java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmIHN3Correction

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmIHN3Correction
extends AlgorithmBase
```
N3 Inhomogeneity correction This is based on code by John G. Sled, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University Information may be found at: http://www.bic.mni.mcgill.ca/software/N3/ Bibliography:

1. J.G. Sled, A.P. Zijdenbos, and A.C. Evans, "A non-parametric method for automatic correction of intensity non-uniformity in MRI data," IEEE Transactions on Medical Imaging, vol. 17, pp. 87-97, February, 1998.

2. J.G. Sled, A.P. Zijdenbos, and A.C. Evans, "A comparison of retrospective intensity non-uniformity correction methods for MRI," in Information Processing in Medical Imaging, pp. 459-464, 1997.

3. J.G. Sled, "A non-parametric method for automatic correction of intensity non-uniformity in MRI data," Master's thesis, McGill University, Montreal, QC, May, 1997.

The N3 method should work with any MR volume including raw (non-stereotaxic) data.

An artifact often seen in MRI is for the signal intensity to vary smoothly across an image. Variously referred to as RF inhomogeneity, shading artifact, or intensity non-uniformity, it is usually attributed to such factors as poor radio frequency(RF) field uniformity, eddy currents driven by switching of field gradients, and patient anatomy both inside and outside the field of view.

This code corrects intensity non-uniformity in MR data without requiring supervision. This method can be applied without a tissue intensity or geometric model. Described as Non-parametric Non_uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction.

From John G. Sled's original N3 code:
```
 Copyright 1996, John G. Sled
 McConnell Brain Imaging Centre,
 Montreal Neurological Institute, McGill University.
 
 Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee
 is hereby granted, provided that the above copyright notice appear in all copies. The author and McGill University
 make no representations about the suitability of this software for any purpose. It is provided "as is" without
 express or implied warranty.
 
```

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 float[][]`	`AtA`	DOCUMENT ME!
`private int`	`AtAP`	DOCUMENT ME!
`private double[][]`	`AtF`	DOCUMENT ME!
`private int`	`AtFP`	DOCUMENT ME!
`private boolean`	`autoThreshold`	If true determines the threshold by histogram analysis.
`private float[][][][]`	`bendingMatrix`	DOCUMENT ME!
`private int`	`binNumber`	DOCUMENT ME!
`private float`	`binWidth`	Histogram bin width.
`private int`	`blockInt`	DOCUMENT ME!
`private float[]`	`blurI`	DOCUMENT ME!
`private float[]`	`blurR`	DOCUMENT ME!
`private float[]`	`buffer`	Buffer for original source image.
`private float[][]`	`bW`	DOCUMENT ME!
`private float[]`	`CArray`	DOCUMENT ME!
`private float`	`class_max`	DOCUMENT ME!
`private float`	`class_min`	DOCUMENT ME!
`private double[][]`	`coef`	DOCUMENT ME!
`private float[]`	`correctedBuffer`	DOCUMENT ME!
`private int`	`currentOffset`	DOCUMENT ME!
`private float[][]`	`d1Spline`	DOCUMENT ME!
`private float[][]`	`DArray`	DOCUMENT ME!
`private float`	`denom`	DOCUMENT ME!
`private int[]`	`derivative`	DOCUMENT ME!
`private int[]`	`dloc_i`	DOCUMENT ME!
`private int[]`	`dloc_j`	DOCUMENT ME!
`private float[][]`	`domain`	DOCUMENT ME!
`private int`	`DP`	DOCUMENT ME!
`private float`	`endTol`	The measure used to terminate the iterations is the coefficient of variation of change in field estimates between successive iterations.
`private boolean`	`entireImage`	Ideally the Weiner filter noise equals the white noise of the image.
`private float[]`	`estimateBuffer`	DOCUMENT ME!
`private float`	`estimateOffset`	DOCUMENT ME!
`private float`	`estimateScale`	DOCUMENT ME!
`private float`	`estimateSlope`	DOCUMENT ME!
`private float[]`	`fHist`	DOCUMENT ME!
`private float[]`	`fHistPaddedI`	DOCUMENT ME!
`private float[]`	`fHistPaddedR`	DOCUMENT ME!
`private float`	`field_floor`	Lowest allowable field value.
`private float[]`	`fieldBuffer`	DOCUMENT ME!
`private float`	`fieldDistance`	Characteristic distance over which the field varies.
`private ModelImage`	`fieldImage`	DOCUMENT ME!
`private float[]`	`filterI`	DOCUMENT ME!
`private float[]`	`filterR`	DOCUMENT ME!
`private float`	`fIndex`	DOCUMENT ME!
`private int`	`first`	DOCUMENT ME!
`private double`	`firstMoment0`	DOCUMENT ME!
`private double`	`firstMoment1`	DOCUMENT ME!
`private float`	`fOffset`	DOCUMENT ME!
`static int`	`FORWARD`	forward FFT
`private int`	`four`	DOCUMENT ME!
`private int`	`FP`	DOCUMENT ME!
`private float`	`frac`	DOCUMENT ME!
`private double`	`fwhm`	DOCUMENT ME!
`private double`	`fwhmFactor`	DOCUMENT ME!
`private double`	`fwhmScale`	DOCUMENT ME!
`private double`	`halfBin`	DOCUMENT ME!
`private int[]`	`hist`	DOCUMENT ME!
`private float`	`histFactor`	DOCUMENT ME!
`private double`	`histMean`	DOCUMENT ME!
`private float`	`histOffset`	DOCUMENT ME!
`private double`	`histSum`	Sum of contents of hisotogram bins.
`private int`	`iLoc`	DOCUMENT ME!
`private float`	`incr`	DOCUMENT ME!
`private int`	`index`	DOCUMENT ME!
`private int`	`index1`	DOCUMENT ME!
`private float[][]`	`integral`	DOCUMENT ME!
`private int`	`interval`	DOCUMENT ME!
`static int`	`INVERSE`	inverse FFT
`private int`	`iters`	DOCUMENT ME!
`private double[][]`	`JArray`	DOCUMENT ME!
`private float`	`kernelfwhm`	Width of deconvolution kernel used to sharpen the histogram.
`private float[][]`	`knots`	DOCUMENT ME!
`private float`	`lambda`	DOCUMENT ME!
`private int`	`last`	DOCUMENT ME!
`private int`	`length`	DOCUMENT ME!
`private float`	`loc`	DOCUMENT ME!
`private int[]`	`locations`	DOCUMENT ME!
`private float[]`	`logBuffer`	Log transformed data.
`private float`	`logOffset`	If minimum value of shrunken buffer
`private int[]`	`lower`	DOCUMENT ME!
`private java.util.BitSet`	`mask`	DOCUMENT ME!
`private int`	`maxIters`	Maximum number of iterations.
`private float`	`mean`	DOCUMENT ME!
`private int`	`mid`	DOCUMENT ME!
`private float[]`	`momentI`	DOCUMENT ME!
`private float[]`	`momentR`	DOCUMENT ME!
`private int[]`	`nArray`	Number of basis functions in each dimension.
`private int`	`nBins`	Number of histogram bins for shrunken buffer.
`private int`	`nDimensions`	DOCUMENT ME!
`private int[]`	`newDim`	DOCUMENT ME!
`private float`	`newRes`	DOCUMENT ME!
`private float[]`	`newResol`	DOCUMENT ME!
`private int`	`newSliceSize`	DOCUMENT ME!
`private int`	`newVolSize`	DOCUMENT ME!
`private int`	`nMax`	DOCUMENT ME!
`private float`	`noise`	Noise used in Weiner filter.
`private int`	`nProduct`	DOCUMENT ME!
`private float`	`numVoxels`	DOCUMENT ME!
`private int`	`offset`	DOCUMENT ME!
`private int`	`offset1`	DOCUMENT ME!
`private int`	`offset2`	DOCUMENT ME!
`private int[][]`	`offsetSp`	DOCUMENT ME!
`private int`	`offsetStep`	DOCUMENT ME!
`private int`	`order`	DOCUMENT ME!
`private int[]`	`orgDim`	DOCUMENT ME!
`private float[]`	`orgResol`	Distance per pixel in millimeters.
`private int`	`padded_size`	DOCUMENT ME!
`private int`	`pDloc_i`	DOCUMENT ME!
`private int`	`pDloc_j`	DOCUMENT ME!
`private int`	`pLocation`	DOCUMENT ME!
`private int`	`pLocation2`	DOCUMENT ME!
`private int`	`pOffset`	DOCUMENT ME!
`private float`	`product`	DOCUMENT ME!
`private int`	`pSpline`	DOCUMENT ME!
`private int`	`pValue`	DOCUMENT ME!
`private int`	`region`	DOCUMENT ME!
`private float[]`	`residueBuffer`	DOCUMENT ME!
`private float`	`rfrac`	DOCUMENT ME!
`private float[]`	`sBuffer`	Buffer for sampled image.
`private float`	`scale`	DOCUMENT ME!
`private float`	`shrink`	The factor by which the data is subsampled to a lower resolution in estimating the slowly varying non-uniformity field.
`private int`	`sizeC`	DOCUMENT ME!
`private int`	`sliceSize`	DOCUMENT ME!
`private double`	`slope`	DOCUMENT ME!
`private int[]`	`smallN`	DOCUMENT ME!
`private java.util.BitSet`	`sMask`	Mask for shrunken buffer.
`private float`	`sMax`	Maximum value of shrunken buffer.
`private float`	`sMin`	Minimum value of shrunken buffer.
`private float`	`sourceMax`	DOCUMENT ME!
`private float`	`sourceMin`	DOCUMENT ME!
`static int`	`spline`	DOCUMENT ME!
`private float`	`spline_lambda`	DOCUMENT ME!
`private float`	`spline_subsample`	DOCUMENT ME!
`private double`	`sqrtNum`	DOCUMENT ME!
`private int`	`start`	DOCUMENT ME!
`private float`	`startK`	DOCUMENT ME!
`private float`	`stddev`	DOCUMENT ME!
`private int[]`	`step`	DOCUMENT ME!
`private float`	`sum2Value`	DOCUMENT ME!
`private float`	`sumValue`	DOCUMENT ME!
`private double`	`Sx`	DOCUMENT ME!
`private double`	`Sy`	DOCUMENT ME!
`private double`	`Sz`	DOCUMENT ME!
`private float`	`temp`	DOCUMENT ME!
`private float`	`temp2`	DOCUMENT ME!
`private float`	`threshold`	Values at less than threshold are treated as part of the background.
`private int`	`tiflat`	DOCUMENT ME!
`private int[]`	`tiindex`	DOCUMENT ME!
`private int[]`	`tistep`	DOCUMENT ME!
`private int`	`tjflat`	DOCUMENT ME!
`private int[]`	`tjindex`	DOCUMENT ME!
`private int[]`	`tjstep`	DOCUMENT ME!
`private java.util.BitSet`	`tMask`	Mask that meets threshold and sMask requirements for shrunken volume.
`private int`	`transformDir`	FORWARD or INVERSE for FFT.
`private int`	`UP`	DOCUMENT ME!
`private int[]`	`upper`	DOCUMENT ME!
`private boolean`	`useScript`	If true, the program is run from a script.
`private float`	`value`	DOCUMENT ME!
`private float`	`value_k`	DOCUMENT ME!
`private float`	`value1`	DOCUMENT ME!
`private float`	`value2`	DOCUMENT ME!
`private float[]`	`values`	DOCUMENT ME!
`private double`	`vari`	DOCUMENT ME!
`private double`	`varMax`	DOCUMENT ME!
`private int`	`volSize`	DOCUMENT ME!
`private float`	`volumeFactor`	Factor by which to shrink volume.
`private float[]`	`workingBuffer`	DOCUMENT ME!
`private float`	`xf`	DOCUMENT ME!
`private int`	`xo`	DOCUMENT ME!
`private float`	`xv`	DOCUMENT ME!
`private int`	`xyo`	DOCUMENT ME!
`private float`	`xyv`	DOCUMENT ME!
`private float[]`	`yMat`	DOCUMENT ME!
`private float[]`	`ys`	DOCUMENT ME!
`private float[]`	`zero`	DOCUMENT ME!
`private double`	`zeroMoment0`	DOCUMENT ME!
`private double`	`zeroMoment1`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, 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
`AlgorithmIHN3Correction(ModelImage destImg, ModelImage fieldImg, ModelImage srcImg, float _threshold, int _maxIters, float _endTol, float _fieldDistance, float _shrink, float _kernelfwhm, float _noise, boolean _entireImage, boolean _autoThreshold, boolean useScript)`	Creates a new AlgorithmIHN3Correction object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`cleanUp()`	Prepares this class for destruction.
`private void`	`fft(float[] rData, float[] iData)`	This is the method that calculates the FFT.
`void`	`finalize()`	Prepares this class for destruction.
`private void`	`fitSplinesToVolumeLookup2D()`	DOCUMENT ME!
`private void`	`fitSplinesToVolumeLookup3D()`	DOCUMENT ME!
`private void`	`IHN3Correction2()`	IHN3Correction2().
`private void`	`IHN3Correction3()`	IHN3Correction3.
`void`	`runAlgorithm()`	Start algorithm.
`private void`	`smoothVolumeLookup2D()`	DOCUMENT ME!
`private void`	`smoothVolumeLookup3D()`	DOCUMENT ME!
`private void`	`TBSplineVolume()`	DOCUMENT ME!
`private void`	`transformBilinear(float[] imgBuf, TransMatrix xfrm)`	Transforms and resamples volume using bilinear interpolation.
`private void`	`transformNearestNeighbor2D(float[] imgBuf, TransMatrix xfrm)`	Transforms and resamples volume using nearest neighbor interpolation.
`private void`	`transformNearestNeighbor3D(float[] imgBuf, TransMatrix xfrm)`	Transforms and resamples volume using nearest neighbor interpolation.
`private void`	`transformTrilinear(float[] imgBuffer, TransMatrix matrix)`	Transforms and resamples volume using trilinear interpolation.
`private void`	`volumeDomain()`	Allocates and initializes important buffers.

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
  - INVERSE
```
public static final int INVERSE
```
    inverse FFT
    
    See Also:
    
    Constant Field Values
  - FORWARD
```
public static final int FORWARD
```
    forward FFT
    
    See Also:
    
    Constant Field Values
  - spline
```
public static final int spline
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - AtA
```
private float[][] AtA
```
    DOCUMENT ME!
  - AtAP
```
private int AtAP
```
    DOCUMENT ME!
  - AtFP
```
private int AtFP
```
    DOCUMENT ME!
  - UP
```
private int UP
```
    DOCUMENT ME!
  - DP
```
private int DP
```
    DOCUMENT ME!
  - FP
```
private int FP
```
    DOCUMENT ME!
  - AtF
```
private double[][] AtF
```
    DOCUMENT ME!
  - autoThreshold
```
private boolean autoThreshold
```
    If true determines the threshold by histogram analysis. If true a VOI cannot be used and the input threshold is ignored.
  - bendingMatrix
```
private float[][][][] bendingMatrix
```
    DOCUMENT ME!
  - binNumber
```
private final int binNumber
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - binWidth
```
private float binWidth
```
    Histogram bin width.
  - blockInt
```
private int blockInt
```
    DOCUMENT ME!
  - currentOffset
```
private int currentOffset
```
    DOCUMENT ME!
  - blurI
```
private float[] blurI
```
    DOCUMENT ME!
  - blurR
```
private float[] blurR
```
    DOCUMENT ME!
  - buffer
```
private float[] buffer
```
    Buffer for original source image.
  - bW
```
private final float[][] bW
```
    DOCUMENT ME!
  - CArray
```
private float[] CArray
```
    DOCUMENT ME!
  - class_max
```
private float class_max
```
    DOCUMENT ME!
  - class_min
```
private float class_min
```
    DOCUMENT ME!
  - coef
```
private double[][] coef
```
    DOCUMENT ME!
  - correctedBuffer
```
private float[] correctedBuffer
```
    DOCUMENT ME!
  - d1Spline
```
private float[][] d1Spline
```
    DOCUMENT ME!
  - DArray
```
private float[][] DArray
```
    DOCUMENT ME!
  - denom
```
private float denom
```
    DOCUMENT ME!
  - derivative
```
private int[] derivative
```
    DOCUMENT ME!
  - dloc_i
```
private int[] dloc_i
```
    DOCUMENT ME!
  - dloc_j
```
private int[] dloc_j
```
    DOCUMENT ME!
  - domain
```
private float[][] domain
```
    DOCUMENT ME!
  - endTol
```
private float endTol
```
    The measure used to terminate the iterations is the coefficient of variation of change in field estimates between successive iterations.
  - entireImage
```
private boolean entireImage
```
    Ideally the Weiner filter noise equals the white noise of the image. The performance of the N3 method is enhanced by supplying a mask for the region of interest. If true, the N3 method is applied to the entire image.
  - estimateBuffer
```
private float[] estimateBuffer
```
    DOCUMENT ME!
  - estimateOffset
```
private float estimateOffset
```
    DOCUMENT ME!
  - estimateScale
```
private float estimateScale
```
    DOCUMENT ME!
  - estimateSlope
```
private float estimateSlope
```
    DOCUMENT ME!
  - fHist
```
private float[] fHist
```
    DOCUMENT ME!
  - fHistPaddedI
```
private float[] fHistPaddedI
```
    DOCUMENT ME!
  - fHistPaddedR
```
private float[] fHistPaddedR
```
    DOCUMENT ME!
  - field_floor
```
private final float field_floor
```
    Lowest allowable field value.
    
    See Also:
    
    Constant Field Values
  - fieldBuffer
```
private float[] fieldBuffer
```
    DOCUMENT ME!
  - fieldDistance
```
private float fieldDistance
```
    Characteristic distance over which the field varies. The distance between adjacent knots in bspline fitting with at least 4 knots going in every dimension. The default in the dialog is one third the distance (resolution * extents) of the smallest dimension.
  - fieldImage
```
private ModelImage fieldImage
```
    DOCUMENT ME!
  - filterI
```
private float[] filterI
```
    DOCUMENT ME!
  - filterR
```
private float[] filterR
```
    DOCUMENT ME!
  - fIndex
```
private float fIndex
```
    DOCUMENT ME!
  - firstMoment0
```
private double firstMoment0
```
    DOCUMENT ME!
  - firstMoment1
```
private double firstMoment1
```
    DOCUMENT ME!
  - fOffset
```
private float fOffset
```
    DOCUMENT ME!
  - fwhm
```
private double fwhm
```
    DOCUMENT ME!
  - fwhmFactor
```
private double fwhmFactor
```
    DOCUMENT ME!
  - fwhmScale
```
private double fwhmScale
```
    DOCUMENT ME!
  - halfBin
```
private double halfBin
```
    DOCUMENT ME!
  - hist
```
private int[] hist
```
    DOCUMENT ME!
  - histFactor
```
private float histFactor
```
    DOCUMENT ME!
  - histMean
```
private double histMean
```
    DOCUMENT ME!
  - histOffset
```
private float histOffset
```
    DOCUMENT ME!
  - histSum
```
private double histSum
```
    Sum of contents of hisotogram bins.
  - iLoc
```
private int iLoc
```
    DOCUMENT ME!
  - incr
```
private float incr
```
    DOCUMENT ME!
  - value_k
```
private float value_k
```
    DOCUMENT ME!
  - index
```
private int index
```
    DOCUMENT ME!
  - index1
```
private int index1
```
    DOCUMENT ME!
  - integral
```
private float[][] integral
```
    DOCUMENT ME!
  - interval
```
private int interval
```
    DOCUMENT ME!
  - iters
```
private int iters
```
    DOCUMENT ME!
  - JArray
```
private double[][] JArray
```
    DOCUMENT ME!
  - kernelfwhm
```
private float kernelfwhm
```
    Width of deconvolution kernel used to sharpen the histogram. Larger values give faster convergence while smaller values give greater accuracy.
  - knots
```
private float[][] knots
```
    DOCUMENT ME!
  - lambda
```
private float lambda
```
    DOCUMENT ME!
  - loc
```
private float loc
```
    DOCUMENT ME!
  - locations
```
private int[] locations
```
    DOCUMENT ME!
  - logBuffer
```
private float[] logBuffer
```
    Log transformed data.
  - logOffset
```
private float logOffset
```
    If minimum value of shrunken buffer
    
    lower
    
    private int[] lower
    
    DOCUMENT ME!
    
    mask
    
    private java.util.BitSet mask
    
    DOCUMENT ME!
    
    maxIters
    
    private int maxIters
    
    Maximum number of iterations.
    
    momentI
    
    private float[] momentI
    
    DOCUMENT ME!
    
    momentR
    
    private float[] momentR
    
    DOCUMENT ME!
    
    nArray
    
    private int[] nArray
    
    Number of basis functions in each dimension.
    
    nBins
    
    private int nBins
    
    Number of histogram bins for shrunken buffer.
    
    nDimensions
    
    private int nDimensions
    
    DOCUMENT ME!
    
    newDim
    
    private int[] newDim
    
    DOCUMENT ME!
    
    newRes
    
    private float newRes
    
    DOCUMENT ME!
    
    newResol
    
    private float[] newResol
    
    DOCUMENT ME!
    
    newSliceSize
    
    private int newSliceSize
    
    DOCUMENT ME!
    
    newVolSize
    
    private int newVolSize
    
    DOCUMENT ME!
    
    nMax
    
    private int nMax
    
    DOCUMENT ME!
    
    noise
    
    private float noise
    
    Noise used in Weiner filter.
    
    nProduct
    
    private int nProduct
    
    DOCUMENT ME!
    
    four
    
    private int four
    
    DOCUMENT ME!
    
    offset
    
    private int offset
    
    DOCUMENT ME!
    
    offset1
    
    private int offset1
    
    DOCUMENT ME!
    
    offset2
    
    private int offset2
    
    DOCUMENT ME!
    
    offsetSp
    
    private int[][] offsetSp
    
    DOCUMENT ME!
    
    offsetStep
    
    private int offsetStep
    
    DOCUMENT ME!
    
    first
    
    private int first
    
    DOCUMENT ME!
    
    last
    
    private int last
    
    DOCUMENT ME!
    
    order
    
    private int order
    
    DOCUMENT ME!
    
    orgDim
    
    private int[] orgDim
    
    DOCUMENT ME!
    
    orgResol
    
    private final float[] orgResol
    
    Distance per pixel in millimeters.
    
    padded_size
    
    private int padded_size
    
    DOCUMENT ME!
    
    pLocation
    
    private int pLocation
    
    DOCUMENT ME!
    
    pLocation2
    
    private int pLocation2
    
    DOCUMENT ME!
    
    pValue
    
    private int pValue
    
    DOCUMENT ME!
    
    pDloc_i
    
    private int pDloc_i
    
    DOCUMENT ME!
    
    pDloc_j
    
    private int pDloc_j
    
    DOCUMENT ME!
    
    product
    
    private float product
    
    DOCUMENT ME!
    
    pSpline
    
    private int pSpline
    
    DOCUMENT ME!
    
    pOffset
    
    private int pOffset
    
    DOCUMENT ME!
    
    region
    
    private int region
    
    DOCUMENT ME!
    
    residueBuffer
    
    private float[] residueBuffer
    
    DOCUMENT ME!
    
    sBuffer
    
    private float[] sBuffer
    
    Buffer for sampled image.
    
    scale
    
    private float scale
    
    DOCUMENT ME!
    
    shrink
    
    private float shrink
    
    The factor by which the data is subsampled to a lower resolution in estimating the slowly varying non-uniformity field. Reduce sampling in the finest sampling direction by the shrink factor. Reduce other sampling directions only if resolution is less than shrink times original minimum resolution. Uses nearest neighbor resampling.
    
    sizeC
    
    private int sizeC
    
    DOCUMENT ME!
    
    sliceSize
    
    private int sliceSize
    
    DOCUMENT ME!
    
    slope
    
    private double slope
    
    DOCUMENT ME!
    
    smallN
    
    private int[] smallN
    
    DOCUMENT ME!
    
    sMask
    
    private java.util.BitSet sMask
    
    Mask for shrunken buffer.
    
    sMax
    
    private float sMax
    
    Maximum value of shrunken buffer.
    
    sMin
    
    private float sMin
    
    Minimum value of shrunken buffer.
    
    sourceMin
    
    private float sourceMin
    
    DOCUMENT ME!
    
    sourceMax
    
    private float sourceMax
    
    DOCUMENT ME!
    
    spline_lambda
    
    private final float spline_lambda
    
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
    
    spline_subsample
    
    private final float spline_subsample
    
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
    
    sqrtNum
    
    private double sqrtNum
    
    DOCUMENT ME!
    
    start
    
    private int start
    
    DOCUMENT ME!
    
    length
    
    private int length
    
    DOCUMENT ME!
    
    mid
    
    private int mid
    
    DOCUMENT ME!
    
    startK
    
    private float startK
    
    DOCUMENT ME!
    
    stddev
    
    private float stddev
    
    DOCUMENT ME!
    
    mean
    
    private float mean
    
    DOCUMENT ME!
    
    numVoxels
    
    private float numVoxels
    
    DOCUMENT ME!
    
    sumValue
    
    private float sumValue
    
    DOCUMENT ME!
    
    sum2Value
    
    private float sum2Value
    
    DOCUMENT ME!
    
    step
    
    private int[] step
    
    DOCUMENT ME!
    
    Sx
    
    private double Sx
    
    DOCUMENT ME!
    
    Sy
    
    private double Sy
    
    DOCUMENT ME!
    
    Sz
    
    private double Sz
    
    DOCUMENT ME!
    
    temp
    
    private float temp
    
    DOCUMENT ME!
    
    temp2
    
    private float temp2
    
    DOCUMENT ME!
    
    threshold
    
    private float threshold
    
    Values at less than threshold are treated as part of the background.
    
    tiflat
    
    private int tiflat
    
    DOCUMENT ME!
    
    tiindex
    
    private int[] tiindex
    
    DOCUMENT ME!
    
    tistep
    
    private int[] tistep
    
    DOCUMENT ME!
    
    tjflat
    
    private int tjflat
    
    DOCUMENT ME!
    
    tjindex
    
    private int[] tjindex
    
    DOCUMENT ME!
    
    tjstep
    
    private int[] tjstep
    
    DOCUMENT ME!
    
    tMask
    
    private java.util.BitSet tMask
    
    Mask that meets threshold and sMask requirements for shrunken volume.
    
    transformDir
    
    private int transformDir
    
    FORWARD or INVERSE for FFT.
    
    upper
    
    private int[] upper
    
    DOCUMENT ME!
    
    useScript
    
    private boolean useScript
    
    If true, the program is run from a script.
    
    value
    
    private float value
    
    DOCUMENT ME!
    
    value1
    
    private float value1
    
    DOCUMENT ME!
    
    value2
    
    private float value2
    
    DOCUMENT ME!
    
    frac
    
    private float frac
    
    DOCUMENT ME!
    
    rfrac
    
    private float rfrac
    
    DOCUMENT ME!
    
    values
    
    private float[] values
    
    DOCUMENT ME!
    
    vari
    
    private double vari
    
    DOCUMENT ME!
    
    varMax
    
    private double varMax
    
    DOCUMENT ME!
    
    volSize
    
    private int volSize
    
    DOCUMENT ME!
    
    volumeFactor
    
    private float volumeFactor
    
    Factor by which to shrink volume.
    
    workingBuffer
    
    private float[] workingBuffer
    
    DOCUMENT ME!
    
    xf
    
    private float xf
    
    DOCUMENT ME!
    
    xo
    
    private int xo
    
    DOCUMENT ME!
    
    xyo
    
    private int xyo
    
    DOCUMENT ME!
    
    xv
    
    private float xv
    
    DOCUMENT ME!
    
    xyv
    
    private float xyv
    
    DOCUMENT ME!
    
    yMat
    
    private float[] yMat
    
    DOCUMENT ME!
    
    ys
    
    private float[] ys
    
    DOCUMENT ME!
    
    zero
    
    private float[] zero
    
    DOCUMENT ME!
    
    zeroMoment0
    
    private double zeroMoment0
    
    DOCUMENT ME!
    
    zeroMoment1
    
    private double zeroMoment1
    
    DOCUMENT ME!
    
    Constructor Detail
    
    AlgorithmIHN3Correction
    
    public AlgorithmIHN3Correction(ModelImage destImg, ModelImage fieldImg, ModelImage srcImg, float _threshold, int _maxIters, float _endTol, float _fieldDistance, float _shrink, float _kernelfwhm, float _noise, boolean _entireImage, boolean _autoThreshold, boolean useScript)
    
    Creates a new AlgorithmIHN3Correction object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    fieldImg - image model where used field is stored
    
    srcImg - source image model
    
    _threshold - Values at less than _threshold are treated as part of the background
    
    _maxIters - Maximum number of iterations
    
    _endTol - The measure used to terminate the iterations is the coefficient of variation of change in field estimates between successive iterations.
    
    _fieldDistance - Characteristic distance over which the field varies. The distance between adjacent knots in bspline fitting with at least 4 knots going in every dimension. The default in the dialog is one third the distance (resolution * extents) of the smallest dimension.
    
    _shrink - The factor by which the data is subsampled to a lower resolution in estimating the slowly varying non-uniformity field. Reduce sampling in the finest sampling direction by the shrink factor.
    
    _kernelfwhm - Width of deconvolution kernel used to sharpen the histogram. Larger values give faster convergence while smaller values give greater accuracy.
    
    _noise - Noise used in Weiner filter
    
    _entireImage - If true, the N3 method is applied to the entire image. If false, the N3 method is applied only to the region of interest.
    
    _autoThreshold - If true determines the threshold by histogram analysis. If true a VOI cannot be used and the input threshold is ignored.
    
    useScript - If true, the program is run from a script
    
    Method Detail
    
    finalize
    
    public void finalize()
    
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
    
    runAlgorithm
    
    public void runAlgorithm()
    
    Start algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
    
    cleanUp
    
    private void cleanUp()
    
    Prepares this class for destruction.
    
    fft
    
    private void fft(float[] rData, float[] iData)
    
    This is the method that calculates the FFT.
    
    Parameters:
    
    rData - real data
    
    iData - imaginary data
    
    fitSplinesToVolumeLookup2D
    
    private void fitSplinesToVolumeLookup2D()
    
    DOCUMENT ME!
    
    fitSplinesToVolumeLookup3D
    
    private void fitSplinesToVolumeLookup3D()
    
    DOCUMENT ME!
    
    IHN3Correction2
    
    private void IHN3Correction2()
    
    IHN3Correction2(). Derived from PERL file nu_estimate_np_and_em.in Iteratively estimates intensity non-uniformity artifacts in MRI areas.
    
    IHN3Correction3
    
    private void IHN3Correction3()
    
    IHN3Correction3. Derived from PERL file nu_estimate_np_and_em.in Iteratively estimates intensity non-uniformity artifacts in MRI volumes.
    
    smoothVolumeLookup2D
    
    private void smoothVolumeLookup2D()
    
    DOCUMENT ME!
    
    smoothVolumeLookup3D
    
    private void smoothVolumeLookup3D()
    
    DOCUMENT ME!
    
    TBSplineVolume
    
    private void TBSplineVolume()
    
    DOCUMENT ME!
    
    transformBilinear
    
    private void transformBilinear(float[] imgBuf, TransMatrix xfrm)
    
    Transforms and resamples volume using bilinear interpolation.
    
    Parameters:
    
    imgBuf - - image array
    
    xfrm - - TransMatrix to be applied
    
    transformNearestNeighbor2D
    
    private void transformNearestNeighbor2D(float[] imgBuf, TransMatrix xfrm)
    
    Transforms and resamples volume using nearest neighbor interpolation.
    
    Parameters:
    
    imgBuf - image array
    
    xfrm - transformation matrix to be applied
    
    transformNearestNeighbor3D
    
    private void transformNearestNeighbor3D(float[] imgBuf, TransMatrix xfrm)
    
    Transforms and resamples volume using nearest neighbor interpolation.
    
    Parameters:
    
    imgBuf - image array
    
    xfrm - transformation matrix to be applied
    
    transformTrilinear
    
    private void transformTrilinear(float[] imgBuffer, TransMatrix matrix)
    
    Transforms and resamples volume using trilinear interpolation.
    
    Parameters:
    
    imgBuffer - image array
    
    xfrm - transformation matrix to be applied
    
    volumeDomain
    
    private void volumeDomain()
    
    Allocates and initializes important buffers.

Class AlgorithmIHN3Correction

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

INVERSE

FORWARD

spline

AtA

AtAP

AtFP

UP

DP

FP

AtF

autoThreshold

bendingMatrix

binNumber

binWidth

blockInt

currentOffset

blurI

blurR

buffer

bW

CArray

class_max

class_min

coef

correctedBuffer

d1Spline

DArray

denom

derivative

dloc_i

dloc_j

domain

endTol

entireImage

estimateBuffer

estimateOffset

estimateScale

estimateSlope

fHist

fHistPaddedI

fHistPaddedR

field_floor

fieldBuffer

fieldDistance

fieldImage

filterI

filterR

fIndex

firstMoment0

firstMoment1

fOffset

fwhm

fwhmFactor

fwhmScale

halfBin

hist

histFactor

histMean

histOffset

histSum

iLoc

incr

value_k

index

index1

integral

interval

iters