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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmRiceWaveletTools
extends AlgorithmBase
```
This "rice-wlet-tools", version 2.4 Released - CONDITIONS FOR USE: Copyright (c) 2000 RICE UNIVERSITY. All rights reserved. This software is distributed and licensed to you on a non-exclusive basis, free-of-charge. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistribution of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistribution in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. All advertising materials mentioning features or use of this software must display the following acknowledgment: This product includes software developed by Rice University, Houston, Texas and its contributors. 4. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY WILLIAM MARSH RICE UNIVERSITY, HOUSTON, TEXAS, AND CONTRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL RICE UNIVERSITY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTIONS) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE), PRODUCT LIABILITY, OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. For information on commercial licenses, contact Rice University's Office of Technology Transfer at techtran@rice.edu or (713) 348-6173

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`(package private) class`	`AlgorithmRiceWaveletTools.EigenvalueComplex`
`(package private) class`	`AlgorithmRiceWaveletTools.EigenvalueComplexComparator`

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[]`	`aArray`
`private double`	`actualThreshold`
`private boolean`	`doBayesShrinkThresholdComputation`
`private boolean`	`doDenoise`
`private boolean`	`doWaveletImages`
`private int`	`error`
`private int[]`	`extents`
`private int`	`filterLength`
`private int`	`filterType`
`static int`	`HARD_THRESHOLDING`
`private double[][]`	`hhA`
`private double[][]`	`hlA`
`private double[][]`	`lhA`
`private double[][]`	`llA`
`static int`	`MAD`
`static int`	`MAXIMUM_PHASE`
`private int`	`maximumLevel`
`static int`	`MID_PHASE`
`static int`	`MINIMUM_PHASE`
`private int`	`minimumLevel`
`private int`	`nDims`
`private double[]`	`noiseStandardDeviation`
`private int`	`numberOfLevels`
`private boolean`	`redundant`
`private double[]`	`scalingFilter`
`private int`	`sliceSize`
`static int`	`SOFT_THRESHOLDING`
`static int`	`STD`
`private int`	`thresholdingType`
`private boolean`	`thresholdLowPass`
`private double`	`thresholdMultiplier`
`private boolean`	`useNoiseStdConstructor`
`private int`	`varianceEstimator`
`private double[]`	`waveletFilter`
`private ModelImage[]`	`waveletImage`
`private int`	`xDim`
`private double[]`	`y`
`private int`	`yDim`
`private double[]`	`yl`
`private int`	`z`
`private int`	`zDim`

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
`AlgorithmRiceWaveletTools()`
`AlgorithmRiceWaveletTools(ModelImage srcImg, double[] noiseStandardDeviation)`
`AlgorithmRiceWaveletTools(ModelImage srcImg, int filterLength, boolean redundant, int numberOfLevels, boolean doWaveletImages, int minimumLevel, int maximumLevel, int filterType, boolean doDenoise, double actualThreshold, int varianceEstimator, double thresholdMultiplier, int thresholdingType, boolean thresholdLowPass, boolean doBayesShrinkThresholdComputation)`
`AlgorithmRiceWaveletTools(ModelImage destImg, ModelImage srcImg, int filterLength, boolean redundant, int numberOfLevels, boolean doWaveletImages, int minimumLevel, int maximumLevel, int filterType, boolean doDenoise, double actualThreshold, int varianceEstimator, double thresholdMultiplier, int thresholdingType, boolean thresholdLowPass, boolean doBayesShrinkThresholdComputation)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private double`	`BayesShrinkThresholdComputation(double[] data, double noise_var)`
`private void`	`bpconv(double[] x_out, int lx, double[] g0, double[] g1, int lh, double[] x_inl, double[] x_inh)`
`private void`	`bpsconv(double[] x_out, int lx, double[] g0, double[] g1, int lhm1, int lhhm1, double[] x_inl, double[] x_inh)`
`private void`	`daubcqf()`	Function computes the Daubechies' scaling and wavelet filters (normalized to sqrt(2)).
`private void`	`fpconv(double[] x_in, int lx, double[] h0, double[] h1, int lh, double[] x_outl, double[] x_outh)`
`private void`	`fpsconv(double[] x_in, int lx, double[] h0, double[] h1, int lhm1, double[] x_outl, double[] x_outh)`
`ModelImage[]`	`getWaveletImages()`	Accessor that returns the image.
`private void`	`makeSig(java.lang.String sigName, int signalLength)`
`private void`	`mdwt()`
`void`	`midwt()`
`void`	`mirdwt()`
`private void`	`mrdwt()`
`void`	`runAlgorithm()`	Actually runs the algorithm.
`void`	`signalTest()`
`void`	`test_denoise_2D()`
`void`	`test_denoise_actual_thresh()`
`void`	`test_denoise_default()`
`void`	`test_denoise_hard()`
`void`	`test_denoise_levels()`
`void`	`test_denoise_std()`
`void`	`test_denoise_thresh_multiplier()`
`void`	`test_denoise_threshold_low()`
`void`	`test_denoise_udwt()`
`void`	`test_denoise_udwt_2d()`
`void`	`test_denoise_udwt_actual_thresh()`
`void`	`test_denoise_udwt_levels()`
`void`	`test_denoise_udwt_soft()`
`void`	`test_denoise_udwt_std()`
`void`	`test_denoise_udwt_thresh_multiplier()`
`void`	`test_denoise_udwt_threshold_low()`
`void`	`test_mdwt_1D()`
`void`	`test_mdwt_2D()`
`void`	`test_midwt_1D()`
`void`	`test_midwt_2D()`
`void`	`test_mirdwt_1()`
`void`	`test_mirdwt_2D()`
`void`	`test_mrdwt_1()`
`void`	`test_mrdwt_2()`
`void`	`test_mrdwt_2L2()`

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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
  - MINIMUM_PHASE
```
public static final int MINIMUM_PHASE
```
    See Also:
    
    Constant Field Values
  - MID_PHASE
```
public static final int MID_PHASE
```
    See Also:
    
    Constant Field Values
  - MAXIMUM_PHASE
```
public static final int MAXIMUM_PHASE
```
    See Also:
    
    Constant Field Values
  - MAD
```
public static final int MAD
```
    See Also:
    
    Constant Field Values
  - STD
```
public static final int STD
```
    See Also:
    
    Constant Field Values
  - SOFT_THRESHOLDING
```
public static final int SOFT_THRESHOLDING
```
    See Also:
    
    Constant Field Values
  - HARD_THRESHOLDING
```
public static final int HARD_THRESHOLDING
```
    See Also:
    
    Constant Field Values
  - filterLength
```
private int filterLength
```
  - filterType
```
private int filterType
```
  - scalingFilter
```
private double[] scalingFilter
```
  - waveletFilter
```
private double[] waveletFilter
```
  - nDims
```
private int nDims
```
  - extents
```
private int[] extents
```
  - xDim
```
private int xDim
```
  - yDim
```
private int yDim
```
  - sliceSize
```
private int sliceSize
```
  - zDim
```
private int zDim
```
  - aArray
```
private double[] aArray
```
  - error
```
private int error
```
  - numberOfLevels
```
private int numberOfLevels
```
  - redundant
```
private boolean redundant
```
  - doWaveletImages
```
private boolean doWaveletImages
```
  - waveletImage
```
private ModelImage[] waveletImage
```
  - yl
```
private double[] yl
```
  - llA
```
private double[][] llA
```
  - lhA
```
private double[][] lhA
```
  - hlA
```
private double[][] hlA
```
  - hhA
```
private double[][] hhA
```
  - y
```
private double[] y
```
  - minimumLevel
```
private int minimumLevel
```
  - maximumLevel
```
private int maximumLevel
```
  - z
```
private int z
```
  - doDenoise
```
private boolean doDenoise
```
  - actualThreshold
```
private double actualThreshold
```
  - varianceEstimator
```
private int varianceEstimator
```
  - thresholdMultiplier
```
private double thresholdMultiplier
```
  - thresholdingType
```
private int thresholdingType
```
  - thresholdLowPass
```
private boolean thresholdLowPass
```
  - noiseStandardDeviation
```
private double[] noiseStandardDeviation
```
  - useNoiseStdConstructor
```
private boolean useNoiseStdConstructor
```
  - doBayesShrinkThresholdComputation
```
private boolean doBayesShrinkThresholdComputation
```
- Constructor Detail
  - AlgorithmRiceWaveletTools
```
public AlgorithmRiceWaveletTools()
```
  - AlgorithmRiceWaveletTools
```
public AlgorithmRiceWaveletTools(ModelImage destImg,
                                 ModelImage srcImg,
                                 int filterLength,
                                 boolean redundant,
                                 int numberOfLevels,
                                 boolean doWaveletImages,
                                 int minimumLevel,
                                 int maximumLevel,
                                 int filterType,
                                 boolean doDenoise,
                                 double actualThreshold,
                                 int varianceEstimator,
                                 double thresholdMultiplier,
                                 int thresholdingType,
                                 boolean thresholdLowPass,
                                 boolean doBayesShrinkThresholdComputation)
```
  - AlgorithmRiceWaveletTools
```
public AlgorithmRiceWaveletTools(ModelImage srcImg,
                                 int filterLength,
                                 boolean redundant,
                                 int numberOfLevels,
                                 boolean doWaveletImages,
                                 int minimumLevel,
                                 int maximumLevel,
                                 int filterType,
                                 boolean doDenoise,
                                 double actualThreshold,
                                 int varianceEstimator,
                                 double thresholdMultiplier,
                                 int thresholdingType,
                                 boolean thresholdLowPass,
                                 boolean doBayesShrinkThresholdComputation)
```
  - AlgorithmRiceWaveletTools
```
public AlgorithmRiceWaveletTools(ModelImage srcImg,
                                 double[] noiseStandardDeviation)
```
- Method Detail
  - signalTest
```
public void signalTest()
```
  - test_mrdwt_1
```
public void test_mrdwt_1()
```
  - test_mrdwt_2
```
public void test_mrdwt_2()
```
  - test_mrdwt_2L2
```
public void test_mrdwt_2L2()
```
  - test_mirdwt_1
```
public void test_mirdwt_1()
```
  - test_mirdwt_2D
```
public void test_mirdwt_2D()
```
  - test_mdwt_1D
```
public void test_mdwt_1D()
```
  - test_mdwt_2D
```
public void test_mdwt_2D()
```
  - test_midwt_1D
```
public void test_midwt_1D()
```
  - test_midwt_2D
```
public void test_midwt_2D()
```
  - test_denoise_default
```
public void test_denoise_default()
```
  - test_denoise_2D
```
public void test_denoise_2D()
```
  - test_denoise_udwt
```
public void test_denoise_udwt()
```
  - test_denoise_udwt_2d
```
public void test_denoise_udwt_2d()
```
  - test_denoise_threshold_low
```
public void test_denoise_threshold_low()
```
  - test_denoise_thresh_multiplier
```
public void test_denoise_thresh_multiplier()
```
  - test_denoise_std
```
public void test_denoise_std()
```
  - test_denoise_hard
```
public void test_denoise_hard()
```
  - test_denoise_levels
```
public void test_denoise_levels()
```
  - test_denoise_actual_thresh
```
public void test_denoise_actual_thresh()
```
  - test_denoise_udwt_threshold_low
```
public void test_denoise_udwt_threshold_low()
```
  - test_denoise_udwt_thresh_multiplier
```
public void test_denoise_udwt_thresh_multiplier()
```
  - test_denoise_udwt_std
```
public void test_denoise_udwt_std()
```
  - test_denoise_udwt_soft
```
public void test_denoise_udwt_soft()
```
  - test_denoise_udwt_levels
```
public void test_denoise_udwt_levels()
```
  - test_denoise_udwt_actual_thresh
```
public void test_denoise_udwt_actual_thresh()
```
  - BayesShrinkThresholdComputation
```
private double BayesShrinkThresholdComputation(double[] data,
                                               double noise_var)
```
  - runAlgorithm
```
public void runAlgorithm()
```
    Description copied from class: AlgorithmBase
    
    Actually runs the algorithm. Implemented by inheriting algorithms.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - makeSig
```
private void makeSig(java.lang.String sigName,
                     int signalLength)
```
  - mdwt
```
private void mdwt()
```
  - mrdwt
```
private void mrdwt()
```
  - fpconv
```
private void fpconv(double[] x_in,
                    int lx,
                    double[] h0,
                    double[] h1,
                    int lh,
                    double[] x_outl,
                    double[] x_outh)
```
  - fpsconv
```
private void fpsconv(double[] x_in,
                     int lx,
                     double[] h0,
                     double[] h1,
                     int lhm1,
                     double[] x_outl,
                     double[] x_outh)
```
  - midwt
```
public void midwt()
```
  - mirdwt
```
public void mirdwt()
```
  - bpsconv
```
private void bpsconv(double[] x_out,
                     int lx,
                     double[] g0,
                     double[] g1,
                     int lhm1,
                     int lhhm1,
                     double[] x_inl,
                     double[] x_inh)
```
  - bpconv
```
private void bpconv(double[] x_out,
                    int lx,
                    double[] g0,
                    double[] g1,
                    int lh,
                    double[] x_inl,
                    double[] x_inh)
```
  - daubcqf
```
private void daubcqf()
```
    Function computes the Daubechies' scaling and wavelet filters (normalized to sqrt(2)). The user specifies an even number filter length and a minimum phase, mid phase, or maximum phase solution. Reference: "Orthonormal Bases of Compactly Supported Wavelets", CPAM, October, 1989. From the original source file: %File Name: daubcqf.m %Last Modification Date: 01/02/96 15:12:57 %Current Version: daubcqf.m 2.4 %File Creation Date: 10/10/88 %Author: Ramesh Gopinath % %Copyright (c) 2000 RICE UNIVERSITY. All rights reserved. %Created by Ramesh Gopinath, Department of ECE, Rice University. Correctly gives scaling and wavelet filters for filter length = 4 minimum phase: Calculated scaling filter: 0.48296291314453416 0.8365163037378078 0.2241438680420134 -0.12940952255126037 Calculated Wavelet filter: 0.12940952255126037 0.2241438680420134 -0.8365163037378078 0.48296291314453416 Correct scaling filter = [0.482962913144534 0.836516303737808 0.224143868042013 -0.129409522551260]; Correct wavelet filter = [0.129409522551260 0.224143868042013 -0.836516303737808 0.482962913144534]; Correctly gives scaling and wavelet filters for filter length = 4 mid phase Calculated scaling filter: 0.48296291314453416 0.8365163037378078 0.2241438680420134 -0.12940952255126037 Calculated wavelet filter: 0.12940952255126037 0.2241438680420134 -0.8365163037378078 0.48296291314453416 Correct scaling filter = [0.482962913144534 0.836516303737808 0.224143868042013 -0.129409522551260]; Corrct wavelet filter = [0.129409522551260 0.224143868042013 -0.836516303737808 0.482962913144534]; Correctly gives scaling and wavelet filters for filter length = 4 maximum phase Calculated scaling filter: -0.12940952255126037 0.2241438680420134 0.8365163037378078 0.48296291314453416 Calculated wavelet filter: -0.48296291314453416 0.8365163037378078 -0.2241438680420134 -0.12940952255126037 Correct scaling filter = [-0.129409522551260 0.224143868042013 0.836516303737808 0.482962913144534]; Correct wavelet filter = [-0.482962913144534 0.836516303737808 -0.224143868042013 -0.129409522551260]; Correctly gives scaling and wavelet filters for filter length = 6 minimum phase Scaling filter: 0.3326705529500828 0.8068915093110931 0.459877502118492 -0.1350110200102549 -0.08544127388202716 0.03522629188570937 Wavelet filter: -0.03522629188570937 -0.08544127388202716 0.1350110200102549 0.459877502118492 -0.8068915093110931 0.3326705529500828 Correctly gives scaling and wavelet filters for filter length = 6 mid phase Scaling filter: 0.3326705529500828 0.8068915093110931 0.459877502118492 -0.1350110200102549 -0.08544127388202716 0.03522629188570937 Wavelet filter: -0.03522629188570937 -0.08544127388202716 0.1350110200102549 0.459877502118492 -0.8068915093110931 0.3326705529500828 Correct scaling filter = [0.332670552950083 0.806891509311093 0.459877502118491 -0.135011020010255 -0.085441273882027 0.035226291885710]; Correct wavelet filter = [-0.035226291885710 -0.085441273882027 0.135011020010255 0.459877502118491 -0.806891509311093 0.332670552950083];
  - getWaveletImages
```
public ModelImage[] getWaveletImages()
```
    Accessor that returns the image.
    
    Returns:
    
    the wavelet image

Class AlgorithmRiceWaveletTools

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

MINIMUM_PHASE

MID_PHASE

MAXIMUM_PHASE

MAD

STD

SOFT_THRESHOLDING

HARD_THRESHOLDING

filterLength

filterType

scalingFilter

waveletFilter

nDims

extents

xDim

yDim

sliceSize

zDim

aArray

error

numberOfLevels

redundant

doWaveletImages

waveletImage

yl

llA

lhA

hlA

hhA

y

minimumLevel

maximumLevel

z

doDenoise

actualThreshold

varianceEstimator

thresholdMultiplier

thresholdingType

thresholdLowPass

noiseStandardDeviation

useNoiseStdConstructor

doBayesShrinkThresholdComputation

Constructor Detail

AlgorithmRiceWaveletTools

AlgorithmRiceWaveletTools

AlgorithmRiceWaveletTools

AlgorithmRiceWaveletTools

Method Detail

signalTest

test_mrdwt_1

test_mrdwt_2

test_mrdwt_2L2

test_mirdwt_1

test_mirdwt_2D

test_mdwt_1D

test_mdwt_2D

test_midwt_1D

test_midwt_2D

test_denoise_default

test_denoise_2D

test_denoise_udwt

test_denoise_udwt_2d

test_denoise_threshold_low

test_denoise_thresh_multiplier

test_denoise_std

test_denoise_hard

test_denoise_levels

test_denoise_actual_thresh

test_denoise_udwt_threshold_low