fiji.plugin.trackmate.action.closegaps

Interface GapClosingMethod

All Known Implementing Classes:

CloseGapsByDetection, CloseGapsByLinearInterpolation

public interface GapClosingMethod

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	GapClosingMethod.GapClosingParameter

Method Summary

Modifier and Type	Method and Description
static int	countMissingSpots(Collection<org.jgrapht.graph.DefaultWeightedEdge> gaps, Model model)
static int	countMissingSpots(org.jgrapht.graph.DefaultWeightedEdge gap, Model model)
void	execute(TrackMate trackmate, Logger logger) Performs the gap closing.
static List<org.jgrapht.graph.DefaultWeightedEdge>	getAllGaps(Model model) Utility method that can return all the edges of a model that have a gap.
String	getInfoText() Returns a html string containing a descriptive information about this module.
default List<GapClosingMethod.GapClosingParameter>	getParameters() Returns the list of parameters required to configure this method.
static List<Spot>	interpolate(Model model, org.jgrapht.graph.DefaultWeightedEdge edge) Returns a list of newly created spots obtained by interpolating the position, radius, quality and time features of the source and target spot of the specified edge.
static void	interpolateFeature(Spot targetSpot, Spot spot1, Spot spot2, double weight, String feature)
static Settings	makeSettingsForRoiAround(Spot spot, double neighborhoodFactor, Settings settings) Returns a new Settings object copied from the specified settings, but configured with a small ROI centered on the specified spot, with a radius proportional to the radius of the specified spot, and set to operate only on the frame in which the specified spot it.

Method Detail

getParameters

default List<GapClosingMethod.GapClosingParameter> getParameters()

Returns the list of parameters required to configure this method.

The list will be used to autogenerate a configuration panel.

Returns:

a list of parameters.

getInfoText

String getInfoText()

Returns a html string containing a descriptive information about this module.

Returns:

a html string.

execute

void execute(TrackMate trackmate,
             Logger logger)

Performs the gap closing.

Parameters:

trackmate -

logger -

getAllGaps

static List<org.jgrapht.graph.DefaultWeightedEdge> getAllGaps(Model model)

Utility method that can return all the edges of a model that have a gap.

A gap corresponds to spots that are missing in one or several consecutive frames within a track. Gaps are returned as a list of edges. Each edge in this list has a source spot and a target spot separated by strictly more than 1 frame.

Parameters:

model - the model to search for gaps.

Returns:

a list of edges corresponding to gaps.

interpolate

static List<Spot> interpolate(Model model,
                              org.jgrapht.graph.DefaultWeightedEdge edge)

Returns a list of newly created spots obtained by interpolating the position, radius, quality and time features of the source and target spot of the specified edge.

The list is not empty only if the edge bridges a gap, or if the source and target spots are separated by strictly more than 1 frame.

In the list, the spots are not added to the model and are not linked be edges. The spots are added in time order, from the frame just after the source spot, to the frame just before the target spot. The source and target spot are not in the list.

Parameters:

model - the model.

edge - the edge to interpolate.

Returns:

a new list of spots.

interpolateFeature

static void interpolateFeature(Spot targetSpot,
                               Spot spot1,
                               Spot spot2,
                               double weight,
                               String feature)

makeSettingsForRoiAround

static Settings makeSettingsForRoiAround(Spot spot,
                                         double neighborhoodFactor,
                                         Settings settings)

Returns a new Settings object copied from the specified settings, but configured with a small ROI centered on the specified spot, with a radius proportional to the radius of the specified spot, and set to operate only on the frame in which the specified spot it.

Parameters:

spot - the spot to read the coordinates and the frame from.

neighborhoodFactor - the ROI proportionality factor. The ROI radius will be equal to the spot radius times this factor.

settings - a source settings to copy from. Its Settings.imp field must not be null.

Returns:

a new Settings object.

countMissingSpots

static int countMissingSpots(Collection<org.jgrapht.graph.DefaultWeightedEdge> gaps,
                             Model model)

countMissingSpots

static int countMissingSpots(org.jgrapht.graph.DefaultWeightedEdge gap,
                             Model model)