fiji.plugin.trackmate.tracking.jaqaman

Class SparseLAPTrackerFactory

java.lang.Object

fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory

fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory

All Implemented Interfaces:

SpotTrackerFactory, TrackMateModule, SciJavaPlugin

Direct Known Subclasses:

SimpleSparseLAPTrackerFactory

public class SparseLAPTrackerFactory
extends SegmentTrackerFactory

Field Summary

Fields

Modifier and Type	Field and Description
static String	THIS_INFO_TEXT
static String	THIS_NAME
static String	THIS_TRACKER_KEY

Fields inherited from class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory

errorMessage

Constructor Summary

Constructors

Constructor and Description
SparseLAPTrackerFactory()

Method Summary

Modifier and Type	Method and Description
boolean	checkSettingsValidity(Map<String,Object> settings) Checks the validity of the given settings map for the tracker.
SparseLAPTrackerFactory	copy() Returns a copy the current instance.
SpotTracker	create(SpotCollection spots, Map<String,Object> settings) Instantiates and returns a new SpotTracker configured to operate on the specified SpotCollection, using the specified settins map.
Map<String,Object>	getDefaultSettings() Returns a new default settings map suitable for the tracker Settings are instantiated with default values.
ImageIcon	getIcon() Returns the icon for this action.
String	getInfoText() Returns a html string containing a descriptive information about this module.
String	getKey() Returns a unique identifier of this module.
String	getName() Returns the human-compliant name of this module.
ConfigurationPanel	getTrackerConfigurationPanel(Model model) Returns a new GUI panel able to configure the settings suitable for the target tracker identified by the key parameter.
boolean	marshall(Map<String,Object> settings, org.jdom2.Element element) Marshall into the Element the settings in the Map that relate to segment linking: gap-closing, merging segments, splitting segments.
String	toString(Map<String,Object> sm) A utility method that builds a string representation of a settings map owing to the currently selected tracker in this provider.
boolean	unmarshall(org.jdom2.Element element, Map<String,Object> settings) Un-marshall a JDom element to update a settings map, and sets the target tracker of this provider from the element.

Methods inherited from class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory

getErrorMessage, unmarshallSegment

Methods inherited from class java.lang.Object

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

Methods inherited from interface fiji.plugin.trackmate.TrackMateModule

forbidMultithreading

Field Detail

THIS_TRACKER_KEY

public static final String THIS_TRACKER_KEY

See Also:

Constant Field Values

THIS_NAME

public static final String THIS_NAME

See Also:

Constant Field Values

THIS_INFO_TEXT

public static final String THIS_INFO_TEXT

See Also:

Constant Field Values

Constructor Detail

SparseLAPTrackerFactory

public SparseLAPTrackerFactory()

Method Detail

getInfoText

public String getInfoText()

Description copied from interface: TrackMateModule

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

Returns:

a html string.

getIcon

public ImageIcon getIcon()

Description copied from interface: TrackMateModule

Returns the icon for this action. Can be null.

Specified by:

getIcon in interface TrackMateModule

Overrides:

getIcon in class SegmentTrackerFactory

Returns:

the icon. Returns null to be safely ignored.

getKey

public String getKey()

Description copied from interface: TrackMateModule

Returns a unique identifier of this module.

Returns:

the action key, as a string.

getName

public String getName()

Description copied from interface: TrackMateModule

Returns the human-compliant name of this module.

Returns:

the name, as a String.

create

public SpotTracker create(SpotCollection spots,
                          Map<String,Object> settings)

Description copied from interface: SpotTrackerFactory

Instantiates and returns a new SpotTracker configured to operate on the specified SpotCollection, using the specified settins map.

Parameters:

spots - the SpotCollection containing the spots to track.

settings - the settings map configuring the tracker.

Returns:

a new SpotTracker instance.

copy

public SparseLAPTrackerFactory copy()

Description copied from interface: SpotTrackerFactory

Returns a copy the current instance.

Returns:

a new instance of this tracker factory.

marshall

public boolean marshall(Map<String,Object> settings,
                        org.jdom2.Element element)

Description copied from class: SegmentTrackerFactory

Marshall into the Element the settings in the Map that relate to segment linking: gap-closing, merging segments, splitting segments.

Specified by:

marshall in interface SpotTrackerFactory

Overrides:

marshall in class SegmentTrackerFactory

Returns:

true if marshalling was successful. If not, check SpotTrackerFactory.getErrorMessage()

unmarshall

public boolean unmarshall(org.jdom2.Element element,
                          Map<String,Object> settings)

Description copied from interface: SpotTrackerFactory

Un-marshall a JDom element to update a settings map, and sets the target tracker of this provider from the element.

Concretely: the the specific settings map for the targeted tracker is updated from the element.

Specified by:

unmarshall in interface SpotTrackerFactory

Overrides:

unmarshall in class SegmentTrackerFactory

Parameters:

element - the JDom element to read from.

settings - the map to update. Is cleared prior to updating, so that it contains only the parameters specific to the target tracker.

Returns:

true if unmarshalling was successful. If not, check SpotTrackerFactory.getErrorMessage()

getDefaultSettings

public Map<String,Object> getDefaultSettings()

Description copied from interface: SpotTrackerFactory

Returns a new default settings map suitable for the tracker Settings are instantiated with default values. is returned.

Specified by:

getDefaultSettings in interface SpotTrackerFactory

Overrides:

getDefaultSettings in class SegmentTrackerFactory

Returns:

a settings map.

checkSettingsValidity

public boolean checkSettingsValidity(Map<String,Object> settings)

Description copied from interface: SpotTrackerFactory

Checks the validity of the given settings map for the tracker. The validity check is strict: we check that all needed parameters are here and are of the right class, and that there is no extra unwanted parameters.

Specified by:

checkSettingsValidity in interface SpotTrackerFactory

Overrides:

checkSettingsValidity in class SegmentTrackerFactory

Returns:

true if the settings map can be used with the target factory. If not, check SpotTrackerFactory.getErrorMessage()

toString

public String toString(Map<String,Object> sm)

Description copied from interface: SpotTrackerFactory

A utility method that builds a string representation of a settings map owing to the currently selected tracker in this provider.

Specified by:

toString in interface SpotTrackerFactory

Overrides:

toString in class SegmentTrackerFactory

Parameters:

sm - the map to echo.

Returns:

a string representation of the map.

getTrackerConfigurationPanel

public ConfigurationPanel getTrackerConfigurationPanel(Model model)

Description copied from interface: SpotTrackerFactory

Returns a new GUI panel able to configure the settings suitable for the target tracker identified by the key parameter.

Parameters:

model - the model that will be modified by the target tracker.

Returns:

a new configuration panel.