java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmMatchForReference

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMatchForReference
extends AlgorithmBase
```
Will take Two 2D images (one Reference, one Adjusted) and use the Reference image's Resolutions to transform the adjusted Image into a new size and resolution that the Reference Image can then be matched to, while preserving all Field of Views (there is no loss of FOV).

Version:

1.0

Author:

Ben Link

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private ModelImage`	`adjImage`	adjusted image.
`private boolean`	`correctDims`	check for 2-dimensionality.
`private boolean`	`hasNewAdj`	was a new adjusted image created.
`private boolean`	`hasNewRef`	was a new reference image created.
`private ModelImage`	`newAdjImage`	new adjusted image.
`private ModelImage`	`newRefImage`	new reference image.
`private ModelImage`	`refImage`	reference image.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmMatchForReference(ModelImage rImage, ModelImage aImage)`	Constructor.. takes in a reference and adjusted modelImage

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disposeLocal()`	Dispose of local variables that may be taking up lots of room.
`void`	`finalize()`	Prepares this class for destruction.
`ModelImage`	`getNewAdjustedImage()`	Gets the new adjusted image created.
`ModelImage`	`getNewReferenceImage()`	Gets the new reference image created.
`boolean`	`newAdjustedCreated()`	tells if new adjusted image was created during run().
`boolean`	`newReferenceCreated()`	tells if new reference image was created during run().
`void`	`runAlgorithm()`	algorithm's run function....

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

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

- Field Detail
  - adjImage
```
private ModelImage adjImage
```
    adjusted image.
  - correctDims
```
private boolean correctDims
```
    check for 2-dimensionality.
  - hasNewAdj
```
private boolean hasNewAdj
```
    was a new adjusted image created.
  - hasNewRef
```
private boolean hasNewRef
```
    was a new reference image created.
  - newAdjImage
```
private ModelImage newAdjImage
```
    new adjusted image.
  - newRefImage
```
private ModelImage newRefImage
```
    new reference image.
  - refImage
```
private ModelImage refImage
```
    reference image.
- Constructor Detail
  - AlgorithmMatchForReference
```
public AlgorithmMatchForReference(ModelImage rImage,
                                  ModelImage aImage)
```
    Constructor.. takes in a reference and adjusted modelImage
    
    Parameters:
    
    rImage - reference image
    
    aImage - adjusted image
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    Dispose of local variables that may be taking up lots of room.
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getNewAdjustedImage
```
public ModelImage getNewAdjustedImage()
```
    Gets the new adjusted image created.
    
    Returns:
    
    new adj image
  - getNewReferenceImage
```
public ModelImage getNewReferenceImage()
```
    Gets the new reference image created.
    
    Returns:
    
    new ref image
  - newAdjustedCreated
```
public boolean newAdjustedCreated()
```
    tells if new adjusted image was created during run().
    
    Returns:
    
    if new was created
  - newReferenceCreated
```
public boolean newReferenceCreated()
```
    tells if new reference image was created during run().
    
    Returns:
    
    if new was created
  - runAlgorithm
```
public void runAlgorithm()
```
    algorithm's run function....
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase

Class AlgorithmMatchForReference

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

adjImage

correctDims

hasNewAdj

hasNewRef

newAdjImage

newRefImage

refImage

Constructor Detail

AlgorithmMatchForReference

Method Detail

disposeLocal

finalize

getNewAdjustedImage

getNewReferenceImage

newAdjustedCreated

newReferenceCreated

runAlgorithm