SubpixelLocalization (ImgLib2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imglib2.algorithm.localextrema.SubpixelLocalization<P,T>

```
public class SubpixelLocalization>
extends Object
```
Refine a set of peaks to subpixel coordinates. This class provides the static refinePeaks(List, RandomAccessible, Interval, boolean, int, boolean, float, boolean[], int) method to do this, but this has a lot of parameters. Therefore, this class can also be instantiated to encapsulate the parameter settings.
A List RefinedPeak for the given list of Localizable is computed by, for each peak, fitting a quadratic function to the image and computing the subpixel coordinates of the extremum. This is an iterative procedure. If the extremum is shifted more than 0.5 in one or more the fit is repeated at the corresponding integer coordinates. This is repeated to convergence, for a maximum number of iterations, or until the integer coordinates move out of the valid image.

Author:

Stephan Preibisch, Tobias Pietzsch

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean[]`	`allowedToMoveInDim`
`protected boolean`	`allowMaximaTolerance`
`protected boolean`	`canMoveOutside`
`protected float`	`maximaTolerance`
`protected int`	`maxNumMoves`
`protected int`	`numThreads`
`protected boolean`	`returnInvalidPeaks`

Constructor Summary

Constructors
Constructor and Description

SubpixelLocalization(int numDimensions)

Constructors
Constructor and Description
`SubpixelLocalization(int numDimensions)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean[]`	`getAllowedToMoveInDim()`
`boolean`	`getAllowMaximaTolerance()`
`boolean`	`getCanMoveOutside()`
`float`	`getMaximaTolerance()`
`int`	`getMaxNumMoves()`
`int`	`getNumThreads()`
`boolean`	`getReturnInvalidPeaks()`
`ArrayList<RefinedPeak<P>>`	`process(List<P> peaks, RandomAccessible<T> img, Interval validInterval)` Refine a set of peaks to subpixel coordinates.
`protected static <T extends RealType<T>> void`	`quadraticFitOffset(Localizable p, RandomAccess<T> access, Matrix g, Matrix H, RealPositionable offset)` Estimate subpixel `offset` of extremum of quadratic function fitted at `p`.
`static <T extends RealType<T>,P extends Localizable> ArrayList<RefinedPeak<P>>`	`refinePeaks(List<P> peaks, RandomAccessible<T> img, Interval validInterval, boolean returnInvalidPeaks, int maxNumMoves, boolean allowMaximaTolerance, float maximaTolerance, boolean[] allowedToMoveInDim)` Refine a set of peaks to subpixel coordinates.
`static <T extends RealType<T>,P extends Localizable> ArrayList<RefinedPeak<P>>`	`refinePeaks(List<P> peaks, RandomAccessible<T> img, Interval validInterval, boolean returnInvalidPeaks, int maxNumMoves, boolean allowMaximaTolerance, float maximaTolerance, boolean[] allowedToMoveInDim, int numThreads)` Refine a set of peaks to subpixel coordinates.
`void`	`setAllowedToMoveInDim(boolean[] allowedToMoveInDim)`
`void`	`setAllowMaximaTolerance(boolean allowMaximaTolerance)`
`void`	`setCanMoveOutside(boolean canMoveOutside)`
`void`	`setMaximaTolerance(float maximaTolerance)`
`void`	`setMaxNumMoves(int maxNumMoves)`
`void`	`setNumThreads(int numThreads)`
`void`	`setReturnInvalidPeaks(boolean returnInvalidPeaks)`

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

- Field Detail
 - maxNumMoves
```
protected int maxNumMoves
```
 - allowMaximaTolerance
```
protected boolean allowMaximaTolerance
```
 - canMoveOutside
```
protected boolean canMoveOutside
```
 - maximaTolerance
```
protected float maximaTolerance
```
 - allowedToMoveInDim
```
protected boolean[] allowedToMoveInDim
```
 - returnInvalidPeaks
```
protected boolean returnInvalidPeaks
```
 - numThreads
```
protected int numThreads
```
- Constructor Detail
 - SubpixelLocalization
```
public SubpixelLocalization(int numDimensions)
```
- Method Detail
 - setAllowMaximaTolerance
```
public void setAllowMaximaTolerance(boolean allowMaximaTolerance)
```
 - setCanMoveOutside
```
public void setCanMoveOutside(boolean canMoveOutside)
```
 - setMaximaTolerance
```
public void setMaximaTolerance(float maximaTolerance)
```
 - setMaxNumMoves
```
public void setMaxNumMoves(int maxNumMoves)
```
 - setAllowedToMoveInDim
```
public void setAllowedToMoveInDim(boolean[] allowedToMoveInDim)
```
 - setReturnInvalidPeaks
```
public void setReturnInvalidPeaks(boolean returnInvalidPeaks)
```
 - setNumThreads
```
public void setNumThreads(int numThreads)
```
 - getAllowMaximaTolerance
```
public boolean getAllowMaximaTolerance()
```
 - getCanMoveOutside
```
public boolean getCanMoveOutside()
```
 - getMaximaTolerance
```
public float getMaximaTolerance()
```
 - getMaxNumMoves
```
public int getMaxNumMoves()
```
 - getAllowedToMoveInDim
```
public boolean[] getAllowedToMoveInDim()
```
 - getReturnInvalidPeaks
```
public boolean getReturnInvalidPeaks()
```
 - getNumThreads
```
public int getNumThreads()
```
 - process
```
public ArrayList<RefinedPeak> process(List peaks,
 RandomAccessible<T> img,
 Interval validInterval)
```
 Refine a set of peaks to subpixel coordinates. Calls refinePeaks(List, RandomAccessible, Interval, boolean, int, boolean, float, boolean[], int) with the parameters set to this object.
 
 Parameters:
 
 peaks - List of integer peaks.
 
 img - Pixel values.
 
 validInterval - In which interval the img contains valid pixels. If null, an infinite img is assumed. Integer peaks must lie within a 1-pixel border of this interval.
 
 Returns:
 
 refined list of peaks.
 - refinePeaks
```
public static <T extends RealType<T>,P extends Localizable> ArrayList<RefinedPeak> refinePeaks(List peaks,
 RandomAccessible<T> img,
 Interval validInterval,
 boolean returnInvalidPeaks,
 int maxNumMoves,
 boolean allowMaximaTolerance,
 float maximaTolerance,
 boolean[] allowedToMoveInDim,
 int numThreads)
```
 Refine a set of peaks to subpixel coordinates. Multi-threaded version.
 A List RefinedPeak for the given list of Localizable is computed by, for each peak, fitting a quadratic function to the image and computing the subpixel coordinates of the extremum. This is an iterative procedure. If the extremum is shifted more than 0.5 in one or more the fit is repeated at the corresponding integer coordinates. This is repeated to convergence, for a maximum number of iterations, or until the integer coordinates move out of the valid image.
 
 Parameters:
 
 peaks - List of integer peaks.
 
 img - Pixel values.
 
 validInterval - In which interval the img contains valid pixels. If null, an infinite img is assumed. Integer peaks must lie within a 1-pixel border of this interval.
 
 returnInvalidPeaks - Whether (invalid) RefinedPeak should be created for peaks where the fitting procedure did not converge.
 
 maxNumMoves - maximum number of iterations for each peak.
 
 allowMaximaTolerance - If we allow an increasing maxima tolerance we will not change the base position that easily. Sometimes it simply jumps from left to right and back, because it is 4.51 (i.e. goto 5), then 4.49 (i.e. goto 4) Then we say, ok, lets keep the base position even if the subpixel location is 0.6...
 
 maximaTolerance - By how much to increase the tolerance per iteration.
 
 allowedToMoveInDim - specifies, per dimension, whether the base location is allowed to be moved in the iterative procedure.
 
 numThreads - How many threads to use for the computation.
 
 Returns:
 
 refined list of peaks.
 - refinePeaks
```
public static <T extends RealType<T>,P extends Localizable> ArrayList<RefinedPeak> refinePeaks(List peaks,
 RandomAccessible<T> img,
 Interval validInterval,
 boolean returnInvalidPeaks,
 int maxNumMoves,
 boolean allowMaximaTolerance,
 float maximaTolerance,
 boolean[] allowedToMoveInDim)
```
 Refine a set of peaks to subpixel coordinates. Single-threaded version.
 A List RefinedPeak for the given list of Localizable is computed by, for each peak, fitting a quadratic function to the image and computing the subpixel coordinates of the extremum. This is an iterative procedure. If the extremum is shifted more than 0.5 in one or more the fit is repeated at the corresponding integer coordinates. This is repeated to convergence, for a maximum number of iterations, or until the integer coordinates move out of the valid image.
 
 Parameters:
 
 peaks - List of integer peaks.
 
 img - Pixel values.
 
 validInterval - In which interval the img contains valid pixels. If null, an infinite img is assumed. Integer peaks must lie within a 1-pixel border of this interval.
 
 returnInvalidPeaks - Whether (invalid) RefinedPeak should be created for peaks where the fitting procedure did not converge.
 
 maxNumMoves - maximum number of iterations for each peak.
 
 allowMaximaTolerance - If we allow an increasing maxima tolerance we will not change the base position that easily. Sometimes it simply jumps from left to right and back, because it is 4.51 (i.e. goto 5), then 4.49 (i.e. goto 4) Then we say, ok, lets keep the base position even if the subpixel location is 0.6...
 
 maximaTolerance - By how much to increase the tolerance per iteration.
 
 allowedToMoveInDim - specifies, per dimension, whether the base location is allowed to be moved in the iterative procedure.
 
 Returns:
 
 refined list of peaks.
 - quadraticFitOffset
```
protected static <T extends RealType<T>> void quadraticFitOffset(Localizable p,
 RandomAccess<T> access,
 Matrix g,
 Matrix H,
 RealPositionable offset)
```
 Estimate subpixel offset of extremum of quadratic function fitted at p.
 
 Parameters:
 
 p - integer position at which to fit quadratic.
 
 access - access to the image values.
 
 g - a n vector where n is the dimensionality of the image. (This is a temporary variable to store the gradient).
 
 H - a n × n matrix where n is the dimensionality of the image. (This is a temporary variable to store the Hessian).
 
 offset - subpixel offset of extremum wrt. p is stored here.

Class SubpixelLocalization<P extends Localizable,T extends RealType<T>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

maxNumMoves

allowMaximaTolerance

canMoveOutside

maximaTolerance

allowedToMoveInDim

returnInvalidPeaks

numThreads

Constructor Detail

SubpixelLocalization

Method Detail

setAllowMaximaTolerance

setCanMoveOutside

setMaximaTolerance

setMaxNumMoves

setAllowedToMoveInDim

setReturnInvalidPeaks

setNumThreads

getAllowMaximaTolerance

getCanMoveOutside

getMaximaTolerance

getMaxNumMoves

getAllowedToMoveInDim

getReturnInvalidPeaks

getNumThreads

process

refinePeaks

refinePeaks

quadraticFitOffset