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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMidsagittal
extends AlgorithmBase
```
Finds the midsagittal line of a brain MRI by:
- Flipping the image horizontally.
- Registering the flipped image against the original.
- Getting the angle that the registration rotated the image.
- Transforming the original image by half the registration rotation.
Version:

0.1 Dec 29, 2004

Author:

Evan McCreedy

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 int`	`baseNumIter`	Limits the number of iterations of Powell's algorithm when registering the original image against the flipped image.
`private int`	`coarseAngle`	The coarse angle step to use in each dimension when registering the original image against the flipped image.
`private int`	`costFunc`	The cost function to use when registering the original image against the flipped image.
`private int`	`dof`	The number of degrees of freedom to use when registering the original image against the flipped image.
`private boolean`	`doMultiThread`
`private boolean`	`doSubsample`	Whether to use subsampling when registering the original image against the flipped image.
`private boolean`	`fastMode`	Whether to skip searching of the parameter space when registering the original image against the flipped image.
`private int`	`fineAngle`	The fine angle step to use in each dimension when registering the original image against the flipped image.
`private int`	`interp`	The interpolation method to use when registering the original image against the flipped image.
`private boolean`	`maxOfMin`	Whether to use the maximum of the minimum resolutions of the 2 images when respampling during registration against the flipped image.
`private int`	`numMinima`	Number of minima from level 8 to test at level 4 when registering the original image against the flipped image.
`private int`	`searchAngle`	The search angles to use in each dimension (from `-searchAngle` to `searchAngle`) when registering the original image against the flipped 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

AlgorithmMidsagittal(ModelImage srcImg)
Construct the midsagittal algorithm.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calc()`	Find the midsagittal line and transform the source image to align it along that line vertically.
`private void`	`calc35D()`
`void`	`finalize()`	Prepares this class for destruction.
`ModelImage`	`getResultImage()`	Get the midsagittal aligned image.
`void`	`runAlgorithm()`	Starts the algorithm.

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
  - baseNumIter
```
private int baseNumIter
```
    Limits the number of iterations of Powell's algorithm when registering the original image against the flipped image.
  - coarseAngle
```
private int coarseAngle
```
    The coarse angle step to use in each dimension when registering the original image against the flipped image.
  - costFunc
```
private int costFunc
```
    The cost function to use when registering the original image against the flipped image.
  - dof
```
private int dof
```
    The number of degrees of freedom to use when registering the original image against the flipped image.
  - doSubsample
```
private boolean doSubsample
```
    Whether to use subsampling when registering the original image against the flipped image.
  - doMultiThread
```
private boolean doMultiThread
```
  - fastMode
```
private boolean fastMode
```
    Whether to skip searching of the parameter space when registering the original image against the flipped image.
  - fineAngle
```
private int fineAngle
```
    The fine angle step to use in each dimension when registering the original image against the flipped image.
  - interp
```
private int interp
```
    The interpolation method to use when registering the original image against the flipped image.
  - maxOfMin
```
private boolean maxOfMin
```
    Whether to use the maximum of the minimum resolutions of the 2 images when respampling during registration against the flipped image.
  - numMinima
```
private int numMinima
```
    Number of minima from level 8 to test at level 4 when registering the original image against the flipped image.
  - searchAngle
```
private int searchAngle
```
    The search angles to use in each dimension (from -searchAngle to searchAngle) when registering the original image against the flipped image.
- Constructor Detail
  - AlgorithmMidsagittal
```
public AlgorithmMidsagittal(ModelImage srcImg)
```
    Construct the midsagittal algorithm.
    
    Parameters:
    
    srcImg - source image model
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultImage
```
public ModelImage getResultImage()
```
    Get the midsagittal aligned image.
    
    Returns:
    
    the aligned image
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - calc
```
private void calc()
```
    Find the midsagittal line and transform the source image to align it along that line vertically.
  - calc35D
```
private void calc35D()
```

Class AlgorithmMidsagittal

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

baseNumIter

coarseAngle

costFunc

dof

doSubsample

doMultiThread

fastMode

fineAngle

interp

maxOfMin

numMinima

searchAngle

Constructor Detail

AlgorithmMidsagittal

Method Detail

finalize

getResultImage

runAlgorithm

calc

calc35D