java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline
    - - gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline25D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmRegBSpline25D
extends AlgorithmRegBSpline
```
BSpline based registration of 2.5D images.

Nested Class Summary
- Nested classes/interfaces inherited from class gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline
  AlgorithmRegBSpline.Options
- 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

protected int m_iSliceTarget
Index of the slice in the input source image to use as the target.
- Fields inherited from class gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline
  m_kImageDeformation, m_kImageResult, m_kImageSource, m_kImageTarget, m_kOptionsPass1, m_kOptionsPass2, m_kRegMeasure
- 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
`AlgorithmRegBSpline25D(ModelImage kImageResult, ModelImage kImageSource, int iSliceTarget, ModelImage kImageDeformation, RegistrationMeasure kRegMeasure, AlgorithmRegBSpline.Options kOptionsPass1, AlgorithmRegBSpline.Options kOptionsPass2)`	Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disposeLocal()`	Prepares this class for destruction.
`void`	`finalize()`	Override of Object method called by garbage collection.
`void`	`runAlgorithm()`	AlgorithmBase abstract method implementation which performs the registration.
`protected BSplineRegistration2Df`	`runPass(ModelSimpleImage kSource, ModelSimpleImage kTarget, AlgorithmRegBSpline.Options kOptions, BSplineRegistration2Df kRegPrev)`	Perform a "pass" of BSpline based registration.
`private void`	`transform2DVOI(ModelImage image, ModelImage destImage, float[] imgBuffer, float[] kImageMapX, float[] kImageMapY, int iSlice, int iNumSlices)`
`private void`	`writeResults(BSplineRegistration2Df[] akReg)`	Save the registration information to a file.

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
  - m_iSliceTarget
```
protected final int m_iSliceTarget
```
    Index of the slice in the input source image to use as the target. If the value is -1, then each slice is registered to its adjacent one.
- Constructor Detail
  - AlgorithmRegBSpline25D
```
public AlgorithmRegBSpline25D(ModelImage kImageResult,
                              ModelImage kImageSource,
                              int iSliceTarget,
                              ModelImage kImageDeformation,
                              RegistrationMeasure kRegMeasure,
                              AlgorithmRegBSpline.Options kOptionsPass1,
                              AlgorithmRegBSpline.Options kOptionsPass2)
```
    Constructor.
    
    Parameters:
    
    kImageResult - ModelImage Reference to an image to store the registered source image. This image must have the same dimensions as the input source image.
    
    kImageSource - ModelImage Reference to the original input image to use as the registration source.
    
    iSliceTarget - int Index of the slice in the input source image that is to be used as the reference. If this index is -1, then each slice is registered to the one before it
    
    kImageDeformation - ModelImage Reference to an image to store the computed deformation. This may be a null reference to indicate that the deformation is not to be computed. If this reference is not null, then the image must have the same dimensions as the input source image.
    
    kRegMeasure - RegistrationMeasure Reference to the particular cost measure to use for this registration. The cost measure is the same for all passes.
    
    kOptionsPass1 - Options Options to use for a first pass of registration. This may *not* be a null reference.
    
    kOptionsPass2 - Options Options to use for a second pass of registration. This may be null to indicate that only a single pass of registration is to be performed.
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    Prepares this class for destruction.
    
    Overrides:
    
    disposeLocal in class AlgorithmRegBSpline
  - finalize
```
public void finalize()
```
    Override of Object method called by garbage collection.
    
    Overrides:
    
    finalize in class AlgorithmRegBSpline
  - runAlgorithm
```
public void runAlgorithm()
```
    AlgorithmBase abstract method implementation which performs the registration.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
    
    Throws:
    
    java.lang.RuntimeException - DOCUMENT ME!
  - transform2DVOI
```
private void transform2DVOI(ModelImage image,
                            ModelImage destImage,
                            float[] imgBuffer,
                            float[] kImageMapX,
                            float[] kImageMapY,
                            int iSlice,
                            int iNumSlices)
```
  - runPass
```
protected BSplineRegistration2Df runPass(ModelSimpleImage kSource,
                                         ModelSimpleImage kTarget,
                                         AlgorithmRegBSpline.Options kOptions,
                                         BSplineRegistration2Df kRegPrev)
```
    Perform a "pass" of BSpline based registration. A "pass" is defined to be one or more iterations using the BSpline basis parameters, gradient descent parameters, and convergence parameters.
    
    Parameters:
    
    kSource - ModelSimpleImage Reference to the original input image to use as the registration source. This image does not have to have the same dimensions as the image to be used as the registration target.
    
    kTarget - ModelSimpleImage Reference to the original input image to use as the registration target.
    
    kOptions - Options Options to use for a this registration pass. This may *not* be a null reference.
    
    kRegPrev - BSplineRegistration2Df Reference to a previous registration which can be used to initialize this registration. This may be a null reference meaning that the this registration uses the default "identity" initialization. If this it not a null reference, then this registration is initialized to provide the a close approximation to the same BSpline mapping as determined by the input registration. The main property of a registration is the position of its control points.
    
    Returns:
    
    BSplineRegistration2Df Registration instance resulting from this pass. This may be needed to provide for the initialization of subsequent passes or to compute the deformation image.
  - writeResults
```
private void writeResults(BSplineRegistration2Df[] akReg)
```
    Save the registration information to a file. This information includes the BSpline parameters; in particular, the coordinates for the lattice of control points.
    
    Parameters:
    
    akReg - BSplineRegistration2Df[] Contains the parameters which define the BSpline for registering each slice of the source image to the particular reference slice.

Class AlgorithmRegBSpline25D

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline

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

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline

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

m_iSliceTarget

Constructor Detail

AlgorithmRegBSpline25D

Method Detail

disposeLocal

finalize

runAlgorithm

transform2DVOI

runPass

writeResults