mpicbg.imglib.algorithm.math

Class PickImagePeaks<T extends RealType<T>>

java.lang.Object

mpicbg.imglib.algorithm.math.PickImagePeaks<T>

Type Parameters:

T - the ComparableType representing information stored in the Image to pick peaks from.

All Implemented Interfaces:

Algorithm, Benchmark, OutputAlgorithm<BitType>

public class PickImagePeaks<T extends RealType<T>>
extends Object
implements OutputAlgorithm<BitType>, Benchmark

This class implements a very simple peak-picker, with optional ellipsoidal peak suppression. Peaks are found by taking the sign of the difference operator in each dimension, differentiating between negative and non-negative differences, then finding transitions from non-negative to negative. This is accomplished in a random-access manner, in other words, with one LocalizableCursor irrespective of how it traverses the Image, and a LocalizableByDimCursor that is set to its 2^n-connected neighbors (where n is dimensionality).

The result is that this is a fairly simple, (hopefully) fast peak-picker, but it is accurate only for strict peaks, that is, peaks that have no neighbors of equal value.

This picker does no pre-processing, so it may be advisable to smooth your peak image before using this.

Author:

Larry Lindsey
modified by Jean-Yves Tinevez to allow for border peaks to be found.

Constructor Summary

Constructors

Constructor and Description
PickImagePeaks(Image<T> inputImage)

Method Summary

Modifier and Type	Method and Description
boolean	checkInput()
String	getErrorMessage()
ArrayList<int[]>	getPeakList() Returns an ArrayList containing the locations of peaks in the image associated with this peak picker, as calculated by running the process() method.
long	getProcessingTime()
Image<BitType>	getResult()
boolean	process()
void	setAllowBorderPeak(boolean allowBorderPeak) Set the behavior for finding peak at the image boundaries.
void	setSuppression(double r) Sets the peak suppression region to a spheroid of radius r.
void	setSuppression(double[] r) Sets the peak suppression region to an ellipsoid with dimensional axes corresponding to the elements in r.

Methods inherited from class java.lang.Object

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

Constructor Detail

PickImagePeaks

public PickImagePeaks(Image<T> inputImage)

Method Detail

checkInput

public boolean checkInput()

Specified by:

checkInput in interface Algorithm

getErrorMessage

public String getErrorMessage()

Specified by:

getErrorMessage in interface Algorithm

process

public boolean process()

Specified by:

process in interface Algorithm

getProcessingTime

public long getProcessingTime()

Specified by:

getProcessingTime in interface Benchmark

getResult

public Image<BitType> getResult()

Specified by:

getResult in interface OutputAlgorithm<BitType>

getPeakList

public ArrayList<int[]> getPeakList()

Returns an ArrayList containing the locations of peaks in the image associated with this peak picker, as calculated by running the process() method. This ArrayList will be populated if it is not already. In the case that there is no peak suppression, the locations are placed in the list as they are returned by calling the LocalizableCursor.getPosition() method, and are not guaranteed to have anything like a natural order. In the case that there is peak suppression, an additional step is taken. The peaks are first collected, then sorted by magnitude. These are then selected in order, and the peaks within a distance defined by the suppressAxis array are rejected. There is no peak suppression if the sum of all values in suppressAxis is less than 1.

Returns:

an ArrayList containing peak locations

setSuppression

public void setSuppression(double r)

Sets the peak suppression region to a spheroid of radius r.

Parameters:

r - the radius of the spheroid of peak suppression.

setAllowBorderPeak

public void setAllowBorderPeak(boolean allowBorderPeak)

Set the behavior for finding peak at the image boundaries. If set to false (the default), peaks will not be found at the top borders of the image.

setSuppression

public void setSuppression(double[] r)

Sets the peak suppression region to an ellipsoid with dimensional axes corresponding to the elements in r.

Parameters:

r - an array with as many elements as there are dimensions in the Image with which this PickImagePeaks was created, and represents the extent of the ellipsoid