double weight)
Creates a new edge between two spots, with the specified weight.
|
boolean |
ModelChangeEvent.addSpot(Spot spot) |
Spot |
Model.addSpotTo(Spot spotToAdd,
Integer toFrame)
Adds a single spot to the collections managed by this model, mark it as
visible, then update its features.
|
void |
SelectionModel.addSpotToSelection(Spot spot) |
int |
Spot.compareTo(Spot o) |
boolean |
TrackModel.containsEdge(Spot source,
Spot target)
Returns
true if this model contains the specified edge. |
double |
Spot.diffTo(Spot s,
String feature)
Returns the difference of the feature value for this spot with the one of
the specified spot.
|
List<org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.dijkstraShortestPath(Spot source,
Spot target)
Returns the shortest path between two connected spot, using Dijkstra's
algorithm.
|
Set<org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.edgesOf(Spot spot)
Returns the set of edges of a spot.
|
Spot |
SpotCollection.getClosestSpot(Spot location,
int frame,
boolean visibleSpotsOnly)
Returns the closest
Spot to the given location (encoded as a
Spot), contained in the frame frame. |
org.jgrapht.traverse.GraphIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.getDepthFirstIterator(Spot start,
boolean directed)
Returns a new depth first iterator over the spots connected by links in
this model.
|
org.jgrapht.graph.DefaultWeightedEdge |
TrackModel.getEdge(Spot source,
Spot target)
Returns the specified edge.
|
Integer |
ModelChangeEvent.getFromFrame(Spot spot) |
SortedDepthFirstIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.getSortedDepthFirstIterator(Spot start,
Comparator<Spot> comparator,
boolean directed)
Returns a new depth first iterator over the spots connected by links in
this model.
|
Spot |
SpotCollection.getSpotAt(Spot location,
int frame,
boolean visibleSpotsOnly)
Returns the
Spot at the given location (encoded as a Spot),
contained in the frame frame. |
Integer |
ModelChangeEvent.getSpotFlag(Spot spot)
Returns the modification flag for the given spot affected by this event.
|
Integer |
ModelChangeEvent.getToFrame(Spot spot) |
Spot |
Model.moveSpotFrom(Spot spotToMove,
Integer fromFrame,
Integer toFrame)
Moves a single spot from a frame to another, make it visible if it was
not, then mark it for feature update.
|
double |
Spot.normalizeDiffTo(Spot s,
String feature)
Returns the absolute normalized difference of the feature value of this
spot with the one of the given spot.
|
Integer |
ModelChangeEvent.putFromFrame(Spot spot,
Integer lFromFrame) |
Integer |
ModelChangeEvent.putSpotFlag(Spot spot,
Integer flag) |
Integer |
ModelChangeEvent.putToFrame(Spot spot,
Integer lToFrame) |
boolean |
SpotCollection.remove(Spot spot,
Integer frame)
Removes the given spot from this collection, at the specified frame.
|
org.jgrapht.graph.DefaultWeightedEdge |
Model.removeEdge(Spot source,
Spot target)
Removes an edge between two spots and returns it.
|
Spot |
Model.removeSpot(Spot spotToRemove)
Removes a single spot from the collections managed by this model.
|
void |
SelectionModel.removeSpotFromSelection(Spot spot) |
<T> IterableInterval<T> |
SpotRoi.sample(Spot spot,
ImgPlus<T> img) |
Integer |
TrackModel.trackIDOf(Spot spot)
Returns the track ID the specified spot belong to, or
null
if the specified spot cannot be found in this model. |
void |
Model.updateFeatures(Spot spotToUpdate)
Mark the specified spot for update.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
ModelChangeEvent.addAllSpots(Collection<Spot> lSpots) |
void |
SelectionModel.addSpotToSelection(Collection<Spot> spots) |
<V> org.jgrapht.graph.SimpleDirectedWeightedGraph<V,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.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. |
<V> org.jgrapht.graph.SimpleDirectedWeightedGraph<V,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.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. |
void |
TrackModel.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.
|
void |
TrackModel.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.
|
static SpotCollection |
SpotCollection.fromCollection(Iterable<Spot> spots)
Creates a new
SpotCollection containing only the specified spots. |
static SpotCollection |
SpotCollection.fromMap(Map<Integer,Set<Spot>> source)
Creates a new
SpotCollection from a copy of the specified map of
sets. |
SortedDepthFirstIterator<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
TrackModel.getSortedDepthFirstIterator(Spot start,
Comparator<Spot> comparator,
boolean directed)
Returns a new depth first iterator over the spots connected by links in
this model.
|
void |
SpotCollection.put(int frame,
Collection<Spot> spots)
Stores the specified spots as the content of the specified frame.
|
void |
SelectionModel.removeSpotFromSelection(Collection<Spot> spots) |
void |
SelectionModel.selectTrack(Collection<Spot> spots,
Collection<org.jgrapht.graph.DefaultWeightedEdge> edges,
int direction)
Search and add all spots and links belonging to the same track(s) that of given
spots and
edges to current selection. |
void |
Model.setTracks(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
boolean doNotify)
Sets the tracks stored in this model in bulk.
|
| Constructor and Description |
|---|
Spot(Spot spot)
Creates a new spot, taking its location, its radius, its quality value
and its name from the specified spot.
|
| Constructor and Description |
|---|
SelectionChangeEvent(Object source,
Map<Spot,Boolean> spots,
Map<org.jgrapht.graph.DefaultWeightedEdge,Boolean> edges)
Represents a change in the selection of a displayed TM model.
|
| Modifier and Type | Method and Description |
|---|---|
static ij.ImagePlus |
ExtractTrackStackAction.trackStack(TrackMate trackmate,
Spot spot,
boolean do3d,
Logger logger) |
static ij.ImagePlus |
ExtractTrackStackAction.trackStack(TrackMate trackmate,
Spot start,
Spot end,
boolean do3d,
Logger logger) |
| Modifier and Type | Method and Description |
|---|---|
static <T extends RealType<T>> |
SpotGaussianFitter.spotSubLocalizer(ImgPlus<T> img,
Iterable<Spot> spots,
boolean fixRadius) |
static ij.ImagePlus |
ExtractTrackStackAction.trackStack(Settings settings,
List<Spot> path,
double radius,
boolean do3d,
Logger logger) |
| Modifier and Type | Field and Description |
|---|---|
protected List<Spot> |
ThresholdDetector.spots
The list of
Spot that will be populated by this detector. |
protected List<Spot> |
LogDetector.spots
The list of
Spot that will be populated by this detector. |
protected List<Spot> |
LabelImageDetector.spots
The list of
Spot that will be populated by this detector. |
| Modifier and Type | Method and Description |
|---|---|
static List<Spot> |
DetectionUtils.findLocalMaxima(RandomAccessibleInterval<FloatType> source,
double threshold,
double[] calibration,
double radius,
boolean doSubPixelLocalization,
int numThreads) |
static <R extends IntegerType<R>> |
MaskUtils.fromLabeling(ImgLabeling<Integer,R> labeling,
Interval interval,
double[] calibration)
Creates spots from a label image.
|
static <R extends IntegerType<R>,S extends NumericType<S>> |
MaskUtils.fromLabelingWithROI(ImgLabeling<Integer,R> labeling,
Interval interval,
double[] calibration,
boolean simplify,
RandomAccessibleInterval<S> qualityImage)
Creates spots with ROIs from a 2D label image.
|
static <T extends RealType<T>> |
MaskUtils.fromThreshold(RandomAccessible<T> input,
Interval interval,
double[] calibration,
double threshold,
int numThreads)
Creates spots from a grayscale image, thresholded to create a mask.
|
static <T extends RealType<T>,R extends RealType<R>> |
MaskUtils.fromThreshold(RandomAccessible<T> input,
Interval interval,
double[] calibration,
double threshold,
int numThreads,
RandomAccessibleInterval<R> qualityImage)
Creates spots from a grayscale image, thresholded to create a mask.
|
static <T extends RealType<T>,S extends NumericType<S>> |
MaskUtils.fromThresholdWithROI(RandomAccessible<T> input,
Interval interval,
double[] calibration,
double threshold,
boolean simplify,
int numThreads,
RandomAccessibleInterval<S> qualityImage)
Creates spots with their ROIs from a 2D grayscale image,
thresholded to create a mask.
|
List<Spot> |
ThresholdDetector.getResult() |
List<Spot> |
LogDetector.getResult() |
List<Spot> |
LabelImageDetector.getResult() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
SemiAutoTracker.exposeSpot(Spot newSpot,
Spot previousSpot) |
protected abstract void |
AbstractSemiAutoTracker.exposeSpot(Spot newSpot,
Spot previousSpot)
This method is a hook for subclassers.
|
protected AbstractSemiAutoTracker.SearchRegion<T> |
SemiAutoTracker.getNeighborhood(Spot spot,
int frame) |
protected abstract AbstractSemiAutoTracker.SearchRegion<T> |
AbstractSemiAutoTracker.getNeighborhood(Spot spot,
int frame)
Returns a small neighborhood around the specified spot, but taken at the
specified frame.
|
void |
AbstractSemiAutoTracker.processSpot(Spot initialSpot)
Recursively investigates a neighborhood to find the most likely successor
of a spot, starting with the specified spot and operating recursively.
|
| Modifier and Type | Method and Description |
|---|---|
static FeatureColorGenerator<Spot> |
FeatureUtils.createSpotColorGenerator(Model model,
DisplaySettings displaySettings) |
| Constructor and Description |
|---|
SpotCollectionDataset(Model model,
SelectionModel selectionModel,
DisplaySettings ds,
String xFeature,
List<String> yFeatures,
List<Spot> spots) |
SpotFeatureGrapher(List<Spot> spots,
String xFeature,
List<String> yFeatures,
Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
| Modifier and Type | Method and Description |
|---|---|
void |
SpotShapeAnalyzer.process(Spot spot) |
void |
SpotIntensityMultiCAnalyzer.process(Spot spot) |
void |
SpotFitEllipseAnalyzer.process(Spot spot) |
void |
SpotContrastAndSNRAnalyzer.process(Spot spot) |
abstract void |
AbstractSpotFeatureAnalyzer.process(Spot spot) |
| Modifier and Type | Method and Description |
|---|---|
void |
SpotAnalyzer.process(Iterable<Spot> spots)
Scores a collection spots for the specified channel.
|
void |
SpotAnalyzer.DummySpotAnalyzer.process(Iterable<Spot> spots) |
void |
AbstractSpotFeatureAnalyzer.process(Iterable<Spot> spots) |
| Modifier and Type | Field and Description |
|---|---|
Collection<List<Spot>> |
ConvexBranchesDecomposition.TrackBranchDecomposition.branches
Branches are returned as list of spot.
|
Collection<List<Spot>> |
ConvexBranchesDecomposition.TrackBranchDecomposition.links
Links, as a collection of 2-elements list.
|
| Modifier and Type | Method and Description |
|---|---|
static org.jgrapht.graph.SimpleDirectedGraph<List<Spot>,org.jgrapht.graph.DefaultEdge> |
ConvexBranchesDecomposition.buildBranchGraph(ConvexBranchesDecomposition.TrackBranchDecomposition branchDecomposition)
Builds a directed graph made of a convex branch decomposition.
|
static Map<Spot,Integer> |
GraphUtils.cumulativeBranchWidth(TrackModel model) |
Collection<List<Spot>> |
ConvexBranchesDecomposition.getBranches()
Returns the collection of branches built by this algorithm.
|
Map<Integer,Collection<List<Spot>>> |
ConvexBranchesDecomposition.getBranchesPerTrack()
Returns the mapping of each source track ID to the branches it was split
in.
|
Collection<List<Spot>> |
ConvexBranchesDecomposition.getLinks()
Returns the links cut by this algorithm when splitting the model in
linear, convex branches.
|
Map<Integer,Collection<List<Spot>>> |
ConvexBranchesDecomposition.getLinksPerTrack()
Returns the mapping of each source track ID to the links that were cut in
it to split it in branches.
|
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
FromContinuousBranches.getResult() |
static Set<Spot> |
GraphUtils.getSibblings(org.jgrapht.alg.util.NeighborCache<Spot,org.jgrapht.graph.DefaultWeightedEdge> cache,
Spot spot) |
List<Spot> |
TimeDirectedNeighborIndex.predecessorListOf(Spot v)
Returns the set of vertices which are the predecessors of a specified
vertex.
|
Set<Spot> |
TimeDirectedNeighborIndex.predecessorsOf(Spot v)
Returns the set of vertices which are the predecessors of a specified
vertex.
|
List<Spot> |
TimeDirectedNeighborIndex.successorListOf(Spot v)
Returns the set of vertices which are the successors of a specified
vertex.
|
Set<Spot> |
TimeDirectedNeighborIndex.successorsOf(Spot v)
Returns the set of vertices which are the successors of a specified
vertex.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
TimeDirectedSortedDepthFirstIterator.addUnseenChildrenOf(Spot vertex) |
protected void |
TimeDirectedDepthFirstIterator.addUnseenChildrenOf(Spot vertex) |
static Set<Spot> |
GraphUtils.getSibblings(org.jgrapht.alg.util.NeighborCache<Spot,org.jgrapht.graph.DefaultWeightedEdge> cache,
Spot spot) |
List<Spot> |
TimeDirectedNeighborIndex.predecessorListOf(Spot v)
Returns the set of vertices which are the predecessors of a specified
vertex.
|
Set<Spot> |
TimeDirectedNeighborIndex.predecessorsOf(Spot v)
Returns the set of vertices which are the predecessors of a specified
vertex.
|
List<Spot> |
TimeDirectedNeighborIndex.successorListOf(Spot v)
Returns the set of vertices which are the successors of a specified
vertex.
|
Set<Spot> |
TimeDirectedNeighborIndex.successorsOf(Spot v)
Returns the set of vertices which are the successors of a specified
vertex.
|
| Modifier and Type | Method and Description |
|---|---|
void |
TimeDirectedNeighborIndex.edgeAdded(org.jgrapht.event.GraphEdgeChangeEvent<Spot,org.jgrapht.graph.DefaultWeightedEdge> e) |
void |
TimeDirectedNeighborIndex.edgeRemoved(org.jgrapht.event.GraphEdgeChangeEvent<Spot,org.jgrapht.graph.DefaultWeightedEdge> e) |
static Set<Spot> |
GraphUtils.getSibblings(org.jgrapht.alg.util.NeighborCache<Spot,org.jgrapht.graph.DefaultWeightedEdge> cache,
Spot spot) |
static boolean |
GraphUtils.isTree(Iterable<Spot> spots,
TimeDirectedNeighborIndex cache) |
void |
TimeDirectedNeighborIndex.vertexAdded(org.jgrapht.event.GraphVertexChangeEvent<Spot> e) |
void |
TimeDirectedNeighborIndex.vertexRemoved(org.jgrapht.event.GraphVertexChangeEvent<Spot> e) |
| Constructor and Description |
|---|
TimeDirectedDepthFirstIterator(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> g,
Spot startVertex) |
TimeDirectedSortedDepthFirstIterator(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> g,
Spot startVertex,
Comparator<Spot> comparator) |
| Constructor and Description |
|---|
FromContinuousBranches(Collection<List<Spot>> branches,
Collection<List<Spot>> links) |
FromContinuousBranches(Collection<List<Spot>> branches,
Collection<List<Spot>> links) |
TimeDirectedDepthFirstIterator(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> g,
Spot startVertex) |
TimeDirectedNeighborIndex(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> g) |
TimeDirectedSortedDepthFirstIterator(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> g,
Spot startVertex,
Comparator<Spot> comparator) |
TimeDirectedSortedDepthFirstIterator(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> g,
Spot startVertex,
Comparator<Spot> comparator) |
| Modifier and Type | Field and Description |
|---|---|
protected ConcurrentHashMap<Integer,Spot> |
TmXmlReader.cache
A map of all spots loaded.
|
| Modifier and Type | Method and Description |
|---|---|
static double |
LAPUtils.computeLinkingCostFor(Spot s0,
Spot s1,
double distanceCutOff,
double blockingValue,
Map<String,Double> featurePenalties)
Compute the cost to link two spots, in the default way for the TrackMate trackmate.
|
| Modifier and Type | Method and Description |
|---|---|
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
KalmanTracker.getResult() |
| Modifier and Type | Field and Description |
|---|---|
protected org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
NearestNeighborTracker.graph |
| Modifier and Type | Method and Description |
|---|---|
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
NearestNeighborTracker.getResult() |
| Modifier and Type | Method and Description |
|---|---|
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
OverlapTracker.getResult() |
| Modifier and Type | Field and Description |
|---|---|
protected org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
SparseLAPFrameToFrameTracker.graph |
| Modifier and Type | Method and Description |
|---|---|
protected CostFunction<Spot,Spot> |
SparseLAPFrameToFrameTracker.getCostFunction(Map<String,Double> featurePenalties)
Creates a suitable cost function.
|
protected CostFunction<Spot,Spot> |
SparseLAPFrameToFrameTracker.getCostFunction(Map<String,Double> featurePenalties)
Creates a suitable cost function.
|
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
SparseLAPTracker.getResult() |
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
SparseLAPSegmentTracker.getResult() |
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> |
SparseLAPFrameToFrameTracker.getResult() |
| Constructor and Description |
|---|
SparseLAPSegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
Map<String,Object> settings) |
| Modifier and Type | Method and Description |
|---|---|
double |
SquareDistCostFunction.linkingCost(Spot source,
Spot target) |
double |
FeaturePenaltyCostFunction.linkingCost(Spot source,
Spot target) |
| Modifier and Type | Method and Description |
|---|---|
protected CostFunction<Spot,Spot> |
JaqamanSegmentCostMatrixCreator.getCostFunctionFor(Map<String,Double> featurePenalties) |
protected CostFunction<Spot,Spot> |
JaqamanSegmentCostMatrixCreator.getCostFunctionFor(Map<String,Double> featurePenalties) |
List<Spot> |
GraphSegmentSplitter.getSegmentEnds() |
List<List<Spot>> |
GraphSegmentSplitter.getSegmentMiddles() |
List<Spot> |
GraphSegmentSplitter.getSegmentStarts() |
List<Spot> |
JaqamanSegmentCostMatrixCreator.getSourceList() |
List<Spot> |
JaqamanSegmentCostMatrixCreator.getTargetList() |
| Modifier and Type | Method and Description |
|---|---|
double |
JaqamanSegmentCostMatrixCreator.getAlternativeCostForSource(Spot source) |
double |
JaqamanSegmentCostMatrixCreator.getAlternativeCostForTarget(Spot target) |
| Constructor and Description |
|---|
GraphSegmentSplitter(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
boolean findMiddlePoints) |
JaqamanSegmentCostMatrixCreator(org.jgrapht.Graph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
Map<String,Object> settings)
Instantiates a cost matrix creator for the top-left quadrant of the
segment linking cost matrix.
|
| Modifier and Type | Method and Description |
|---|---|
static <T extends RealType<T>> |
SpotUtil.iterable(Spot spot,
ImgPlus<T> img) |
static void |
TMUtils.localize(Spot spot,
double[] coords)
Store the x, y, z coordinates of the specified spot in the first 3
elements of the specified double array.
|
| Constructor and Description |
|---|
SpotNeighborhood(Spot spot,
ImgPlus<T> img) |
| Modifier and Type | Method and Description |
|---|---|
void |
TrackMateModelView.centerViewOn(Spot spot)
Centers the view on the given spot.
|
Color |
UniformSpotColorGenerator.color(Spot obj) |
Color |
SpotColorGeneratorPerTrackFeature.color(Spot spot) |
Color |
SpotColorGeneratorPerEdgeFeature.color(Spot spot) |
Color |
SpotColorGenerator.color(Spot spot) |
Color |
ManualSpotPerEdgeColorGenerator.color(Spot spot) |
Color |
ManualSpotColorGenerator.color(Spot spot) |
| Modifier and Type | Field and Description |
|---|---|
protected Spot |
SpotOverlay.editingSpot |
| Modifier and Type | Field and Description |
|---|---|
protected Collection<Spot> |
SpotOverlay.spotSelection |
| Modifier and Type | Method and Description |
|---|---|
void |
HyperStackDisplayer.centerViewOn(Spot spot) |
protected void |
TrackOverlay.drawEdge(Graphics2D g2d,
Spot source,
Spot target,
int xcorner,
int ycorner,
double magnification) |
protected void |
TrackOverlay.drawEdge(Graphics2D g2d,
Spot source,
Spot target,
int xcorner,
int ycorner,
double magnification,
float transparency) |
protected void |
SpotOverlay.drawSpot(Graphics2D g2d,
Spot spot,
double zslice,
int xcorner,
int ycorner,
double magnification,
boolean filled) |
| Modifier and Type | Method and Description |
|---|---|
void |
SpotOverlay.setSpotSelection(Collection<Spot> spots) |
| Modifier and Type | Method and Description |
|---|---|
static TablePanel<Spot> |
AllSpotsTableView.createSpotTable(Model model,
DisplaySettings ds) |
TablePanel<Spot> |
TrackTableView.getSpotTable() |
| Modifier and Type | Method and Description |
|---|---|
void |
TrackTableView.centerViewOn(Spot spot) |
void |
BranchTableView.centerViewOn(Spot spot) |
void |
AllSpotsTableView.centerViewOn(Spot spot) |
| Modifier and Type | Method and Description |
|---|---|
Spot |
JGraphXAdapter.getSpotFor(com.mxgraph.model.mxICell cell) |
| Modifier and Type | Method and Description |
|---|---|
com.mxgraph.model.mxCell |
JGraphXAdapter.addJGraphTVertex(Spot vertex) |
void |
TrackScheme.centerViewOn(Spot spot) |
com.mxgraph.model.mxCell |
JGraphXAdapter.getCellFor(Spot spot) |
String |
SpotImageUpdater.getImageString(Spot spot,
double radiusFactor)
Returns the image string of the given spot, based on the raw images
contained in the given model.
|
String |
SpotIconGrabber.getImageString(Spot spot,
double radiusFactor)
Returns the image string for the specified spot.
|
void |
JGraphXAdapter.removeMapping(Spot spot) |
| Modifier and Type | Method and Description |
|---|---|
void |
JGraphXAdapter.edgeAdded(org.jgrapht.event.GraphEdgeChangeEvent<Spot,org.jgrapht.graph.DefaultWeightedEdge> e) |
void |
JGraphXAdapter.edgeRemoved(org.jgrapht.event.GraphEdgeChangeEvent<Spot,org.jgrapht.graph.DefaultWeightedEdge> e) |
void |
JGraphXAdapter.vertexAdded(org.jgrapht.event.GraphVertexChangeEvent<Spot> e) |
void |
JGraphXAdapter.vertexRemoved(org.jgrapht.event.GraphVertexChangeEvent<Spot> e) |
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