Constructor Detail

• AbstractEdgeAnalyzer

  public AbstractEdgeAnalyzer(String key,
                              String name,
                              List<String> features,
                              Map<String,String> featureNames,
                              Map<String,String> featureShortNames,
                              Map<String,Dimension> featureDimensions,
                              Map<String,Boolean> isInts)

Method Detail

• getProcessingTime

  public long getProcessingTime()

  Specified by:

  getProcessingTime in interface Benchmark

• isManualFeature

  public final 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.

• 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 final boolean isLocal()

  Description copied from interface: EdgeAnalyzer
  Returns true if this analyzer is a local analyzer. That is: a modification that affects only one edge requires the edge features to be re-calculated only for this edge. If false, any model modification involving an edge will trigger a recalculation over the whole track this edge belong to.

  Example of local edge feature: the edge length (distance between the two spots). This one does not depend on other edge values.

  Example of non-local edge feature: the local curvature of the trajectory, which depends on the neighbor edges.

  Specified by:

  isLocal in interface EdgeAnalyzer

• 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.

• 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

• 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

• 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

• 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

• process

  public void process(Collection<org.jgrapht.graph.DefaultWeightedEdge> edges,
                      Model model)

  Description copied from interface: EdgeAnalyzer
  Scores a collection of link between two spots. The results must be stored in the FeatureModel.

  Note: ideally concrete implementation should work in a multi-threaded fashion for performance reason, when possible.

  Specified by:

  process in interface EdgeAnalyzer

  Parameters:

  edges - the collection of edges whose features are to be calculated.

  model - the Model they belong to.

• analyze

  protected abstract void analyze(org.jgrapht.graph.DefaultWeightedEdge edge,
                                  Model model)