SubpixelLocalization (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.imglib.algorithm.scalespace.SubpixelLocalization<T>

All Implemented Interfaces:: Algorithm, Benchmark, MultiThreaded

public class SubpixelLocalization<T extends RealType<T>>
extends Object
implements Algorithm, Benchmark, MultiThreaded

TODO

Author:: Stephan Preibisch

Constructor Summary

Constructors
Constructor and Description

SubpixelLocalization(Image<T> laPlacian, List<DifferenceOfGaussianPeak<T>> peaks)

Constructors
Constructor and Description
`SubpixelLocalization(Image<T> laPlacian, List<DifferenceOfGaussianPeak<T>> peaks)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`analyzePeak(DifferenceOfGaussianPeak<T> peak)`
`boolean`	`checkInput()`
`static <T extends RealType<T>> Image<DoubleType>`	`computeDerivativeVector(LocalizableByDimCursor<T> cursor)` Computes the n-dimensional 1st derivative vector in 3x3x3...x3 environment for a certain `Image` location defined by the position of the `LocalizableByDimCursor`.
`static <T extends RealType<T>> void`	`computeDerivativeVector(LocalizableByDimCursor<T> cursor, Image<DoubleType> derivativeVector)` Computes the n-dimensional 1st derivative vector in 3x3x3...x3 environment for a certain `Image` location defined by the position of the `LocalizableByDimCursor`.
`static <T extends RealType<T>> Image<DoubleType>`	`computeHessianMatrix(LocalizableByDimCursor<T> cursor)` Computes the n-dimensional Hessian Matrix in 3x3x3...x3 environment for a certain `Image` location defined by the position of the `LocalizableByDimCursor`.
`static <T extends RealType<T>> void`	`computeHessianMatrix(LocalizableByDimCursor<T> cursor, Image<DoubleType> hessianMatrix)` Computes the n-dimensional Hessian Matrix in 3x3x3...x3 environment for a certain `Image` location defined by the position of the `LocalizableByDimCursor`.
`static Matrix`	`computePseudoInverseMatrix(Matrix M, double threshold)` Computes the pseudo-inverse of a matrix using Singular Value Decomposition
`boolean[]`	`getAllowedToMoveInDim()`
`boolean`	`getAllowMaximaTolerance()`
`boolean`	`getCanMoveOutside()`
`protected Image<DoubleType>`	`getDerivativeVector(LocalizableByDimCursor<T> cursor, Image<DoubleType> derivativeVector)` This method is called by the process method to allow to override how the derivative vector is computed
`List<DifferenceOfGaussianPeak<T>>`	`getDoGPeaks()`
`String`	`getErrorMessage()`
`protected Image<DoubleType>`	`getHessianMatrix(LocalizableByDimCursor<T> cursor, Image<DoubleType> hessianMatrix)` This method is called by the process method to allow to override how the hessian matrix is computed
`Image<T>`	`getLaPlaceImage()`
`static <S extends RealType<S>> Matrix`	`getMatrix(Image<S> maxtrixImage)` Converts an `Image` into a matrix
`float`	`getMaximaTolerance()`
`int`	`getMaxNumMoves()`
`int`	`getNumThreads()` The number of threads used by the algorithm
`long`	`getProcessingTime()`
`protected boolean`	`handleFailure(DifferenceOfGaussianPeak<T> peak, String error)`
`protected Matrix`	`invertMatrix(Image<DoubleType> matrixImage)` This method is called by the process method to allow to override how the matrix is inverted
`boolean`	`process()`
`void`	`setAllowedToMoveInDim(boolean[] allowedToMoveInDim)`
`void`	`setAllowMaximaTolerance(boolean allowMaximaTolerance)`
`void`	`setCanMoveOutside(boolean canMoveOutside)`
`void`	`setDoGPeaks(List<DifferenceOfGaussianPeak<T>> peaks)`
`void`	`setLaPlaceImage(Image<T> laPlacian)`
`void`	`setMaximaTolerance(float maximaTolerance)`
`void`	`setMaxNumMoves(int maxNumMoves)`
`void`	`setNumThreads()` Sets the number of threads to the amount of processors available
`void`	`setNumThreads(int numThreads)` Sets the number of threads

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

- Constructor Detail
  - SubpixelLocalization
```
public SubpixelLocalization(Image<T> laPlacian,
                            List<DifferenceOfGaussianPeak<T>> peaks)
```
- Method Detail
  - setAllowMaximaTolerance
```
public void setAllowMaximaTolerance(boolean allowMaximaTolerance)
```
  - setCanMoveOutside
```
public void setCanMoveOutside(boolean canMoveOutside)
```
  - setMaximaTolerance
```
public void setMaximaTolerance(float maximaTolerance)
```
  - setLaPlaceImage
```
public void setLaPlaceImage(Image<T> laPlacian)
```
  - setDoGPeaks
```
public void setDoGPeaks(List<DifferenceOfGaussianPeak<T>> peaks)
```
  - setMaxNumMoves
```
public void setMaxNumMoves(int maxNumMoves)
```
  - setAllowedToMoveInDim
```
public void setAllowedToMoveInDim(boolean[] allowedToMoveInDim)
```
  - getAllowMaximaTolerance
```
public boolean getAllowMaximaTolerance()
```
  - getCanMoveOutside
```
public boolean getCanMoveOutside()
```
  - getMaximaTolerance
```
public float getMaximaTolerance()
```
  - getLaPlaceImage
```
public Image<T> getLaPlaceImage()
```
  - getDoGPeaks
```
public List<DifferenceOfGaussianPeak<T>> getDoGPeaks()
```
  - getMaxNumMoves
```
public int getMaxNumMoves()
```
  - getAllowedToMoveInDim
```
public boolean[] getAllowedToMoveInDim()
```
  - handleFailure
```
protected boolean handleFailure(DifferenceOfGaussianPeak<T> peak,
                                String error)
```
  - process
```
public boolean process()
```
    Specified by:
    
    process in interface Algorithm
  - analyzePeak
```
public boolean analyzePeak(DifferenceOfGaussianPeak<T> peak)
```
  - invertMatrix
```
protected Matrix invertMatrix(Image<DoubleType> matrixImage)
```
    This method is called by the process method to allow to override how the matrix is inverted
  - getDerivativeVector
```
protected Image<DoubleType> getDerivativeVector(LocalizableByDimCursor<T> cursor,
                                                Image<DoubleType> derivativeVector)
```
    This method is called by the process method to allow to override how the derivative vector is computed
  - getHessianMatrix
```
protected Image<DoubleType> getHessianMatrix(LocalizableByDimCursor<T> cursor,
                                             Image<DoubleType> hessianMatrix)
```
    This method is called by the process method to allow to override how the hessian matrix is computed
  - getMatrix
```
public static <S extends RealType<S>> Matrix getMatrix(Image<S> maxtrixImage)
```
    Converts an Image into a matrix
    
    Parameters:
    
    maxtrixImage - - the input Image
    
    Returns:
    
    a Matrix or null if the Image is not one or two-dimensional
  - computePseudoInverseMatrix
```
public static final Matrix computePseudoInverseMatrix(Matrix M,
                                                      double threshold)
```
    Computes the pseudo-inverse of a matrix using Singular Value Decomposition
    
    Parameters:
    
    M - - the input Matrix
    
    threshold - - the threshold for inverting diagonal elements (suggested 0.001)
    
    Returns:
    
    the inverted Matrix or an approximation with lowest possible squared error
  - computeDerivativeVector
```
public static final <T extends RealType<T>> Image<DoubleType> computeDerivativeVector(LocalizableByDimCursor<T> cursor)
```
    Computes the n-dimensional 1st derivative vector in 3x3x3...x3 environment for a certain Image location defined by the position of the LocalizableByDimCursor.
    
    Parameters:
    
    cursor - - the position for which to compute the Hessian Matrix
    
    Returns:
    
    Image - the derivative, which is essentially a one-dimensional DoubleType Image of size [numDimensions]
  - computeDerivativeVector
```
public static final <T extends RealType<T>> void computeDerivativeVector(LocalizableByDimCursor<T> cursor,
                                                                         Image<DoubleType> derivativeVector)
```
    Computes the n-dimensional 1st derivative vector in 3x3x3...x3 environment for a certain Image location defined by the position of the LocalizableByDimCursor.
    
    Parameters:
    
    cursor - - the position for which to compute the Hessian Matrix
    
    Image - - the derivative, which is essentially a one-dimensional DoubleType Image of size [numDimensions]
  - computeHessianMatrix
```
public static final <T extends RealType<T>> Image<DoubleType> computeHessianMatrix(LocalizableByDimCursor<T> cursor)
```
    Computes the n-dimensional Hessian Matrix in 3x3x3...x3 environment for a certain Image location defined by the position of the LocalizableByDimCursor.
    
    Parameters:
    
    cursor - - the position for which to compute the Hessian Matrix
    
    Returns:
    
    Image - the hessian matrix, which is essentially a two-dimensional DoubleType Image of size [numDimensions][numDimensions]
  - computeHessianMatrix
```
public static final <T extends RealType<T>> void computeHessianMatrix(LocalizableByDimCursor<T> cursor,
                                                                      Image<DoubleType> hessianMatrix)
```
    Computes the n-dimensional Hessian Matrix in 3x3x3...x3 environment for a certain Image location defined by the position of the LocalizableByDimCursor.
    
    Parameters:
    
    cursor - - the position for which to compute the Hessian Matrix
    
    Image - - the hessian matrix, which is essentially a two-dimensional DoubleType Image of size [numDimensions][numDimensions]
  - checkInput
```
public boolean checkInput()
```
    Specified by:
    
    checkInput in interface Algorithm
  - setNumThreads
```
public void setNumThreads()
```
    Description copied from interface: MultiThreaded
    
    Sets the number of threads to the amount of processors available
    
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads(int numThreads)
```
    Description copied from interface: MultiThreaded
    
    Sets the number of threads
    
    Specified by:
    
    setNumThreads in interface MultiThreaded
    
    Parameters:
    
    numThreads - - number of threads to use
  - getNumThreads
```
public int getNumThreads()
```
    Description copied from interface: MultiThreaded
    
    The number of threads used by the algorithm
    
    Specified by:
    
    getNumThreads in interface MultiThreaded
    
    Returns:
    
    - the number of threads
  - getErrorMessage
```
public String getErrorMessage()
```
    Specified by:
    
    getErrorMessage in interface Algorithm
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark

Class SubpixelLocalization<T extends RealType<T>>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SubpixelLocalization

Method Detail

setAllowMaximaTolerance

setCanMoveOutside

setMaximaTolerance

setLaPlaceImage

setDoGPeaks

setMaxNumMoves

setAllowedToMoveInDim

getAllowMaximaTolerance

getCanMoveOutside

getMaximaTolerance

getLaPlaceImage

getDoGPeaks

getMaxNumMoves

getAllowedToMoveInDim

handleFailure

process

analyzePeak

invertMatrix

getDerivativeVector

getHessianMatrix

getMatrix

computePseudoInverseMatrix

computeDerivativeVector

computeDerivativeVector

computeHessianMatrix

computeHessianMatrix

checkInput

setNumThreads

setNumThreads

getNumThreads

getErrorMessage

getProcessingTime