java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.filters.AlgorithmN4MRIBiasFieldCorrectionFilter

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmN4MRIBiasFieldCorrectionFilter
extends AlgorithmBase
```
Version:

0.1 May 16, 2014

Author:

William Gandler This a a port of itkN4MRIBiasFieldCorrectionImageFilter.txx, itkN4MRIBiasFieldCorrectionImageFilter.h, itkCoxDeBoorBSplineKernelFunctionTest2.cxx, itkBSplineScatteredDataPointSetToImageFilterTest, itkBSplineScatteredDataPointSetToImageFilterTest2, and itkBSplineControlPointImageFilterTest from the itk package. Here is the original itk header: Program: Advanced Normalization Tools Module: $RCSfile: itkN4MRIBiasFieldCorrectionImageFilter.txx,v $ Language: C++ Date: $Date: 2009/06/09 16:22:05 $ Version: $Revision: 1.6 $ Copyright (c) ConsortiumOfANTS. All rights reserved. See accompanying COPYING.txt or http://sourceforge.net/projects/advants/files/ANTS/ANTSCopyright.txt for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information.

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 double`	`biasFieldFullWidthAtHalfMaximum`
`private boolean`	`BSplineControlPointImageFilterTest`
`private boolean`	`BSplineKernelFunctionTest`
`private boolean`	`BSplineScatteredDataPointSetToImageFilterTest`
`private boolean`	`BSplineScatteredDataPointSetToImageFilterTest2`
`private double[]`	`confidence`
`private ModelImage`	`confidenceImage`
`private int`	`controlPoints`
`private double`	`convergenceThreshold`
`private boolean`	`CoxDeBoorBSplineKernelFunctionTest`
`private boolean`	`CoxDeBoorBSplineKernelFunctionTest2`
`private boolean`	`entireImage`	Flag, if true, indicates that the whole image should be processed.
`private ModelImage`	`fieldImage`
`private int`	`fittingLevels`
`private int[]`	`latticeExtents`
`private int`	`latticeExtentsLength`
`private int`	`length`
`private ModelImage`	`logBiasFieldControlPointLattice`
`private int[]`	`maskExtents`
`private int[]`	`maskIndex`
`private int[]`	`maskLargest`
`private float[]`	`maskOrigin`
`private int`	`maximumIterations`
`private int[]`	`maximumNumberOfIterations`
`private int`	`nDims`
`private int`	`numberOfHistogramBins`
`private float[]`	`origin`
`private int[]`	`originalNumberOfControlPoints`
`private int[]`	`originalNumberOfFittingLevels`
`private float[]`	`resolutions`
`private boolean`	`selfTest`
`private double`	`sigmoidNormalizedAlpha`
`private double`	`sigmoidNormalizedBeta`
`private int`	`sliceSize`
`private int[]`	`splineOrder`
`private double`	`WienerFilterNoise`
`private int`	`xDim`
`private int`	`xyzSize`

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
`AlgorithmN4MRIBiasFieldCorrectionFilter(ModelImage destImg, ModelImage fieldImage, ModelImage srcImg, int maximumIterations, double convergenceThreshold, double biasFieldFullWidthAtHalfMaximum, double WienerFilterNoise, int fittingLevels, int controlPoints, ModelImage confidenceImage, boolean maskFlag)`	Constructor which sets the source and destination images

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private double`	`calculateConvergenceMeasurement(double[] fieldEstimate1, double[] fieldEstimate2)`
`void`	`finalize()`	Prepares this class for destruction.
`void`	`runAlgorithm()`	Starts the program.
`private void`	`selfTest()`
`private double[]`	`sharpen(double[] unsharpened)`
`private double[]`	`updateBiasFieldEstimate(double[] fieldEstimate)`

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

fieldImage
```
private ModelImage fieldImage
```

entireImage
```
private boolean entireImage
```
Flag, if true, indicates that the whole image should be processed. If false either: 1.) Process where the mask is set true 2.) Make sure the mask is set false and process where the confidence image is > 0.0

confidenceImage
```
private ModelImage confidenceImage
```

confidence
```
private double[] confidence
```

nDims
```
private int nDims
```

numberOfHistogramBins
```
private int numberOfHistogramBins
```

logBiasFieldControlPointLattice

private ModelImage logBiasFieldControlPointLattice

WienerFilterNoise
```
private double WienerFilterNoise
```

biasFieldFullWidthAtHalfMaximum

private double biasFieldFullWidthAtHalfMaximum

splineOrder
```
private int[] splineOrder
```

fittingLevels
```
private int fittingLevels
```

originalNumberOfFittingLevels

private int[] originalNumberOfFittingLevels

controlPoints
```
private int controlPoints
```

originalNumberOfControlPoints

private int[] originalNumberOfControlPoints

sigmoidNormalizedAlpha
```
private double sigmoidNormalizedAlpha
```

sigmoidNormalizedBeta
```
private double sigmoidNormalizedBeta
```

maximumIterations
```
private int maximumIterations
```

maximumNumberOfIterations

private int[] maximumNumberOfIterations

convergenceThreshold
```
private double convergenceThreshold
```

length
```
private int length
```

origin
```
private float[] origin
```

resolutions
```
private float[] resolutions
```

xDim
```
private int xDim
```

sliceSize
```
private int sliceSize
```

xyzSize
```
private int xyzSize
```

maskOrigin
```
private float[] maskOrigin
```

maskIndex
```
private int[] maskIndex
```

maskLargest
```
private int[] maskLargest
```

maskExtents
```
private int[] maskExtents
```

latticeExtents
```
private int[] latticeExtents
```

latticeExtentsLength
```
private int latticeExtentsLength
```

selfTest
```
private boolean selfTest
```

CoxDeBoorBSplineKernelFunctionTest

private boolean CoxDeBoorBSplineKernelFunctionTest

CoxDeBoorBSplineKernelFunctionTest2

private boolean CoxDeBoorBSplineKernelFunctionTest2

BSplineScatteredDataPointSetToImageFilterTest

private boolean BSplineScatteredDataPointSetToImageFilterTest

BSplineScatteredDataPointSetToImageFilterTest2

private boolean BSplineScatteredDataPointSetToImageFilterTest2

BSplineControlPointImageFilterTest

private boolean BSplineControlPointImageFilterTest

BSplineKernelFunctionTest

private boolean BSplineKernelFunctionTest

Constructor Detail

AlgorithmN4MRIBiasFieldCorrectionFilter

public AlgorithmN4MRIBiasFieldCorrectionFilter(ModelImage destImg,
                                               ModelImage fieldImage,
                                               ModelImage srcImg,
                                               int maximumIterations,
                                               double convergenceThreshold,
                                               double biasFieldFullWidthAtHalfMaximum,
                                               double WienerFilterNoise,
                                               int fittingLevels,
                                               int controlPoints,
                                               ModelImage confidenceImage,
                                               boolean maskFlag)

Constructor which sets the source and destination images

Parameters:: destImg - the destination image; fieldImage -; srcImg - the source image; confidenceImage -; maskFlag - the mask flag

Method Detail

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

Overrides:

finalize in class AlgorithmBase

runAlgorithm
```
public void runAlgorithm()
```
Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

sharpen

private double[] sharpen(double[] unsharpened)

updateBiasFieldEstimate

private double[] updateBiasFieldEstimate(double[] fieldEstimate)

calculateConvergenceMeasurement

private double calculateConvergenceMeasurement(double[] fieldEstimate1,
                                               double[] fieldEstimate2)

selfTest
```
private void selfTest()
```

Class AlgorithmN4MRIBiasFieldCorrectionFilter

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

fieldImage

entireImage

confidenceImage

confidence

nDims

numberOfHistogramBins

logBiasFieldControlPointLattice

WienerFilterNoise

biasFieldFullWidthAtHalfMaximum

splineOrder

fittingLevels

originalNumberOfFittingLevels

controlPoints

originalNumberOfControlPoints

sigmoidNormalizedAlpha

sigmoidNormalizedBeta

maximumIterations

maximumNumberOfIterations

convergenceThreshold

length

origin

resolutions

xDim

sliceSize

xyzSize

maskOrigin

maskIndex

maskLargest

maskExtents

latticeExtents

latticeExtentsLength

selfTest

CoxDeBoorBSplineKernelFunctionTest

CoxDeBoorBSplineKernelFunctionTest2

BSplineScatteredDataPointSetToImageFilterTest

BSplineScatteredDataPointSetToImageFilterTest2

BSplineControlPointImageFilterTest

BSplineKernelFunctionTest

Constructor Detail

AlgorithmN4MRIBiasFieldCorrectionFilter

Method Detail

finalize

runAlgorithm

sharpen

updateBiasFieldEstimate

calculateConvergenceMeasurement

selfTest