ThresholdDetectorFactory (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.detection.ThresholdDetectorFactory<T>

All Implemented Interfaces:

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

Direct Known Subclasses:

MaskDetectorFactory
```
public class ThresholdDetectorFactory<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`	`KEY_INTENSITY_THRESHOLD`
`static String`	`KEY_SIMPLIFY_CONTOURS`
`static String`	`NAME` The pretty name of the target detector.
`protected Map<String,Object>`	`settings`

Constructor Summary

Constructors
Constructor and Description

ThresholdDetectorFactory()

Constructors
Constructor and Description
`ThresholdDetectorFactory()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkSettings(Map<String,Object> lSettings)` Check that the given settings map is suitable for target detector.
`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
  - KEY_SIMPLIFY_CONTOURS
```
public static final String KEY_SIMPLIFY_CONTOURS
```
    See Also:
    
    Constant Field Values
  - KEY_INTENSITY_THRESHOLD
```
public static final String KEY_INTENSITY_THRESHOLD
```
    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
  - ThresholdDetectorFactory
```
public ThresholdDetectorFactory()
```
- 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.

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface fiji.plugin.trackmate.TrackMateModule

Field Detail

DETECTOR_KEY

NAME

INFO_TEXT

KEY_SIMPLIFY_CONTOURS

KEY_INTENSITY_THRESHOLD

img

settings

errorMessage

Constructor Detail

ThresholdDetectorFactory

Method Detail

setTarget

getDetector

has2Dsegmentation

getKey

getErrorMessage

checkSettings

marshall

unmarshall

getDetectorConfigurationPanel

getInfoText

getName

getDefaultSettings

getIcon