OverlapTrackerFactory (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory

All Implemented Interfaces:: SpotTrackerFactory, TrackMateModule, SciJavaPlugin

public class OverlapTrackerFactory
extends Object
implements SpotTrackerFactory

Field Summary

Fields
Modifier and Type	Field and Description
`static Double`	`DEFAULT_MIN_IOU`
`static Double`	`DEFAULT_SCALE_FACTOR`
`static String`	`FAST_CALCULATION` Value for the fast IoU calculation method.
`static String`	`KEY_IOU_CALCULATION` The key to the parameter that stores how the IoU should be calculated.
`static String`	`KEY_MIN_IOU` The key to the parameter that stores the minimal IoU below which links are not created.
`static String`	`KEY_SCALE_FACTOR` The key to the parameter that stores scale factor parameter.
`static String`	`PRECISE_CALCULATION` Value for the precise IoU calculation method.
`static String`	`TRACKER_INFO_TEXT`
`static String`	`TRACKER_KEY`
`static String`	`TRACKER_NAME`

Constructor Summary

Constructors
Constructor and Description

OverlapTrackerFactory()

Constructors
Constructor and Description
`OverlapTrackerFactory()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkSettingsValidity(Map<String,Object> settings)` Checks the validity of the given settings map for the tracker.
`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.
`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.
`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)` Marshalls a settings map to a JDom element, ready for saving to XML.
`String`	`toString(Map<String,Object> settings)` 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 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
  - KEY_SCALE_FACTOR
```
public static final String KEY_SCALE_FACTOR
```
    The key to the parameter that stores scale factor parameter. The scale factor allows for enlarging (>1) or shrinking (<1) the spot shapes before computing their IoU. Values are strictly positive Doubles.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_SCALE_FACTOR
```
public static final Double DEFAULT_SCALE_FACTOR
```
  - KEY_MIN_IOU
```
public static final String KEY_MIN_IOU
```
    The key to the parameter that stores the minimal IoU below which links are not created. Values are strictly positive Doubles.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_MIN_IOU
```
public static final Double DEFAULT_MIN_IOU
```
  - KEY_IOU_CALCULATION
```
public static final String KEY_IOU_CALCULATION
```
    The key to the parameter that stores how the IoU should be calculated. There are two methods specified as strings: FAST_CALCULATION and PRECISE_CALCULATION.
    
    See Also:
    
    Constant Field Values
  - FAST_CALCULATION
```
public static final String FAST_CALCULATION
```
    Value for the fast IoU calculation method.
    
    See Also:
    
    KEY_IOU_CALCULATION
  - PRECISE_CALCULATION
```
public static final String PRECISE_CALCULATION
```
    Value for the precise IoU calculation method.
    
    See Also:
    
    KEY_IOU_CALCULATION
  - TRACKER_KEY
```
public static final String TRACKER_KEY
```
    See Also:
    
    Constant Field Values
  - TRACKER_NAME
```
public static final String TRACKER_NAME
```
    See Also:
    
    Constant Field Values
  - TRACKER_INFO_TEXT
```
public static final String TRACKER_INFO_TEXT
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - OverlapTrackerFactory
```
public OverlapTrackerFactory()
```
- Method Detail
  - 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.
  - 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.
  - 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.
  - 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.
  - 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.
    
    Specified by:
    
    create in interface SpotTrackerFactory
    
    Parameters:
    
    spots - the SpotCollection containing the spots to track.
    
    settings - the settings map configuring the tracker.
    
    Returns:
    
    a new SpotTracker instance.
  - 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.
    
    Specified by:
    
    getTrackerConfigurationPanel in interface SpotTrackerFactory
    
    Parameters:
    
    model - the model that will be modified by the target tracker.
    
    Returns:
    
    a new configuration panel.
  - marshall
```
public boolean marshall(Map<String,Object> settings,
                        org.jdom2.Element element)
```
    Description copied from interface: SpotTrackerFactory
    
    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 concrete tracker factory are marshalled. The element also always receive an attribute named that saves the target SpotTracker key.
    
    Specified by:
    
    marshall in interface SpotTrackerFactory
    
    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
    
    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()
  - toString
```
public String toString(Map<String,Object> settings)
```
    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
    
    Parameters:
    
    settings - the map to echo.
    
    Returns:
    
    a string representation of the map.
  - 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
    
    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
    
    Returns:
    
    true if the settings map can be used with the target factory. If not, check SpotTrackerFactory.getErrorMessage()
  - getErrorMessage
```
public String getErrorMessage()
```
    Description copied from interface: SpotTrackerFactory
    
    Returns a meaningful error message for the last action on this factory.
    
    Specified by:
    
    getErrorMessage in interface SpotTrackerFactory
    
    Returns:
    
    an error message.
    
    See Also:
    
    SpotTrackerFactory.marshall(Map, Element), SpotTrackerFactory.unmarshall(Element, Map), SpotTrackerFactory.checkSettingsValidity(Map)

Class OverlapTrackerFactory

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface fiji.plugin.trackmate.TrackMateModule

Field Detail

KEY_SCALE_FACTOR

DEFAULT_SCALE_FACTOR

KEY_MIN_IOU

DEFAULT_MIN_IOU

KEY_IOU_CALCULATION

FAST_CALCULATION

PRECISE_CALCULATION

TRACKER_KEY

TRACKER_NAME

TRACKER_INFO_TEXT

Constructor Detail

OverlapTrackerFactory

Method Detail

getKey

getName

getInfoText

getIcon

create

getTrackerConfigurationPanel

marshall

unmarshall

toString

getDefaultSettings

checkSettingsValidity

getErrorMessage