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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmSWI
extends AlgorithmBase
```
This class recalculates mo and dceFullTre to provide better estimates using the inverse Ernst equation

Author:

Justin Senseney (SenseneyJ@mail.nih.gov)

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`	`brainMask`	Denotes which pixels undergo SWI processing.
`private ModelImage`	`iCenter`
`private ModelImage`	`iFinal`
`private ModelImage`	`iImage`
`private boolean`	`inScript`	Denotes whether the algorithm is run in a script/JIST, if so showInterImages just stores images for later access.
`private ModelImage`	`kCenterImage`
`private ModelImage`	`kImage`
`private ModelImage`	`magImage`
`private double`	`maskThreshold`
`private int`	`multFactor`
`private ModelImage`	`phaseImage`
`private ModelImage`	`phaseMask`
`private boolean`	`showInterImages`	Whether intermediate images should be displayed during pipeline processing
`private int`	`xDim`	X dimension length
`private int`	`xFilterSize`
`private double`	`xFilterTopLeft`
`private int`	`yDim`	Y dimension length
`private int`	`yFilterSize`
`private double`	`yFilterTopLeft`
`private int`	`zDim`	Z dimension length

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
`AlgorithmSWI(boolean inScript, ModelImage resultImage, ModelImage magImage, ModelImage phaseImage, double maskThreshold, int roFilterSize, int peFilterSize, int multFactor, boolean showInterImages)`	Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calc2D()`
`private void`	`calc3D()`
`private ModelImage`	`createBrainMask()`
`private ModelImage`	`createiImage(double[] realData, double[] imagData)`
`private ModelImage`	`createKCenterImage(ModelImage kImage)`
`private ModelImage`	`createkImage(ModelImage iImage)`
`void`	`finalize()`	Prepares this class for destruction.
`private ModelImage`	`generateIFinal(ModelImage iImage, ModelImage iCenterImage, java.util.BitSet brainMaskSet, double[] ixRealFinal, double[] ixImagFinal)`
`private ModelImage`	`generateMagEnhanced(double[] phaseMaskData, ModelImage magnitude)`
`private ModelImage`	`generatePhaseMask(java.util.BitSet brainMaskSet, double[] ixRealFinal, double[] ixImagFinal, double[] phaseMaskData)`
`ModelImage`	`getBrainMask()`
`ModelImage`	`getiCenter()`
`ModelImage`	`getiFinal()`
`ModelImage`	`getiImage()`
`ModelImage`	`getkCenterImage()`
`ModelImage`	`getkImage()`
`ModelImage`	`getPhaseMask()`
`private void`	`rescaleToComplex(ModelImage magImage, ModelImage phaseImage, double[] realData, double[] imagData)`
`void`	`runAlgorithm()`	Starts the algorithm.
`private ModelImage`	`runiFFTonKCenter(ModelImage kCenterImage)`

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

magImage
```
private ModelImage magImage
```

phaseImage
```
private ModelImage phaseImage
```

maskThreshold
```
private double maskThreshold
```

xFilterSize
```
private int xFilterSize
```

yFilterSize
```
private int yFilterSize
```

multFactor
```
private int multFactor
```

xDim
```
private int xDim
```
X dimension length

yDim
```
private int yDim
```
Y dimension length

zDim
```
private int zDim
```
Z dimension length

xFilterTopLeft
```
private double xFilterTopLeft
```

yFilterTopLeft
```
private double yFilterTopLeft
```

showInterImages
```
private boolean showInterImages
```
Whether intermediate images should be displayed during pipeline processing

kImage
```
private ModelImage kImage
```

iImage
```
private ModelImage iImage
```

brainMask
```
private ModelImage brainMask
```
Denotes which pixels undergo SWI processing.

kCenterImage
```
private ModelImage kCenterImage
```

iFinal
```
private ModelImage iFinal
```

phaseMask
```
private ModelImage phaseMask
```

inScript
```
private boolean inScript
```
Denotes whether the algorithm is run in a script/JIST, if so showInterImages just stores images for later access.

iCenter
```
private ModelImage iCenter
```

Constructor Detail

AlgorithmSWI

public AlgorithmSWI(boolean inScript,
                    ModelImage resultImage,
                    ModelImage magImage,
                    ModelImage phaseImage,
                    double maskThreshold,
                    int roFilterSize,
                    int peFilterSize,
                    int multFactor,
                    boolean showInterImages)

Constructor.

Parameters:: resultImage - Result image model; srcImg - Source image model.

Method Detail

finalize
```
public void finalize()
```
Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm
```
public void runAlgorithm()
```
Starts the algorithm. At the conclusion of this method, AlgorithmBase reports to any algorithm listeners that this algorithm has completed. This method is not usually called explicitly by a controlling dialog. Instead, see AlgorithmBase.run() or start().

Specified by:

runAlgorithm in class AlgorithmBase

calc2D
```
private void calc2D()
```

calc3D
```
private void calc3D()
```

generateMagEnhanced

private ModelImage generateMagEnhanced(double[] phaseMaskData,
                                       ModelImage magnitude)

generatePhaseMask

private ModelImage generatePhaseMask(java.util.BitSet brainMaskSet,
                                     double[] ixRealFinal,
                                     double[] ixImagFinal,
                                     double[] phaseMaskData)

generateIFinal

private ModelImage generateIFinal(ModelImage iImage,
                                  ModelImage iCenterImage,
                                  java.util.BitSet brainMaskSet,
                                  double[] ixRealFinal,
                                  double[] ixImagFinal)

runiFFTonKCenter

private ModelImage runiFFTonKCenter(ModelImage kCenterImage)

createKCenterImage

private ModelImage createKCenterImage(ModelImage kImage)

createkImage

private ModelImage createkImage(ModelImage iImage)

createiImage

private ModelImage createiImage(double[] realData,
                                double[] imagData)

createBrainMask
```
private ModelImage createBrainMask()
```

rescaleToComplex

private void rescaleToComplex(ModelImage magImage,
                              ModelImage phaseImage,
                              double[] realData,
                              double[] imagData)

getkImage
```
public ModelImage getkImage()
```

getiImage
```
public ModelImage getiImage()
```

getBrainMask
```
public ModelImage getBrainMask()
```

getkCenterImage
```
public ModelImage getkCenterImage()
```

getiFinal
```
public ModelImage getiFinal()
```

getPhaseMask
```
public ModelImage getPhaseMask()
```

getiCenter
```
public ModelImage getiCenter()
```

Class AlgorithmSWI

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

magImage

phaseImage

maskThreshold

xFilterSize

yFilterSize

multFactor

xDim

yDim

zDim

xFilterTopLeft

yFilterTopLeft

showInterImages

kImage

iImage

brainMask

kCenterImage

iFinal

phaseMask

inScript

iCenter

Constructor Detail

AlgorithmSWI

Method Detail

finalize

runAlgorithm

calc2D

calc3D

generateMagEnhanced

generatePhaseMask

generateIFinal

runiFFTonKCenter

createKCenterImage

createkImage

createiImage

createBrainMask

rescaleToComplex

getkImage

getiImage

getBrainMask

getkCenterImage

getiFinal

getPhaseMask

getiCenter