fiji.plugin.trackmate.detection

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

java.lang.Object

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

All Implemented Interfaces:

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

public class LabelImageDetectorFactory<T extends RealType<T> & NativeType<T>>
extends Object
implements SpotDetectorFactory<T>

Field Summary

Fields

Modifier and Type	Field and Description
static String	DETECTOR_KEY A string key identifying this factory.
protected String	errorMessage
protected ImgPlus<T>	img The image to operate on.
static String	INFO_TEXT An html information text.
static String	NAME The pretty name of the target detector.
protected Map<String,Object>	settings

Constructor Summary

Constructors

Constructor and Description
LabelImageDetectorFactory()

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.
LabelImageDetectorFactory<T>	copy() Returns a copy the current instance.
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	getErrorMessage() Returns a meaningful error message for the last action on this factory.
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.
boolean	has2Dsegmentation() Return true for the detectors that can provide a spot with a 2D SpotRoi when they operate on 2D images.
boolean	marshall(Map<String,Object> lSettings, org.jdom2.Element element) Marshalls a settings map to a JDom element, ready for saving to XML.
boolean	setTarget(ImgPlus<T> img, Map<String,Object> settings) Configure this factory to operate on the given source image (possibly 5D), with the given settings map.
boolean	unmarshall(org.jdom2.Element element, Map<String,Object> lSettings) Un-marshalls a JDom element to update a settings map.

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

DETECTOR_KEY

public static final String DETECTOR_KEY

A string key identifying this factory.

See Also:

Constant Field Values

NAME

public static final String NAME

The pretty name of the target detector.

See Also:

Constant Field Values

INFO_TEXT

public static final String INFO_TEXT

An html information text.

See Also:

Constant Field Values

img

protected ImgPlus<T extends RealType<T> & NativeType<T>> img

The image to operate on. Multiple frames, multiple channels.

settings

protected Map<String,Object> settings

errorMessage

protected String errorMessage

Constructor Detail

LabelImageDetectorFactory

public LabelImageDetectorFactory()

Method Detail

setTarget

public boolean setTarget(ImgPlus<T> img,
                         Map<String,Object> settings)

Description copied from interface: SpotDetectorFactoryBase

Configure this factory to operate on the given source image (possibly 5D), with the given settings map.

Also checks the validity of the given settings map for this factory. If check fails, return false, an error message can be obtained through SpotDetectorFactoryBase.getErrorMessage().

Specified by:

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

Parameters:

img - the ImgPlus to operate on, possible 5D.

settings - the settings map, must be suitable for this detector factory.

Returns:

false is the given settings map is not suitable for this detector factory.

See Also:

SpotDetectorFactoryBase.getErrorMessage()

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>>

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

has2Dsegmentation

public boolean has2Dsegmentation()

Description copied from interface: SpotDetectorFactoryBase

Return true for the detectors that can provide a spot with a 2D SpotRoi when they operate on 2D images.

This flag may be used by clients to exploit the fact that the spots created with this detector will have a contour that can be used e.g. to compute morphological features. The default is false, indicating that this detector provides spots as a X, Y, Z, radius tuple.

Specified by:

has2Dsegmentation in interface SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>>

Returns:

true if the spots created by this detector have a 2D contour.

getKey

public String getKey()

Description copied from interface: TrackMateModule

Returns a unique identifier of this module.

Specified by:

getKey in interface TrackMateModule

Returns:

the action key, as a string.

getErrorMessage

public String getErrorMessage()

Description copied from interface: SpotDetectorFactoryBase

Returns a meaningful error message for the last action on this factory.

Specified by:

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

See Also:

SpotDetectorFactoryBase.setTarget(ImgPlus, Map), SpotDetectorFactoryBase.marshall(Map, Element), SpotDetectorFactoryBase.unmarshall(Element, Map)

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>>

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>>

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>>

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>>

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

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

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>>

Returns:

a new map.

getIcon

public ImageIcon getIcon()

Description copied from interface: TrackMateModule

Returns the icon for this action. Can be null.

Specified by:

getIcon in interface TrackMateModule

Returns:

the icon. Returns null to be safely ignored.

copy

public LabelImageDetectorFactory<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>>

Returns:

a new instance of this detector factory.