TrackMotilityAnalyzer (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer

All Implemented Interfaces:

FeatureAnalyzer, TrackAnalyzer, TrackMateModule, Benchmark, MultiThreaded, SciJavaPlugin
```
public class TrackMotilityAnalyzer
extends Object
implements TrackAnalyzer
```

Field Summary

Fields
Modifier and Type	Field and Description
`static Map<String,Dimension>`	`FEATURE_DIMENSIONS`
`static Map<String,String>`	`FEATURE_NAMES`
`static Map<String,String>`	`FEATURE_SHORT_NAMES`
`static List<String>`	`FEATURES`
`static Map<String,Boolean>`	`IS_INT`
`static String`	`KEY`
`static String`	`TRACK_CONFINMENT_RATIO`
`static String`	`TRACK_LINEARITY_OF_FORWARD_PROGRESSION`
`static String`	`TRACK_MAX_DISTANCE_TRAVELED`
`static String`	`TRACK_MEAN_DIRECTIONAL_CHANGE_RATE`
`static String`	`TRACK_MEAN_STRAIGHT_LINE_SPEED`
`static String`	`TRACK_TOTAL_DISTANCE_TRAVELED`

Constructor Summary

Constructors
Constructor and Description

TrackMotilityAnalyzer()

Constructors
Constructor and Description
`TrackMotilityAnalyzer()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Map<String,Dimension>`	`getFeatureDimensions()` Returns the map of feature dimension this analyzer can compute.
`Map<String,String>`	`getFeatureNames()` Returns the map of names for any feature this analyzer can compute.
`List<String>`	`getFeatures()` Returns the list of features this analyzer can compute.
`Map<String,String>`	`getFeatureShortNames()` Returns the map of short names for any feature the analyzer can compute.
`ImageIcon`	`getIcon()` Returns the icon for this action.
`String`	`getInfoText()` Returns a html string containing a descriptive information about this module.
`Map<String,Boolean>`	`getIsIntFeature()` Returns the map that states whether the key feature is a feature that returns integers.
`String`	`getKey()` Returns a unique identifier of this module.
`String`	`getName()` Returns the human-compliant name of this module.
`int`	`getNumThreads()`
`long`	`getProcessingTime()`
`boolean`	`isLocal()` Returns `true` if this analyzer is a local analyzer.
`boolean`	`isManualFeature()` Returns whether all the features declared in this `FeatureAnalyzer` are manual features.
`void`	`process(Collection<Integer> trackIDs, Model model)` Compute the features of the track whose ID is given.
`void`	`setNumThreads()`
`void`	`setNumThreads(int numThreads)`

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
```
public static final String KEY
```
    See Also:
    
    Constant Field Values
  - TRACK_TOTAL_DISTANCE_TRAVELED
```
public static final String TRACK_TOTAL_DISTANCE_TRAVELED
```
    See Also:
    
    Constant Field Values
  - TRACK_MAX_DISTANCE_TRAVELED
```
public static final String TRACK_MAX_DISTANCE_TRAVELED
```
    See Also:
    
    Constant Field Values
  - TRACK_CONFINMENT_RATIO
```
public static final String TRACK_CONFINMENT_RATIO
```
    See Also:
    
    Constant Field Values
  - TRACK_MEAN_STRAIGHT_LINE_SPEED
```
public static final String TRACK_MEAN_STRAIGHT_LINE_SPEED
```
    See Also:
    
    Constant Field Values
  - TRACK_LINEARITY_OF_FORWARD_PROGRESSION
```
public static final String TRACK_LINEARITY_OF_FORWARD_PROGRESSION
```
    See Also:
    
    Constant Field Values
  - TRACK_MEAN_DIRECTIONAL_CHANGE_RATE
```
public static final String TRACK_MEAN_DIRECTIONAL_CHANGE_RATE
```
    See Also:
    
    Constant Field Values
  - FEATURES
```
public static final List<String> FEATURES
```
  - FEATURE_NAMES
```
public static final Map<String,String> FEATURE_NAMES
```
  - FEATURE_SHORT_NAMES
```
public static final Map<String,String> FEATURE_SHORT_NAMES
```
  - FEATURE_DIMENSIONS
```
public static final Map<String,Dimension> FEATURE_DIMENSIONS
```
  - IS_INT
```
public static final Map<String,Boolean> IS_INT
```
- Constructor Detail
  - TrackMotilityAnalyzer
```
public TrackMotilityAnalyzer()
```
- Method Detail
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark
  - getFeatureDimensions
```
public Map<String,Dimension> getFeatureDimensions()
```
    Description copied from interface: FeatureAnalyzer
    
    Returns the map of feature dimension this analyzer can compute.
    
    Specified by:
    
    getFeatureDimensions in interface FeatureAnalyzer
  - getFeatureNames
```
public Map<String,String> getFeatureNames()
```
    Description copied from interface: FeatureAnalyzer
    
    Returns the map of names for any feature this analyzer can compute.
    
    Specified by:
    
    getFeatureNames in interface FeatureAnalyzer
  - getFeatureShortNames
```
public Map<String,String> getFeatureShortNames()
```
    Description copied from interface: FeatureAnalyzer
    
    Returns the map of short names for any feature the analyzer can compute.
    
    Specified by:
    
    getFeatureShortNames in interface FeatureAnalyzer
  - getFeatures
```
public List<String> getFeatures()
```
    Description copied from interface: FeatureAnalyzer
    
    Returns the list of features this analyzer can compute.
    
    Specified by:
    
    getFeatures in interface FeatureAnalyzer
  - getIsIntFeature
```
public Map<String,Boolean> getIsIntFeature()
```
    Description copied from interface: FeatureAnalyzer
    
    Returns the map that states whether the key feature is a feature that returns integers. If true, then special treatment is applied when saving/loading, etc. for clarity and precision.
    
    Specified by:
    
    getIsIntFeature in interface FeatureAnalyzer
  - isManualFeature
```
public boolean isManualFeature()
```
    Description copied from interface: FeatureAnalyzer
    
    Returns whether all the features declared in this FeatureAnalyzer are manual features.
    Manual features are not calculated normally using an analyzer, nor cleared at each recalculation. Another classes are responsible to set their value. The concrete FeatureAnalyzer calculation method is not called by TrackMate when a change happens to the model. Therefore the calculation routine of the FeatureAnalyzer can be used to discard the manually stored value of these features.
    
    Specified by:
    
    isManualFeature in interface FeatureAnalyzer
    
    Returns:
    
    true if the features declared in this analyzer are manual feature.
  - 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.
  - 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.
  - 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.
  - getNumThreads
```
public int getNumThreads()
```
    Specified by:
    
    getNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads()
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads(int numThreads)
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - isLocal
```
public boolean isLocal()
```
    Description copied from interface: TrackAnalyzer
    
    Returns true if this analyzer is a local analyzer. That is: a modification that affects only one track requires the track features to be re-calculated only for this track. If false, any model modification involving edges will trigger a recalculation over all the visible tracks of the model.
    Example of a local track feature: the number of spots in a track. It does not depend on the number of spots in other tracks.
    Example of a non-local track feature: the rank of the track sorted by its number of spots, compared to other tracks.
    
    Specified by:
    
    isLocal in interface TrackAnalyzer
  - process
```
public void process(Collection<Integer> trackIDs,
                    Model model)
```
    Description copied from interface: TrackAnalyzer
    
    Compute the features of the track whose ID is given.
    
    Specified by:
    
    process in interface TrackAnalyzer
    
    Parameters:
    
    trackIDs - the IDs of the track whose features are to be calculated.
    
    model - the Model from which actual tracks are to be retrieved.

Class TrackMotilityAnalyzer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface fiji.plugin.trackmate.TrackMateModule

Field Detail

KEY

TRACK_TOTAL_DISTANCE_TRAVELED

TRACK_MAX_DISTANCE_TRAVELED

TRACK_CONFINMENT_RATIO

TRACK_MEAN_STRAIGHT_LINE_SPEED

TRACK_LINEARITY_OF_FORWARD_PROGRESSION

TRACK_MEAN_DIRECTIONAL_CHANGE_RATE

FEATURES

FEATURE_NAMES

FEATURE_SHORT_NAMES

FEATURE_DIMENSIONS

IS_INT

Constructor Detail

TrackMotilityAnalyzer

Method Detail

getProcessingTime

getFeatureDimensions

getFeatureNames

getFeatureShortNames

getFeatures

getIsIntFeature

isManualFeature

getIcon

getInfoText

getKey

getName

getNumThreads

setNumThreads

setNumThreads

isLocal

process