ROIAlgorithm (Fiji Javadocs 0-SNAPSHOT API)

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

Type Parameters:

T -

S -

All Implemented Interfaces:

Algorithm, Benchmark, OutputAlgorithm<S>

Direct Known Subclasses:

DirectConvolution, StatisticalOperation
```
public abstract class ROIAlgorithm<T extends RealType<T>,S extends RealType<S>>
extends Object
implements OutputAlgorithm<S>, Benchmark
```
ROIAlgorithm implements a framework against which to build operations of one image against another, like convolution, cross-correlation, or morphological operations. It operates by creating a RegionOfInterestCursor from the input image, and an output image, which is assumed to be of the same size as the input. The process() method curses over the output image, and at each step calls the abstract method patchOperation(), giving it the current location in the output and input images, as well as the RegionOfInterestCursor, which will curse over a patch of a given size in the input image. patchOperation() is responsible for setting the value of the pixel at the given position in the output image.

Author:

Larry Lindsey

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`ROIAlgorithm(S type, Image<T> imageIn, int[] patchSize)` Creates an ROIAlgorithm with default `OutOfBoundsStrategyValueFactory`, with value Zero.
`protected`	`ROIAlgorithm(S type, Image<T> imageIn, int[] patchSize, OutOfBoundsStrategyFactory<T> inOutFactory)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`void`	`close()`
`String`	`getErrorMessage()`
`String`	`getName()`
`protected Image<S>`	`getOutputImage()` Returns the `Image` that will eventually become the result of this `OutputAlgorithm`, and creates it if it has not yet been created.
`int[]`	`getPatchSize()`
`long`	`getProcessingTime()`
`Image<S>`	`getResult()`
`protected abstract boolean`	`patchOperation(int[] position, RegionOfInterestCursor<T> cursor)` Performs this algorithm's operation on the patch represented by a `RegionOfInterestCursor`
`protected int[]`	`positionOffset(int[] position, int[] offsetPosition)` Offsets the given position to reflect the origin of the patch being in its center, rather than at the top-left corner as is usually the case.
`boolean`	`process()`
`protected void`	`setErrorMessage(String message)`
`void`	`setImageFactory(ImageFactory<S> factory)` Set the `ImageFactory` used to create the output `Image`
`void`	`setName(String inName)` Set the name given to the output image.

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

- Constructor Detail
  - ROIAlgorithm
```
protected ROIAlgorithm(S type,
                       Image<T> imageIn,
                       int[] patchSize)
```
    Creates an ROIAlgorithm with default OutOfBoundsStrategyValueFactory, with value Zero.
    
    Parameters:
    
    type - a representative type for the output image.
    
    imageIn - the image over which to iterate.
    
    patchSize - the size of the patch that will be examined at each iteration.
  - ROIAlgorithm
```
protected ROIAlgorithm(S type,
                       Image<T> imageIn,
                       int[] patchSize,
                       OutOfBoundsStrategyFactory<T> inOutFactory)
```
    Parameters:
    
    type - a representative type for the output image.
    
    imageIn - the image over which to iterate.
    
    patchSize - the size of the patch that will be examined at each iteration.
    
    inOutFactory - an OutOfBoundsStrategyFactory to handle the border phenomenon.
- Method Detail
  - patchOperation
```
protected abstract boolean patchOperation(int[] position,
                                          RegionOfInterestCursor<T> cursor)
```
    Performs this algorithm's operation on the patch represented by a RegionOfInterestCursor
    
    Parameters:
    
    position - the position in the input image at the center of the patch represented by the RegionOfInterestCursor
    
    cursor - a RegionOfInterestCursor that iterates over the given patch-of-interest
    
    Returns:
    
    true if the operation on the given patch was successful, false otherwise. If false is returned by this method, process() will abort.
  - setImageFactory
```
public void setImageFactory(ImageFactory<S> factory)
```
    Set the ImageFactory used to create the output Image
    
    Parameters:
    
    factory - the ImageFactory used to create the output Image
  - setName
```
public void setName(String inName)
```
    Set the name given to the output image.
    
    Parameters:
    
    inName - the name to give to the output image.
  - getName
```
public String getName()
```
  - getPatchSize
```
public int[] getPatchSize()
```
  - getOutputImage
```
protected Image<S> getOutputImage()
```
    Returns the Image that will eventually become the result of this OutputAlgorithm, and creates it if it has not yet been created.
    
    Returns:
    
    the Image that will eventually become the result of this OutputAlgorithm.
  - getResult
```
public Image<S> getResult()
```
    Specified by:
    
    getResult in interface OutputAlgorithm<S extends RealType<S>>
  - getErrorMessage
```
public String getErrorMessage()
```
    Specified by:
    
    getErrorMessage in interface Algorithm
  - setErrorMessage
```
protected void setErrorMessage(String message)
```
  - positionOffset
```
protected int[] positionOffset(int[] position,
                               int[] offsetPosition)
```
    Offsets the given position to reflect the origin of the patch being in its center, rather than at the top-left corner as is usually the case.
    
    Parameters:
    
    position - the position to be offset
    
    offsetPosition - an int array to contain the newly offset position coordinates
    
    Returns:
    
    offsetPosition, for convenience.
  - process
```
public boolean process()
```
    Specified by:
    
    process in interface Algorithm
  - checkInput
```
public boolean checkInput()
```
    Specified by:
    
    checkInput in interface Algorithm
  - close
```
public void close()
```
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ROIAlgorithm

ROIAlgorithm

Method Detail

patchOperation

setImageFactory

setName

getName

getPatchSize

getOutputImage

getResult

getErrorMessage

setErrorMessage

positionOffset

process

checkInput

close

getProcessingTime