java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.filters.BM3D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class BM3D
extends AlgorithmBase
```

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class BM3D.indexValueComparator

private class BM3D.indexValueItem
- 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[]`	`destImage`
`private boolean`	`estimateNoiseStandardDeviation`
`private int`	`k_H`
`private int`	`k_W`
`private double`	`lambda3D_H`
`private int`	`n_H`
`private int`	`N_H`
`private int`	`n_W`
`private int`	`N_W`
`private int`	`p_H`
`private int`	`p_W`
`private double`	`sigma`
`private java.lang.String`	`tau_2D_H`
`private java.lang.String`	`tau_2D_W`
`private double`	`tauMatch_H`
`private double`	`tauMatch_W`
`private boolean`	`useSD_H`
`private boolean`	`useSD_W`

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, 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
`BM3D(ModelImage[] destImage, ModelImage srcImg, boolean estimateNoiseStandardDeviation, double sigma, int n_H, int N_H, int p_H, boolean useSD_H, java.lang.String tau_2D_H, double lambda3D_H, int n_W, int N_W, int p_W, boolean useSD_W, java.lang.String tau_2D_W)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private double[][]`	`bm3d_1st_step(double sigma, ModelImage img_noisy, int nHard, int kHard, int NHard, int pHard, double lambdaHard3D, double tauMatch, boolean useSD, java.lang.String tau_2D)`
`private double[][]`	`bm3d_2nd_step(double sigma, ModelImage img_noisy, ModelImage img_basic, int nWien, int kWien, int NWien, int pWien, double tauMatch, boolean useSD, java.lang.String tau_2D)`
`private double[][][]`	`build_3D_group(java.util.Vector<java.util.Vector<double[][]>> fre_all_patches, int[][] N__ni_nj, int nSx_r)`
`private int[]`	`closest_power_of_2(int[] M, int max_)`
`private void`	`get_add_patch_matrix(int h, int w, int nHW, int kHW, double[][] row_add_mat, double[][] column_add_mat)`
`private double[][]`	`get_kaiserWindow(int kHW)`
`private double[][][]`	`ht_filtering_hadamard(double[][][] group_3D, double sigma, double lambdaHard3D, boolean doWeight, double[] weight)`
`private java.util.Vector<java.util.Vector<double[][]>>`	`image2patches(ModelImage im, int patch_h, int patch_w)`
`private int[]`	`ind_initialize(int max_size, int N, int step)`
`private double[]`	`kaiser(int M, double beta)`
`private double`	`log2(double x)`
`private int[][][][]`	`precompute_BM(ModelImage img, int kHW, int NHW, int nHW, double tauMatch, int[][] threshold_count)`
`void`	`runAlgorithm()`	Actually runs the algorithm.
`private double`	`sd_weighting(double[][][] group_3D)`
`private ModelImage`	`symetrize(ModelImage img, int pad)`
`private double[][]`	`translation_2d_mat(double[][] mat, int right, int down)`
`private double[][][]`	`wiener_filtering_hadamard(double[][][] group_3D_img, double[][][] group_3D_est, double sigma, boolean doWeight, double[] weight)`

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

destImage
```
private ModelImage[] destImage
```

estimateNoiseStandardDeviation

private boolean estimateNoiseStandardDeviation

sigma
```
private double sigma
```

n_H
```
private int n_H
```

k_H
```
private int k_H
```

N_H
```
private int N_H
```

p_H
```
private int p_H
```

tauMatch_H
```
private double tauMatch_H
```

useSD_H
```
private boolean useSD_H
```

tau_2D_H
```
private java.lang.String tau_2D_H
```

lambda3D_H
```
private double lambda3D_H
```

n_W
```
private int n_W
```

k_W
```
private int k_W
```

N_W
```
private int N_W
```

p_W
```
private int p_W
```

tauMatch_W
```
private double tauMatch_W
```

useSD_W
```
private boolean useSD_W
```

tau_2D_W
```
private java.lang.String tau_2D_W
```

Constructor Detail

BM3D

public BM3D(ModelImage[] destImage,
            ModelImage srcImg,
            boolean estimateNoiseStandardDeviation,
            double sigma,
            int n_H,
            int N_H,
            int p_H,
            boolean useSD_H,
            java.lang.String tau_2D_H,
            double lambda3D_H,
            int n_W,
            int N_W,
            int p_W,
            boolean useSD_W,
            java.lang.String tau_2D_W)

Method Detail

runAlgorithm
```
public void runAlgorithm()
```
Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

bm3d_2nd_step

private double[][] bm3d_2nd_step(double sigma,
                                 ModelImage img_noisy,
                                 ModelImage img_basic,
                                 int nWien,
                                 int kWien,
                                 int NWien,
                                 int pWien,
                                 double tauMatch,
                                 boolean useSD,
                                 java.lang.String tau_2D)

wiener_filtering_hadamard

private double[][][] wiener_filtering_hadamard(double[][][] group_3D_img,
                                               double[][][] group_3D_est,
                                               double sigma,
                                               boolean doWeight,
                                               double[] weight)

symetrize

private ModelImage symetrize(ModelImage img,
                             int pad)

bm3d_1st_step

private double[][] bm3d_1st_step(double sigma,
                                 ModelImage img_noisy,
                                 int nHard,
                                 int kHard,
                                 int NHard,
                                 int pHard,
                                 double lambdaHard3D,
                                 double tauMatch,
                                 boolean useSD,
                                 java.lang.String tau_2D)

sd_weighting

private double sd_weighting(double[][][] group_3D)

ht_filtering_hadamard

private double[][][] ht_filtering_hadamard(double[][][] group_3D,
                                           double sigma,
                                           double lambdaHard3D,
                                           boolean doWeight,
                                           double[] weight)

build_3D_group

private double[][][] build_3D_group(java.util.Vector<java.util.Vector<double[][]>> fre_all_patches,
                                    int[][] N__ni_nj,
                                    int nSx_r)

log2
```
private double log2(double x)
```

image2patches

private java.util.Vector<java.util.Vector<double[][]>> image2patches(ModelImage im,
                                                                     int patch_h,
                                                                     int patch_w)

precompute_BM

private int[][][][] precompute_BM(ModelImage img,
                                  int kHW,
                                  int NHW,
                                  int nHW,
                                  double tauMatch,
                                  int[][] threshold_count)

closest_power_of_2

private int[] closest_power_of_2(int[] M,
                                 int max_)

get_add_patch_matrix

private void get_add_patch_matrix(int h,
                                  int w,
                                  int nHW,
                                  int kHW,
                                  double[][] row_add_mat,
                                  double[][] column_add_mat)

translation_2d_mat

private double[][] translation_2d_mat(double[][] mat,
                                      int right,
                                      int down)

get_kaiserWindow

private double[][] get_kaiserWindow(int kHW)

kaiser

private double[] kaiser(int M,
                        double beta)

ind_initialize

private int[] ind_initialize(int max_size,
                             int N,
                             int step)

Modifier and Type	Class	Description
`private class`	`BM3D.indexValueComparator`
`private class`	`BM3D.indexValueItem`

Class BM3D

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

destImage

estimateNoiseStandardDeviation

sigma

n_H

k_H

N_H

p_H

tauMatch_H

useSD_H

tau_2D_H

lambda3D_H

n_W

k_W

N_W

p_W

tauMatch_W

useSD_W

tau_2D_W

Constructor Detail

BM3D

Method Detail

runAlgorithm

bm3d_2nd_step

wiener_filtering_hadamard

symetrize

bm3d_1st_step

sd_weighting

ht_filtering_hadamard

build_3D_group

log2

image2patches

precompute_BM

closest_power_of_2

get_add_patch_matrix

translation_2d_mat

get_kaiserWindow

kaiser

ind_initialize