fiji.plugin.trackmate.detection

Class HessianDetectorFactory<T extends RealType<T> & NativeType<T>>

java.lang.Object

fiji.plugin.trackmate.detection.LogDetectorFactory<T>

fiji.plugin.trackmate.detection.HessianDetectorFactory<T>

All Implemented Interfaces:

SpotDetectorFactory<T>, SpotDetectorFactoryBase<T>, TrackMateModule, SciJavaPlugin

public class HessianDetectorFactory<T extends RealType<T> & NativeType<T>>
extends LogDetectorFactory<T>

Field Summary

Fields

Modifier and Type	Field and Description
static String	DETECTOR_KEY
static String	INFO_TEXT
static String	NAME

Fields inherited from class fiji.plugin.trackmate.detection.LogDetectorFactory

errorMessage, img, settings

Constructor Summary

Constructors

Constructor and Description
HessianDetectorFactory()

Method Summary

Modifier and Type	Method and Description
boolean	checkSettings(Map<String,Object> lSettings) Check that the given settings map is suitable for target detector.
HessianDetectorFactory<T>	copy() Returns a copy the current instance.
boolean	forbidMultithreading() Returns a flag that tells TrackMate whether it should strictly forbid running this module concurrently.
Map<String,Object>	getDefaultSettings() Returns a new default settings map suitable for the target detector.
SpotDetector<T>	getDetector(Interval interval, int frame) Returns a new SpotDetector configured to operate on the given target frame.
ConfigurationPanel	getDetectorConfigurationPanel(Settings lSettings, Model model) Returns a new GUI panel able to configure the settings suitable for this specific detector factory.
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.
boolean	marshall(Map<String,Object> lSettings, org.jdom2.Element element) Marshalls a settings map to a JDom element, ready for saving to XML.
boolean	unmarshall(org.jdom2.Element element, Map<String,Object> lSettings) Un-marshalls a JDom element to update a settings map.

Methods inherited from class fiji.plugin.trackmate.detection.LogDetectorFactory

getErrorMessage, getIcon, prepareFrameImg, setTarget

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.detection.SpotDetectorFactoryBase

has2Dsegmentation

Field Detail

DETECTOR_KEY

public static final String DETECTOR_KEY

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

INFO_TEXT

public static final String INFO_TEXT

See Also:

Constant Field Values

Constructor Detail

HessianDetectorFactory

public HessianDetectorFactory()

Method Detail

getDetector

public SpotDetector<T> getDetector(Interval interval,
                                   int frame)

Description copied from interface: SpotDetectorFactory

Returns a new SpotDetector configured to operate on the given target frame. This factory must be first given the ImgPlus and the settings map, through the #setTarget(ImgPlus, Map) method.

Specified by:

getDetector in interface SpotDetectorFactory<T extends RealType<T> & NativeType<T>>

Overrides:

getDetector in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Parameters:

interval - the interval that determines the region in the source image to operate on. This must not have a dimension for time (e.g. if the source image is 2D+T (3D), then the interval must be 2D; if the source image is 3D without time, then the interval must be 3D).

frame - the frame index in the source image to operate on

forbidMultithreading

public boolean forbidMultithreading()

Description copied from interface: TrackMateModule

Returns a flag that tells TrackMate whether it should strictly forbid running this module concurrently.

This might be the case for instance if you have a spot detector that you want to run strictly one frame after another, to save resources or because the multi-threading of the detector cannot be controlled. In that case this flag should be set to true.

If false (the default), the multi-threading will be decided by TrackMate.

Returns:

whether to forbid running this module concurrently

getKey

public String getKey()

Description copied from interface: TrackMateModule

Returns a unique identifier of this module.

Specified by:

getKey in interface TrackMateModule

Overrides:

getKey in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Returns:

the action key, as a string.

checkSettings

public boolean checkSettings(Map<String,Object> lSettings)

Description copied from interface: SpotDetectorFactoryBase

Check that the given settings map is suitable for target detector.

Specified by:

checkSettings in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Overrides:

checkSettings in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Parameters:

lSettings - the map to test.

Returns:

true if the settings map is valid.

marshall

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

Description copied from interface: SpotDetectorFactoryBase

Marshalls a settings map to a JDom element, ready for saving to XML. The element is updated with new attributes.

Only parameters specific to the specific detector factory are marshalled. The element also always receive an attribute named that saves the target SpotDetectorFactory key.

Specified by:

marshall in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Overrides:

marshall in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Returns:

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

unmarshall

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

Description copied from interface: SpotDetectorFactoryBase

Un-marshalls a JDom element to update a settings map.

Specified by:

unmarshall in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Overrides:

unmarshall in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Parameters:

element - the JDom element to read from.

lSettings - the map to update. Is cleared prior to updating, so that it contains only the parameters specific to the target detector factory.

Returns:

true if un-marshalling was successful. If not, check SpotDetectorFactoryBase.getErrorMessage()

getDetectorConfigurationPanel

public ConfigurationPanel getDetectorConfigurationPanel(Settings lSettings,
                                                        Model model)

Description copied from interface: SpotDetectorFactoryBase

Returns a new GUI panel able to configure the settings suitable for this specific detector factory.

Specified by:

getDetectorConfigurationPanel in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Overrides:

getDetectorConfigurationPanel in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Parameters:

lSettings - the current settings, used to get info to display on the GUI panel.

model - the current model, used to get info to display on the GUI panel.

getInfoText

public String getInfoText()

Description copied from interface: TrackMateModule

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

Specified by:

getInfoText in interface TrackMateModule

Overrides:

getInfoText in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Returns:

a html string.

getName

public String getName()

Description copied from interface: TrackMateModule

Returns the human-compliant name of this module.

Specified by:

getName in interface TrackMateModule

Overrides:

getName in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Returns:

the name, as a String.

getDefaultSettings

public Map<String,Object> getDefaultSettings()

Description copied from interface: SpotDetectorFactoryBase

Returns a new default settings map suitable for the target detector. Settings are instantiated with default values.

Specified by:

getDefaultSettings in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Overrides:

getDefaultSettings in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Returns:

a new map.

copy

public HessianDetectorFactory<T> copy()

Description copied from interface: SpotDetectorFactoryBase

Returns a copy the current instance.

Specified by:

copy in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Overrides:

copy in class LogDetectorFactory<T extends RealType<T> & NativeType<T>>

Returns:

a new instance of this detector factory.