fiji.plugin.trackmate.action.fit

Class AbstractSpotFitter

java.lang.Object

fiji.plugin.trackmate.action.fit.AbstractSpotFitter

All Implemented Interfaces:

SpotFitter, Benchmark, MultiThreaded

Direct Known Subclasses:

SpotGaussianFitter2D, SpotGaussianFitter2DFixedRadius, SpotGaussianFitter3D, SpotGaussianFitter3DFixedRadius

public abstract class AbstractSpotFitter
extends Object
implements SpotFitter

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AbstractSpotFitter.Observation

Field Summary

Fields

Modifier and Type	Field and Description
protected double[]	calibration
protected int	channel
protected ImgPlus<RealType>	img
protected LevenbergMarquardtOptimizer	optimizer

Constructor Summary

Constructors

Constructor and Description
AbstractSpotFitter(ij.ImagePlus imp, int channel)

Method Summary

Modifier and Type	Method and Description
protected static void	clipBackground(AbstractSpotFitter.Observation obs)
abstract void	fit(Spot spot)
protected AbstractSpotFitter.Observation	gatherObservationData(Point point, long[] span, int frame)
int	getNumThreads()
long	getProcessingTime()
protected RandomAccessibleInterval<RealType>	getSlice(int frame)
void	process(Iterable<Spot> spots, Logger logger)
void	setNumThreads()
void	setNumThreads(int numThreads)

Methods inherited from class java.lang.Object

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

Field Detail

img

protected final ImgPlus<RealType> img

channel

protected final int channel

calibration

protected final double[] calibration

optimizer

protected final LevenbergMarquardtOptimizer optimizer

Constructor Detail

AbstractSpotFitter

public AbstractSpotFitter(ij.ImagePlus imp,
                          int channel)

Method Detail

process

public void process(Iterable<Spot> spots,
                    Logger logger)

Specified by:

process in interface SpotFitter

getSlice

protected RandomAccessibleInterval<RealType> getSlice(int frame)

fit

public abstract void fit(Spot spot)

Specified by:

fit in interface SpotFitter

setNumThreads

public void setNumThreads()

Specified by:

setNumThreads in interface MultiThreaded

setNumThreads

public void setNumThreads(int numThreads)

Specified by:

setNumThreads in interface MultiThreaded

getNumThreads

public int getNumThreads()

Specified by:

getNumThreads in interface MultiThreaded

getProcessingTime

public long getProcessingTime()

Specified by:

getProcessingTime in interface Benchmark

clipBackground

protected static void clipBackground(AbstractSpotFitter.Observation obs)

gatherObservationData

protected AbstractSpotFitter.Observation gatherObservationData(Point point,
                                                               long[] span,
                                                               int frame)