PhaseCorrelation (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.imglib.algorithm.fft.PhaseCorrelation<T,S>

All Implemented Interfaces:: Algorithm, Benchmark, MultiThreaded

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

TODO

Author:: Stephan Preibisch

Constructor Summary

Constructors
Constructor and Description
`PhaseCorrelation(Image<T> image1, Image<S> image2)`
`PhaseCorrelation(Image<T> image1, Image<S> image2, int numPeaks, boolean verifyWithCrossCorrelation)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`protected boolean`	`computeFFT(FourierTransform<T,ComplexFloatType> fft1, FourierTransform<S,ComplexFloatType> fft2)`
`protected ArrayList<PhaseCorrelationPeak>`	`extractPhaseCorrelationPeaks(Image<FloatType> invPCM, int numPeaks, FourierTransform<?,?> fft1, FourierTransform<?,?> fft2)`
`ArrayList<PhaseCorrelationPeak>`	`getAllShifts()`
`boolean`	`getComputeFFTinParalell()`
`String`	`getErrorMessage()`
`int`	`getInvestigateNumPeaks()`
`boolean`	`getKeepPhaseCorrelationMatrix()`
`protected static int[]`	`getMaxDim(Image<?> image1, Image<?> image2)`
`int[]`	`getMinimalPixelOverlap()`
`float`	`getNormalizationThreshold()`
`int`	`getNumThreads()` The number of threads used by the algorithm
`Image<FloatType>`	`getPhaseCorrelationMatrix()`
`long`	`getProcessingTime()`
`PhaseCorrelationPeak`	`getShift()`
`boolean`	`getVerifyWithCrossCorrelation()`
`protected void`	`multiplyInPlace(Image<ComplexFloatType> fftImage1, Image<ComplexFloatType> fftImage2)`
`protected void`	`normalizeAndConjugate(Image<ComplexFloatType> fftImage1, Image<ComplexFloatType> fftImage2)`
`boolean`	`process()`
`void`	`setComputeFFTinParalell(boolean computeFFTinParalell)`
`void`	`setInvestigateNumPeaks(int numPeaks)`
`void`	`setKeepPhaseCorrelationMatrix(boolean keepPCM)`
`void`	`setMinimalPixelOverlap(int minOverlapPx)`
`void`	`setMinimalPixelOverlap(int[] minOverlapPx)`
`void`	`setNormalizationThreshold(int normalizationThreshold)`
`void`	`setNumThreads()` Sets the number of threads to the amount of processors available
`void`	`setNumThreads(int numThreads)` Sets the number of threads
`void`	`setVerifyWithCrossCorrelation(boolean verifyWithCrossCorrelation)`
`static <T extends RealType<T>,S extends RealType<S>> double`	`testCrossCorrelation(int[] shift, Image<T> image1, Image<S> image2)`
`static <T extends RealType<T>,S extends RealType<S>> double`	`testCrossCorrelation(int[] shift, Image<T> image1, Image<S> image2, int minOverlapPx)`
`static <T extends RealType<T>,S extends RealType<S>> double`	`testCrossCorrelation(int[] shift, Image<T> image1, Image<S> image2, int[] minOverlapPx)`
`static <T extends RealType<T>,S extends RealType<S>> double`	`testCrossCorrelation(int[] shift, Image<T> image1, Image<S> image2, int[] minOverlapPx, long[] numPixels)`
`static <T extends RealType<T>,S extends RealType<S>> double`	`testCrossCorrelation(int[] shift, Image<T> image1, Image<S> image2, int minOverlapPx, long[] numPixels)`
`protected void`	`verifyWithCrossCorrelation(ArrayList<PhaseCorrelationPeak> peakList, int[] dimInvPCM, Image<T> image1, Image<S> image2)`

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

Constructor Detail

PhaseCorrelation

public PhaseCorrelation(Image<T> image1,
                        Image<S> image2,
                        int numPeaks,
                        boolean verifyWithCrossCorrelation)

PhaseCorrelation

public PhaseCorrelation(Image<T> image1,
                        Image<S> image2)

Method Detail

setComputeFFTinParalell

public void setComputeFFTinParalell(boolean computeFFTinParalell)

setInvestigateNumPeaks

public void setInvestigateNumPeaks(int numPeaks)

setKeepPhaseCorrelationMatrix

public void setKeepPhaseCorrelationMatrix(boolean keepPCM)

setNormalizationThreshold

public void setNormalizationThreshold(int normalizationThreshold)

setVerifyWithCrossCorrelation

public void setVerifyWithCrossCorrelation(boolean verifyWithCrossCorrelation)

setMinimalPixelOverlap

public void setMinimalPixelOverlap(int[] minOverlapPx)

setMinimalPixelOverlap

public void setMinimalPixelOverlap(int minOverlapPx)

getComputeFFTinParalell

public boolean getComputeFFTinParalell()

getInvestigateNumPeaks
```
public int getInvestigateNumPeaks()
```

getKeepPhaseCorrelationMatrix

public boolean getKeepPhaseCorrelationMatrix()

getNormalizationThreshold

public float getNormalizationThreshold()

getVerifyWithCrossCorrelation

public boolean getVerifyWithCrossCorrelation()

getMinimalPixelOverlap
```
public int[] getMinimalPixelOverlap()
```

getPhaseCorrelationMatrix

public Image<FloatType> getPhaseCorrelationMatrix()

getShift

public PhaseCorrelationPeak getShift()

getAllShifts

public ArrayList<PhaseCorrelationPeak> getAllShifts()

process
```
public boolean process()
```
Specified by:

process in interface Algorithm

verifyWithCrossCorrelation

protected void verifyWithCrossCorrelation(ArrayList<PhaseCorrelationPeak> peakList,
                                          int[] dimInvPCM,
                                          Image<T> image1,
                                          Image<S> image2)

testCrossCorrelation

public static <T extends RealType<T>,S extends RealType<S>> double testCrossCorrelation(int[] shift,
                                                                                        Image<T> image1,
                                                                                        Image<S> image2)

testCrossCorrelation

public static <T extends RealType<T>,S extends RealType<S>> double testCrossCorrelation(int[] shift,
                                                                                        Image<T> image1,
                                                                                        Image<S> image2,
                                                                                        int minOverlapPx)

testCrossCorrelation

public static <T extends RealType<T>,S extends RealType<S>> double testCrossCorrelation(int[] shift,
                                                                                        Image<T> image1,
                                                                                        Image<S> image2,
                                                                                        int minOverlapPx,
                                                                                        long[] numPixels)

testCrossCorrelation

public static <T extends RealType<T>,S extends RealType<S>> double testCrossCorrelation(int[] shift,
                                                                                        Image<T> image1,
                                                                                        Image<S> image2,
                                                                                        int[] minOverlapPx)

testCrossCorrelation

public static <T extends RealType<T>,S extends RealType<S>> double testCrossCorrelation(int[] shift,
                                                                                        Image<T> image1,
                                                                                        Image<S> image2,
                                                                                        int[] minOverlapPx,
                                                                                        long[] numPixels)

extractPhaseCorrelationPeaks

protected ArrayList<PhaseCorrelationPeak> extractPhaseCorrelationPeaks(Image<FloatType> invPCM,
                                                                       int numPeaks,
                                                                       FourierTransform<?,?> fft1,
                                                                       FourierTransform<?,?> fft2)

getMaxDim

protected static int[] getMaxDim(Image<?> image1,
                                 Image<?> image2)

multiplyInPlace

protected void multiplyInPlace(Image<ComplexFloatType> fftImage1,
                               Image<ComplexFloatType> fftImage2)

normalizeAndConjugate

protected void normalizeAndConjugate(Image<ComplexFloatType> fftImage1,
                                     Image<ComplexFloatType> fftImage2)

computeFFT

protected boolean computeFFT(FourierTransform<T,ComplexFloatType> fft1,
                             FourierTransform<S,ComplexFloatType> fft2)

getProcessingTime
```
public long getProcessingTime()
```
Specified by:

getProcessingTime in interface Benchmark

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

checkInput
```
public boolean checkInput()
```
Specified by:

checkInput in interface Algorithm

getErrorMessage
```
public String getErrorMessage()
```
Specified by:

getErrorMessage in interface Algorithm

Class PhaseCorrelation<T extends RealType<T>,S extends RealType<S>>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PhaseCorrelation

PhaseCorrelation

Method Detail

setComputeFFTinParalell

setInvestigateNumPeaks

setKeepPhaseCorrelationMatrix

setNormalizationThreshold

setVerifyWithCrossCorrelation

setMinimalPixelOverlap

setMinimalPixelOverlap

getComputeFFTinParalell

getInvestigateNumPeaks

getKeepPhaseCorrelationMatrix

getNormalizationThreshold

getVerifyWithCrossCorrelation

getMinimalPixelOverlap

getPhaseCorrelationMatrix

getShift

getAllShifts

process

verifyWithCrossCorrelation

testCrossCorrelation

testCrossCorrelation

testCrossCorrelation

testCrossCorrelation

testCrossCorrelation

extractPhaseCorrelationPeaks

getMaxDim

multiplyInPlace

normalizeAndConjugate

computeFFT

getProcessingTime

setNumThreads

setNumThreads

getNumThreads

checkInput

getErrorMessage