FourierConvolution (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:: Algorithm, Benchmark, MultiThreaded, OutputAlgorithm<T>

Direct Known Subclasses:: InverseFourierConvolution

public class FourierConvolution<T extends RealType<T>,S extends RealType<S>>
extends Object
implements MultiThreaded, OutputAlgorithm<T>, Benchmark

TODO

Author:: Stephan Preibisch

Constructor Summary

Constructors
Constructor and Description

FourierConvolution(Image<T> image, Image<S> kernel)

Constructors
Constructor and Description
`FourierConvolution(Image<T> image, Image<S> kernel)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`void`	`close()`
`static Image<FloatType>`	`createGaussianKernel(ContainerFactory factory, double[] sigmas)`
`static Image<FloatType>`	`createGaussianKernel(ContainerFactory factory, double[] sigmas, int precision)`
`static Image<FloatType>`	`createGaussianKernel(ContainerFactory factory, double sigma, int numDimensions)`
`String`	`getErrorMessage()`
`boolean`	`getExtendImageByKernelSize()`
`static <T extends RealType<T>> Image<T>`	`getGaussianKernel(ImageFactory<T> imgFactory, double[] sigma)`
`static <T extends RealType<T>> Image<T>`	`getGaussianKernel(ImageFactory<T> imgFactory, double sigma, int numDimensions)`
`Image<T>`	`getImage()`
`OutOfBoundsStrategyFactory<T>`	`getImageOutOfBoundsStrategy()`
`boolean`	`getKeepImgFFT()`
`Image<S>`	`getKernel()`
`int`	`getNumThreads()` The number of threads used by the algorithm
`long`	`getProcessingTime()`
`Image<T>`	`getResult()`
`protected void`	`multiply(Image<ComplexFloatType> a, Image<ComplexFloatType> b)` Multiply in Fourier Space
`boolean`	`process()`
`boolean`	`replaceImage(Image<T> img)`
`boolean`	`replaceKernel(Image<S> knl)`
`void`	`setExtendImageByKernelSize(boolean extend)` Defines if the image is extended by half the kernelsize all around its edges before computation.
`void`	`setImageOutOfBoundsStrategy(OutOfBoundsStrategyFactory<T> strategy)`
`void`	`setKeepImgFFT(boolean keepImgFFT)` By default, he will not do the computation in-place
`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

FourierConvolution

public FourierConvolution(Image<T> image,
                          Image<S> kernel)

Method Detail

getImage
```
public Image<T> getImage()
```

getKernel
```
public Image<S> getKernel()
```

setImageOutOfBoundsStrategy

public void setImageOutOfBoundsStrategy(OutOfBoundsStrategyFactory<T> strategy)

getImageOutOfBoundsStrategy

public OutOfBoundsStrategyFactory<T> getImageOutOfBoundsStrategy()

replaceImage

public boolean replaceImage(Image<T> img)

setExtendImageByKernelSize
```
public void setExtendImageByKernelSize(boolean extend)
```
Defines if the image is extended by half the kernelsize all around its edges before computation. This way, the outoufbounds will be correct.

Parameters:

extend -

getExtendImageByKernelSize

public boolean getExtendImageByKernelSize()

setKeepImgFFT
```
public void setKeepImgFFT(boolean keepImgFFT)
```
By default, he will not do the computation in-place

Parameters:

keepImgFFT -

getKeepImgFFT
```
public boolean getKeepImgFFT()
```

replaceKernel

public boolean replaceKernel(Image<S> knl)

createGaussianKernel

public static final Image<FloatType> createGaussianKernel(ContainerFactory factory,
                                                          double sigma,
                                                          int numDimensions)

createGaussianKernel

public static final Image<FloatType> createGaussianKernel(ContainerFactory factory,
                                                          double[] sigmas)

createGaussianKernel

public static final Image<FloatType> createGaussianKernel(ContainerFactory factory,
                                                          double[] sigmas,
                                                          int precision)

getGaussianKernel

public static final <T extends RealType<T>> Image<T> getGaussianKernel(ImageFactory<T> imgFactory,
                                                                       double sigma,
                                                                       int numDimensions)

getGaussianKernel

public static final <T extends RealType<T>> Image<T> getGaussianKernel(ImageFactory<T> imgFactory,
                                                                       double[] sigma)

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

process in interface Algorithm

multiply

protected void multiply(Image<ComplexFloatType> a,
                        Image<ComplexFloatType> b)

Multiply in Fourier Space

Parameters:: a -; b -

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

getResult
```
public Image<T> getResult()
```
Specified by:

getResult in interface OutputAlgorithm<T extends RealType<T>>

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

checkInput in interface Algorithm

close
```
public void close()
```

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

getErrorMessage in interface Algorithm

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FourierConvolution

Method Detail

getImage

getKernel

setImageOutOfBoundsStrategy

getImageOutOfBoundsStrategy

replaceImage

setExtendImageByKernelSize

getExtendImageByKernelSize

setKeepImgFFT

getKeepImgFFT

replaceKernel

createGaussianKernel

createGaussianKernel

createGaussianKernel

getGaussianKernel

getGaussianKernel

process

multiply

getProcessingTime

setNumThreads

setNumThreads

getNumThreads

getResult

checkInput

close

getErrorMessage