AbstractRegionalExtremaFinder (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder<T>

All Implemented Interfaces:

Algorithm, Benchmark, RegionalExtremaFinder<T>

Direct Known Subclasses:

RegionalExtremaFinder2D, RegionalExtremaFinder3D
```
public abstract class AbstractRegionalExtremaFinder<T extends RealType<T>>
extends Object
implements RegionalExtremaFinder<T>
```
TODO

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`allowEdgeMax`
`protected boolean`	`doInterpolate`
`protected Image<T>`	`image`
`protected ArrayList<ArrayList<int[]>>`	`maxima`
`protected OutOfBoundsStrategyFactory<T>`	`outOfBoundsFactory`
`protected T`	`threshold`

Constructor Summary

Constructors
Constructor and Description

AbstractRegionalExtremaFinder()

Constructors
Constructor and Description
`AbstractRegionalExtremaFinder()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`allowEdgeExtrema(boolean flag)` If set to true before the `Algorithm.process()` method is called, then extrema found at the edges of the image bounds (including time edges) will not be pruned, and will be included in the result array.
`protected float[]`	`findAveragePosition(ArrayList<int[]> coords)` Given an ArrayList of int[] (coordinates), computes the averaged coordinates and returns them.
`ArrayList<ArrayList<int[]>>`	`getRegionalExtrema()` Returns the ArrayList containing the coordinates of the local extrema found.
`ArrayList<float[]>`	`getRegionalExtremaCenters()` Computes the average coordinate of the extrema locations.
`void`	`setOutOfBoundsStrategyFactory(OutOfBoundsStrategyFactory<T> strategy)` Set the strategy used by this extrema finder to deal with edge pixels.
`void`	`setThreshold(T threshold)` Set the threshold value under which (or over which, in the case of a minima finder) pixels are ignored.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface mpicbg.imglib.algorithm.Algorithm
checkInput, getErrorMessage, process

Methods inherited from interface mpicbg.imglib.algorithm.Benchmark
getProcessingTime

- Field Detail
  - outOfBoundsFactory
```
protected OutOfBoundsStrategyFactory<T extends RealType<T>> outOfBoundsFactory
```
  - allowEdgeMax
```
protected boolean allowEdgeMax
```
  - doInterpolate
```
protected boolean doInterpolate
```
  - image
```
protected Image<T extends RealType<T>> image
```
  - maxima
```
protected final ArrayList<ArrayList<int[]>> maxima
```
  - threshold
```
protected T extends RealType<T> threshold
```
- Constructor Detail
  - AbstractRegionalExtremaFinder
```
public AbstractRegionalExtremaFinder()
```
- Method Detail
  - allowEdgeExtrema
```
public void allowEdgeExtrema(boolean flag)
```
    Description copied from interface: RegionalExtremaFinder
    
    If set to true before the Algorithm.process() method is called, then extrema found at the edges of the image bounds (including time edges) will not be pruned, and will be included in the result array.
    
    Specified by:
    
    allowEdgeExtrema in interface RegionalExtremaFinder<T extends RealType<T>>
  - getRegionalExtrema
```
public ArrayList<ArrayList<int[]>> getRegionalExtrema()
```
    Description copied from interface: RegionalExtremaFinder
    
    Returns the ArrayList containing the coordinates of the local extrema found. Each element of the ArrayList is a int array, representing the coordinate of the found extrema, in the same order that of the source Image.
    
    Specified by:
    
    getRegionalExtrema in interface RegionalExtremaFinder<T extends RealType<T>>
    
    Returns:
    
    the ArrayList containing the extrema coordinates
  - getRegionalExtremaCenters
```
public ArrayList<float[]> getRegionalExtremaCenters()
```
    Description copied from interface: RegionalExtremaFinder
    
    Computes the average coordinate of the extrema locations. This average coordinates are returned, and represents the "center" of the regional maximum. Note that this is not guaranteed to be in the regional maximum itself (imagine a regional maximum that is a ring shape; the direct center is not part of the regional maximum itself, but is what would be computed by this function). Return null if the Algorithm.process() method has not bee called.
    
    Specified by:
    
    getRegionalExtremaCenters in interface RegionalExtremaFinder<T extends RealType<T>>
    
    Returns:
    
    The coordinates of the "center pixel" of the regional maximum. It will always be a 3-elements float arrays, even for 2D case.
  - setThreshold
```
public void setThreshold(T threshold)
```
    Description copied from interface: RegionalExtremaFinder
    
    Set the threshold value under which (or over which, in the case of a minima finder) pixels are ignored. If null, then all pixels are taken into account.
    
    Specified by:
    
    setThreshold in interface RegionalExtremaFinder<T extends RealType<T>>
  - findAveragePosition
```
protected float[] findAveragePosition(ArrayList<int[]> coords)
```
    Given an ArrayList of int[] (coordinates), computes the averaged coordinates and returns them. This will always return a 3-elements arrays, even for 2D.
    
    Parameters:
    
    searched -
    
    Returns:
  - setOutOfBoundsStrategyFactory
```
public void setOutOfBoundsStrategyFactory(OutOfBoundsStrategyFactory<T> strategy)
```
    Description copied from interface: RegionalExtremaFinder
    
    Set the strategy used by this extrema finder to deal with edge pixels. By default, it is an OutOfBoundsStrategyValueFactory set with the value 0 to avoid nasty edge effects.
    
    Specified by:
    
    setOutOfBoundsStrategyFactory in interface RegionalExtremaFinder<T extends RealType<T>>
    
    Parameters:
    
    strategy - the strategy to set

Class AbstractRegionalExtremaFinder<T extends RealType<T>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface mpicbg.imglib.algorithm.Algorithm

Methods inherited from interface mpicbg.imglib.algorithm.Benchmark

Field Detail

outOfBoundsFactory

allowEdgeMax

doInterpolate

image

maxima

threshold

Constructor Detail

AbstractRegionalExtremaFinder

Method Detail

allowEdgeExtrema

getRegionalExtrema

getRegionalExtremaCenters

setThreshold

findAveragePosition

setOutOfBoundsStrategyFactory