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

All Implemented Interfaces:

de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmEntropyMinimization
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
```
DOCUMENT ME!

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`	`ac1`	DOCUMENT ME!
`private double`	`ac2`	DOCUMENT ME!
`private double`	`ac3`	DOCUMENT ME!
`private double`	`ac4`	DOCUMENT ME!
`private double`	`ac5`	DOCUMENT ME!
`private double`	`ac6`	DOCUMENT ME!
`private double`	`ac7`	DOCUMENT ME!
`private double`	`ac8`	DOCUMENT ME!
`private double`	`ac9`	DOCUMENT ME!
`private double`	`ad1`	DOCUMENT ME!
`private double`	`ad2`	DOCUMENT ME!
`private double`	`ad3`	DOCUMENT ME!
`private double`	`ad4`	DOCUMENT ME!
`private double`	`ad5`	DOCUMENT ME!
`private double`	`ad6`	DOCUMENT ME!
`private double`	`ad7`	DOCUMENT ME!
`private double`	`ad8`	DOCUMENT ME!
`private double`	`ad9`	DOCUMENT ME!
`private int`	`area`	DOCUMENT ME!
`private boolean`	`backgroundPresent`	DOCUMENT ME!
`private float[]`	`buffer`	DOCUMENT ME!
`private double`	`grayCount`	DOCUMENT ME!
`private int`	`histogramAvailable`	Number of pixels available for histogram formation.
`private double[]`	`idealBuffer`	Buffer holding calculation for noiseless U(x,y).
`private int`	`iter`	DOCUMENT ME!
`private double`	`maximum`	original image maximum.
`private double`	`maximumB`	DOCUMENT ME!
`private double`	`maximumG`	DOCUMENT ME!
`private double`	`maximumR`	DOCUMENT ME!
`private double`	`mc1`	DOCUMENT ME!
`private double`	`mc10`	DOCUMENT ME!
`private double`	`mc11`	DOCUMENT ME!
`private double`	`mc12`	DOCUMENT ME!
`private double`	`mc13`	DOCUMENT ME!
`private double`	`mc14`	DOCUMENT ME!
`private double`	`mc15`	DOCUMENT ME!
`private double`	`mc16`	DOCUMENT ME!
`private double`	`mc17`	DOCUMENT ME!
`private double`	`mc18`	DOCUMENT ME!
`private double`	`mc19`	DOCUMENT ME!
`private double`	`mc2`	DOCUMENT ME!
`private double`	`mc3`	DOCUMENT ME!
`private double`	`mc4`	DOCUMENT ME!
`private double`	`mc5`	DOCUMENT ME!
`private double`	`mc6`	DOCUMENT ME!
`private double`	`mc7`	DOCUMENT ME!
`private double`	`mc8`	DOCUMENT ME!
`private double`	`mc9`	DOCUMENT ME!
`private double`	`md1`	DOCUMENT ME!
`private double`	`md10`	DOCUMENT ME!
`private double`	`md11`	DOCUMENT ME!
`private double`	`md12`	DOCUMENT ME!
`private double`	`md13`	DOCUMENT ME!
`private double`	`md14`	DOCUMENT ME!
`private double`	`md15`	DOCUMENT ME!
`private double`	`md16`	DOCUMENT ME!
`private double`	`md17`	DOCUMENT ME!
`private double`	`md18`	DOCUMENT ME!
`private double`	`md19`	DOCUMENT ME!
`private double`	`md2`	DOCUMENT ME!
`private double`	`md3`	DOCUMENT ME!
`private double`	`md4`	DOCUMENT ME!
`private double`	`md5`	DOCUMENT ME!
`private double`	`md6`	DOCUMENT ME!
`private double`	`md7`	DOCUMENT ME!
`private double`	`md8`	DOCUMENT ME!
`private double`	`md9`	DOCUMENT ME!
`private double`	`minimum`	original image minimum.
`private double`	`minimumB`	DOCUMENT ME!
`private double`	`minimumG`	DOCUMENT ME!
`private double`	`minimumR`	DOCUMENT ME!
`static int`	`NOISE_M2`	Quadratic multiplicative noise.
`static int`	`NOISE_M3`	Cubic multiplicative noise.
`static int`	`NOISE_MA2`	The user can choose to use thresholding to exclude the background from any processing.
`private int`	`noiseType`	NOISE_MA2 or NOISE_M2.
`private int`	`nParams`	Numbering of shading correction parameters.
`private boolean[]`	`objectBuffer`	DOCUMENT ME!
`private int`	`pixelIncrement`	pixelIncrement is increased above 1 if subsampling.
`private double`	`powellTolerance`	Tolerance passed to Powell's algorithm.
`private int`	`sliceSize`	xDim * yDim.
`private boolean`	`subsample`	If true, subsample image for histogram formation.
`private float`	`thresholdLevel`	DOCUMENT ME!
`private boolean`	`thresholdSelected`	If true don't use pixels below thresholdLevel that are 4 or 6 neighbor connected to boundary pixels below thresholdLevel.
`private boolean[]`	`validBuffer`	True for source input locations not having image min or image max values.
`private int`	`volSize`	DOCUMENT ME!
`private int`	`volume`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private int`	`zDim`	DOCUMENT ME!
`private int`	`zPixelIncrement`	Handle case where zDim is far less than xDim and yDim

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
`AlgorithmEntropyMinimization(ModelImage srcImage, boolean thresholdSelected, float thresholdLevel, boolean subsample, int noiseType)`	Creates a new AlgorithmEntropyMinimization object.
`AlgorithmEntropyMinimization(ModelImage resultImage, ModelImage srcImage, boolean thresholdSelected, float thresholdLevel, boolean subsample, int noiseType)`	Creates a new AlgorithmEntropyMinimization object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private double`	`entropyFunction(double[] p)`	DOCUMENT ME!
`double`	`eval(double[] x)`
`void`	`finalize()`	Prepares this class for destruction.
`int`	`getNumberOfVariables()`
`private void`	`powell(double[] p, double[][] xi, double ftol)`	Minimization of entropy function of nParams variables.
`private void`	`run2Da2m2()`	DOCUMENT ME!
`private void`	`run2Dm2()`	DOCUMENT ME!
`private void`	`run2Dm3()`	DOCUMENT ME!
`private void`	`run3Da2m2()`	DOCUMENT ME!
`private void`	`run3Dm2()`	DOCUMENT ME!
`private void`	`run3Dm3()`	DOCUMENT ME!
`void`	`runAlgorithm()`	DOCUMENT ME!

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
  - NOISE_MA2
```
public static final int NOISE_MA2
```
    The user can choose to use thresholding to exclude the background from any processing. Excluded pixels will have the same values as the original source image. All pixels with values below threshold that are 4 or 6 neighbor connected thru below threshold pixels to a boundary pixel which is below threshold will be excluded from processing. By default image subsampling is used in histogram formation since using 5000 images samples is sufficient to form the histogram. If subsampling is selected, pixelIncrement for both x and y is set equal to: Math.max(1,(int)Math.sqrt(histogramAvailable/5000)) If subsampling is not selected, pixelIncrement equals 1 Powell's algorithm is used to search for the values of the 10 shading parameters that minimize the entropy of the blurred histogram of the U(x,y) image. A histogram is formed to represent integers from the floor(image U minimum) to the ceiling(image U maximum). For each floating point gray value gp in U(x,y) a count of 1 is split between the 2 integer bins encompassing it. Let the bins be k and k+1. k+1-gp is added to bin k and gp - k is added to bin k+1. Gray values in locations corresponding to the image minimum or image maximum in the original input image are not used in creating this histogram, since they may represent regions where saturation effects are occurring. Then, a blurred histogram is created from the original histogram. The original histogram is blurred with a triangular window of size 5: blurredHistogram[i] = originalHistogram[i-2] + 2* originalHistogram[i-1] + 3*originalHistogram[i] + 2*originalHistogram[i+1] + originalHistogram[i+2] The blurred histogram is normalized to give probabilities by dividing the count in each bin by the total number of counts in the blurred histogram. The entropy is formed by summing the -probability(n)*log(probability(n)) over all bins n with nonzero counts. References: This software implements the algorithm discussed in: 1.) Retrospective shading correction based on entropy minimization by B. Likar, J. B. A. Maintz, M. A. Viergever, and F. Pernus, Journal of Microscopy, Vol. 197, Pt 3., March, 2000, pp. 285-295. 2.) Retrospective Correction of MR Intensity Inhomogeneity by Information Minimization by Bostjan Likar, Max Viergever, and Franjo Pernus, IEEE Transactions on Medical Imaging, Vol. 20, No. 12, December, 2001, pp. 1398-1410. 3.) Real-time automated visual inspection of color tablets in pharmaceutical blisters by Joze Derganc, Bostjan Likar, Rok Bernard, Dejan Tomazevic, and Franjo Pernus, Real-Time Imaging, Vol. 9, 2003, pp. 113-124.
    
    See Also:
    
    Constant Field Values
  - NOISE_M2
```
public static final int NOISE_M2
```
    Quadratic multiplicative noise.
    
    See Also:
    
    Constant Field Values
  - NOISE_M3
```
public static final int NOISE_M3
```
    Cubic multiplicative noise.
    
    See Also:
    
    Constant Field Values
  - ac1
```
private double ac1
```
    DOCUMENT ME!
  - ac2
```
private double ac2
```
    DOCUMENT ME!
  - ac3
```
private double ac3
```
    DOCUMENT ME!
  - ac4
```
private double ac4
```
    DOCUMENT ME!
  - ac5
```
private double ac5
```
    DOCUMENT ME!
  - ac6
```
private double ac6
```
    DOCUMENT ME!
  - ac7
```
private double ac7
```
    DOCUMENT ME!
  - ac8
```
private double ac8
```
    DOCUMENT ME!
  - ac9
```
private double ac9
```
    DOCUMENT ME!
  - ad1
```
private double ad1
```
    DOCUMENT ME!
  - ad2
```
private double ad2
```
    DOCUMENT ME!
  - ad3
```
private double ad3
```
    DOCUMENT ME!
  - ad4
```
private double ad4
```
    DOCUMENT ME!
  - ad5
```
private double ad5
```
    DOCUMENT ME!
  - ad6
```
private double ad6
```
    DOCUMENT ME!
  - ad7
```
private double ad7
```
    DOCUMENT ME!
  - ad8
```
private double ad8
```
    DOCUMENT ME!
  - ad9
```
private double ad9
```
    DOCUMENT ME!
  - area
```
private int area
```
    DOCUMENT ME!
  - backgroundPresent
```
private boolean backgroundPresent
```
    DOCUMENT ME!
  - buffer
```
private float[] buffer
```
    DOCUMENT ME!
  - grayCount
```
private double grayCount
```
    DOCUMENT ME!
  - histogramAvailable
```
private int histogramAvailable
```
    Number of pixels available for histogram formation.
  - idealBuffer
```
private double[] idealBuffer
```
    Buffer holding calculation for noiseless U(x,y).
  - iter
```
private int iter
```
    DOCUMENT ME!
  - maximum
```
private double maximum
```
    original image maximum.
  - maximumR
```
private double maximumR
```
    DOCUMENT ME!
  - maximumG
```
private double maximumG
```
    DOCUMENT ME!
  - maximumB
```
private double maximumB
```
    DOCUMENT ME!
  - mc1
```
private double mc1
```
    DOCUMENT ME!
  - mc2
```
private double mc2
```
    DOCUMENT ME!
  - mc3
```
private double mc3
```
    DOCUMENT ME!
  - mc4
```
private double mc4
```
    DOCUMENT ME!
  - mc5
```
private double mc5
```
    DOCUMENT ME!
  - mc6
```
private double mc6
```
    DOCUMENT ME!
  - mc7
```
private double mc7
```
    DOCUMENT ME!
  - mc8
```
private double mc8
```
    DOCUMENT ME!
  - mc9
```
private double mc9
```
    DOCUMENT ME!
  - mc10
```
private double mc10
```
    DOCUMENT ME!
  - mc11
```
private double mc11
```
    DOCUMENT ME!
  - mc12
```
private double mc12
```
    DOCUMENT ME!
  - mc13
```
private double mc13
```
    DOCUMENT ME!
  - mc14
```
private double mc14
```
    DOCUMENT ME!
  - mc15
```
private double mc15
```
    DOCUMENT ME!
  - mc16
```
private double mc16
```
    DOCUMENT ME!
  - mc17
```
private double mc17
```
    DOCUMENT ME!
  - mc18
```
private double mc18
```
    DOCUMENT ME!
  - mc19
```
private double mc19
```
    DOCUMENT ME!
  - md1
```
private double md1
```
    DOCUMENT ME!
  - md2
```
private double md2
```
    DOCUMENT ME!
  - md3
```
private double md3
```
    DOCUMENT ME!
  - md4
```
private double md4
```
    DOCUMENT ME!
  - md5
```
private double md5
```
    DOCUMENT ME!
  - md6
```
private double md6
```
    DOCUMENT ME!
  - md7
```
private double md7
```
    DOCUMENT ME!
  - md8
```
private double md8
```
    DOCUMENT ME!
  - md9
```
private double md9
```
    DOCUMENT ME!
  - md10
```
private double md10
```
    DOCUMENT ME!
  - md11
```
private double md11
```
    DOCUMENT ME!
  - md12
```
private double md12
```
    DOCUMENT ME!
  - md13
```
private double md13
```
    DOCUMENT ME!
  - md14
```
private double md14
```
    DOCUMENT ME!
  - md15
```
private double md15
```
    DOCUMENT ME!
  - md16
```
private double md16
```
    DOCUMENT ME!
  - md17
```
private double md17
```
    DOCUMENT ME!
  - md18
```
private double md18
```
    DOCUMENT ME!
  - md19
```
private double md19
```
    DOCUMENT ME!
  - minimum
```
private double minimum
```
    original image minimum.
  - minimumR
```
private double minimumR
```
    DOCUMENT ME!
  - minimumG
```
private double minimumG
```
    DOCUMENT ME!
  - minimumB
```
private double minimumB
```
    DOCUMENT ME!
  - noiseType
```
private int noiseType
```
    NOISE_MA2 or NOISE_M2.
  - nParams
```
private int nParams
```
    Numbering of shading correction parameters.
  - objectBuffer
```
private boolean[] objectBuffer
```
    DOCUMENT ME!
  - pixelIncrement
```
private int pixelIncrement
```
    pixelIncrement is increased above 1 if subsampling.
  - zPixelIncrement
```
private int zPixelIncrement
```
    Handle case where zDim is far less than xDim and yDim
  - powellTolerance
```
private double powellTolerance
```
    Tolerance passed to Powell's algorithm.
  - sliceSize
```
private int sliceSize
```
    xDim * yDim.
  - subsample
```
private boolean subsample
```
    If true, subsample image for histogram formation.
  - thresholdLevel
```
private float thresholdLevel
```
    DOCUMENT ME!
  - thresholdSelected
```
private boolean thresholdSelected
```
    If true don't use pixels below thresholdLevel that are 4 or 6 neighbor connected to boundary pixels below thresholdLevel.
  - validBuffer
```
private boolean[] validBuffer
```
    True for source input locations not having image min or image max values.
  - volSize
```
private int volSize
```
    DOCUMENT ME!
  - volume
```
private int volume
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - zDim
```
private int zDim
```
    DOCUMENT ME!
- Constructor Detail
  - AlgorithmEntropyMinimization
```
public AlgorithmEntropyMinimization(ModelImage srcImage,
                                    boolean thresholdSelected,
                                    float thresholdLevel,
                                    boolean subsample,
                                    int noiseType)
```
    Creates a new AlgorithmEntropyMinimization object.
    
    Parameters:
    
    srcImage - original image
    
    thresholdSelected - If true, don't use pixels that are 4 or 6 neighbor connected to boundary pixels below thresholdLevel
    
    thresholdLevel - DOCUMENT ME!
    
    subsample - DOCUMENT ME!
    
    noiseType - DOCUMENT ME!
  - AlgorithmEntropyMinimization
```
public AlgorithmEntropyMinimization(ModelImage resultImage,
                                    ModelImage srcImage,
                                    boolean thresholdSelected,
                                    float thresholdLevel,
                                    boolean subsample,
                                    int noiseType)
```
    Creates a new AlgorithmEntropyMinimization object.
    
    Parameters:
    
    resultImage - entropy minimized image
    
    srcImage - original image
    
    thresholdSelected - If true, don't use pixels that are 4 or 6 neighbor connected to boundary pixels below thresholdLevel
    
    thresholdLevel - DOCUMENT ME!
    
    subsample - DOCUMENT ME!
    
    noiseType - DOCUMENT ME!
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    DOCUMENT ME!
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - entropyFunction
```
private double entropyFunction(double[] p)
```
    DOCUMENT ME!
    
    Parameters:
    
    p - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - powell
```
private void powell(double[] p,
                    double[][] xi,
                    double ftol)
```
    Minimization of entropy function of nParams variables. Input consists of an initial starting point p[0...nParams-1]; an initial matrix xi[0...nParams-1][0...nParams-1], whose columns contain the initial set of directions (usually the nParams unit vectors); and ftol, the fractional tolerance in the function value such that failure to decrease by more than this amount on one iteration signals doneness. On output, p is set to the best point found, xi is the then-current direction set, fret is the returned function value at p, and iter is the number of iterations taken.
    
    Parameters:
    
    p - DOCUMENT ME!
    
    xi - DOCUMENT ME!
    
    ftol - DOCUMENT ME!
  - run2Da2m2
```
private void run2Da2m2()
```
    DOCUMENT ME!
  - run2Dm2
```
private void run2Dm2()
```
    DOCUMENT ME!
  - run2Dm3
```
private void run2Dm3()
```
    DOCUMENT ME!
  - run3Da2m2
```
private void run3Da2m2()
```
    DOCUMENT ME!
  - run3Dm2
```
private void run3Dm2()
```
    DOCUMENT ME!
  - run3Dm3
```
private void run3Dm3()
```
    DOCUMENT ME!
  - eval
```
public double eval(double[] x)
```
    Specified by:
    
    eval in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
  - getNumberOfVariables
```
public int getNumberOfVariables()
```
    Specified by:
    
    getNumberOfVariables in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables

Class AlgorithmEntropyMinimization

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

NOISE_MA2

NOISE_M2

NOISE_M3

ac1

ac2

ac3

ac4

ac5

ac6

ac7

ac8

ac9

ad1

ad2

ad3

ad4

ad5

ad6

ad7

ad8

ad9

area

backgroundPresent

buffer

grayCount

histogramAvailable

idealBuffer

iter

maximum

maximumR

maximumG

maximumB

mc1

mc2

mc3

mc4

mc5

mc6

mc7

mc8

mc9

mc10

mc11

mc12

mc13

mc14

mc15

mc16

mc17

mc18

mc19

md1

md2

md3

md4

md5

md6

md7

md8

md9

md10

md11

md12

md13

md14

md15

md16

md17