GaussianConvolution3 (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.imglib.algorithm.gauss.GaussianConvolution3<A,B,C>

Type Parameters:

A - - The input Type

B - - The NumericType used to compute the gaussian convolution

C - - The output Type

All Implemented Interfaces:

Algorithm, Benchmark, MultiThreaded, OutputAlgorithm<C>

Direct Known Subclasses:

GaussianConvolution, GaussianConvolution2, GaussianConvolution4
```
public class GaussianConvolution3<A extends Type<A>,B extends NumericType<B>,C extends Type<C>>
extends Object
implements MultiThreaded, OutputAlgorithm<C>, Benchmark
```
Computes a Gaussian Convolution on any Type(A) for which is defined how to convert it into a NumericType(B) on which the convolution is performed and back to the desired output Type(C). Of course A and C can be same. Note that the kernel precision is limited to double here.

Author:

Stephan Preibisch

Constructor Summary

Constructors
Constructor and Description
`GaussianConvolution3(Image<A> image, ImageFactory<B> factoryProcess, ImageFactory<C> factoryOut, OutOfBoundsStrategyFactory<B> outOfBoundsFactory, Converter<A,B> converterIn, Converter<B,C> converterOut, double sigma)`
`GaussianConvolution3(Image<A> image, ImageFactory<B> factoryProcess, ImageFactory<C> factoryOut, OutOfBoundsStrategyFactory<B> outOfBoundsFactory, Converter<A,B> converterIn, Converter<B,C> converterOut, double[] sigma)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`protected void`	`computeKernel()`
`protected void`	`convolve(LocalizableByDimCursor<B> inputIterator, LocalizableCursor<B> outputIterator, int dim, double[] kernel, long startPos, long loopSize)`
`protected void`	`convolveDim(LocalizableByDimCursor<B> inputIterator, LocalizableCursor<B> outputIterator, int currentDim, long startPos, long loopSize)`
`protected static double[]`	`createArray(Image<?> image, double sigma)`
`protected Image<C>`	`getConvolvedImage()`
`String`	`getErrorMessage()`
`Image<A>`	`getImage()`
`protected Image<B>`	`getInputImage()`
`protected LocalizableByDimCursor<B>`	`getInputIterator(Image<B> temp1, Image<B> temp2, int currentDim)`
`int`	`getKernelSize(int dim)`
`int`	`getNumThreads()` The number of threads used by the algorithm
`protected LocalizableCursor<B>`	`getOutputIterator(Image<B> temp1, Image<B> temp2, int currentDim)`
`long`	`getProcessingTime()`
`Image<C>`	`getResult()`
`double[]`	`getSigma()`
`double[]`	`getSigmas()` The sigma the image was convolved with
`protected Image<B>`	`getTempImage1(int currentDim)`
`protected Image<B>`	`getTempImage2(int currentDim)`
`boolean`	`process()`
`protected boolean`	`processWithOptimizedMethod()`
`void`	`setImage(Image<A> image)`
`void`	`setNumThreads()` Sets the number of threads to the amount of processors available
`void`	`setNumThreads(int numThreads)` Sets the number of threads
`void`	`setSigma(double sigma)`
`void`	`setSigma(double[] sigma)`

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

Constructor Detail

GaussianConvolution3

public GaussianConvolution3(Image<A> image,
                            ImageFactory<B> factoryProcess,
                            ImageFactory<C> factoryOut,
                            OutOfBoundsStrategyFactory<B> outOfBoundsFactory,
                            Converter<A,B> converterIn,
                            Converter<B,C> converterOut,
                            double[] sigma)

GaussianConvolution3

public GaussianConvolution3(Image<A> image,
                            ImageFactory<B> factoryProcess,
                            ImageFactory<C> factoryOut,
                            OutOfBoundsStrategyFactory<B> outOfBoundsFactory,
                            Converter<A,B> converterIn,
                            Converter<B,C> converterOut,
                            double sigma)

Method Detail

createArray

protected static double[] createArray(Image<?> image,
                                      double sigma)

computeKernel
```
protected void computeKernel()
```

setSigma
```
public void setSigma(double sigma)
```

setSigma
```
public void setSigma(double[] sigma)
```

getSigma
```
public double[] getSigma()
```

setImage
```
public void setImage(Image<A> image)
```

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

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

getSigmas
```
public double[] getSigmas()
```
The sigma the image was convolved with

Returns:

- double sigma

getKernelSize
```
public int getKernelSize(int dim)
```

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

getResult in interface OutputAlgorithm<C extends Type<C>>

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

checkInput in interface Algorithm

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

getErrorMessage in interface Algorithm

getInputImage
```
protected Image<B> getInputImage()
```

getTempImage1

protected Image<B> getTempImage1(int currentDim)

getTempImage2

protected Image<B> getTempImage2(int currentDim)

getInputIterator

protected LocalizableByDimCursor<B> getInputIterator(Image<B> temp1,
                                                     Image<B> temp2,
                                                     int currentDim)

getOutputIterator

protected LocalizableCursor<B> getOutputIterator(Image<B> temp1,
                                                 Image<B> temp2,
                                                 int currentDim)

getConvolvedImage

protected Image<C> getConvolvedImage()

processWithOptimizedMethod

protected boolean processWithOptimizedMethod()

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

process in interface Algorithm

convolveDim

protected void convolveDim(LocalizableByDimCursor<B> inputIterator,
                           LocalizableCursor<B> outputIterator,
                           int currentDim,
                           long startPos,
                           long loopSize)

convolve

protected void convolve(LocalizableByDimCursor<B> inputIterator,
                        LocalizableCursor<B> outputIterator,
                        int dim,
                        double[] kernel,
                        long startPos,
                        long loopSize)

Class GaussianConvolution3<A extends Type<A>,B extends NumericType<B>,C extends Type<C>>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GaussianConvolution3

GaussianConvolution3

Method Detail

createArray

computeKernel

setSigma

setSigma

getSigma

setImage

getImage

getProcessingTime

setNumThreads

setNumThreads

getNumThreads

getSigmas

getKernelSize

getResult

checkInput

getErrorMessage

getInputImage

getTempImage1

getTempImage2

getInputIterator

getOutputIterator

getConvolvedImage

processWithOptimizedMethod

process

convolveDim

convolve