de.mpg.biochem.mars.image

Class PeakTracker

java.lang.Object

de.mpg.biochem.mars.image.PeakTracker

public class PeakTracker
extends java.lang.Object

PeakTracker tracks the relative position of peaks over time based on peak feature differences, minimum distance change, and minimum total track length. Parameters are maintained for multiple rounds of tracking. The main processing method (track) accepts a map of all peaks for each position T, the final SingleMoleculeArchive that will contain the molecule records resulting from tracking and the channel to set in the molecule records.

Constructor Summary

Constructors

Constructor and Description
PeakTracker(double[] maxDifference, boolean[] ckMaxDifference, int minimumDistance, int minTrajectoryLength, boolean writeIntegration, boolean verbose, org.scijava.log.LogService logService, double pixelSize)
PeakTracker(double maxDifferenceX, double maxDifferenceY, double maxDifferenceT, int minimumDistance, int minTrajectoryLength, boolean verbose, org.scijava.log.LogService logService, double pixelSize)

Method Summary

Modifier and Type	Method and Description
void	track(java.util.concurrent.ConcurrentMap<java.lang.Integer,java.util.List<Peak>> peakStack, MoleculeArchive<?,?,?,?> archive, int channel, int nThreads)
void	track(java.util.concurrent.ConcurrentMap<java.lang.Integer,java.util.List<Peak>> peakStack, MoleculeArchive<?,?,?,?> archive, int channel, java.util.List<java.lang.Integer> trackingTimePoints, int nThreads)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PeakTracker

public PeakTracker(double maxDifferenceX,
                   double maxDifferenceY,
                   double maxDifferenceT,
                   int minimumDistance,
                   int minTrajectoryLength,
                   boolean verbose,
                   org.scijava.log.LogService logService,
                   double pixelSize)

PeakTracker

public PeakTracker(double[] maxDifference,
                   boolean[] ckMaxDifference,
                   int minimumDistance,
                   int minTrajectoryLength,
                   boolean writeIntegration,
                   boolean verbose,
                   org.scijava.log.LogService logService,
                   double pixelSize)

Method Detail

track

public void track(java.util.concurrent.ConcurrentMap<java.lang.Integer,java.util.List<Peak>> peakStack,
                  MoleculeArchive<?,?,?,?> archive,
                  int channel,
                  int nThreads)

track

public void track(java.util.concurrent.ConcurrentMap<java.lang.Integer,java.util.List<Peak>> peakStack,
                  MoleculeArchive<?,?,?,?> archive,
                  int channel,
                  java.util.List<java.lang.Integer> trackingTimePoints,
                  int nThreads)