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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMode
extends AlgorithmBase
```
AlgorithmMode applies one of the user specified kernels to a 2D or 3D BYTE, SHORT, INTEGER, UBYTE, USHORT, UINTEGER. AlgorithmMode is a spatial filtering technique that replaces the central kernel pixel with the mode of the pixels under the kernelMask. The mode of a set of values is the value that occurs most frequently. If all values are unique, that is, all numbers occur once in the kernelMask, the algorithm does NOT change the value of the central pixel.
Mode filtering is currently thought to be useful in filtering a segmented image to get rid of small clusters of one value within a large cluser of a different value. We are currently investigating mode filtering in cleaning up a C-Means classification of brain images, which were detected using the Brain Extraction Tool (BET). Mode filtering can be applied to gray scale images to remove some noise, however, we have found that a 3X3X3 cube kernel significantly blurs the image, while an axis kernel appear to clean up some of the noise without too much blurring. The utility more filtering on gray scale images need more investigation.

Giving credit where credit is due, this algorithm and its associated dialog, JDialogMode started with the AlgorithmMedian and JDialogMedian code. The color image stuff, iteration control, and standard deviation were removed. Furthermore, all processing is done using integer images and buffers, as finding the mode of floating (real) numbers is not meaningful.

Version:

1.0 June 24, 2004

Author:

Paul Hemler

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
`static int`	`AXIAL_KERNEL`	(3D only).
`(package private) int`	`bdrBufferDepth`	Border buffer number of slices.
`(package private) int`	`bdrBufferHeight`	Border buffer number of rows.
`(package private) int`	`bdrBufferWidth`	Border buffer number of columns.
`static int`	`CROSS_KERNEL`	cross (2D only).
`static int`	`CUBE_KERNEL`	(3D only).
`private int`	`currentSlice`	Used for 3D loop control.
`private boolean`	`entireImage`	true means apply to entire image, false only region.
`private int`	`halfK`	The kernel radius.
`static int`	`HORZ_KERNEL`	horizontal (2D only).
`private byte[]`	`kernel`	mask to determine the region of pixels used in the mode filter.
`private int`	`kernelCenter`	The index of the kernel center.
`private int[]`	`kernelMask`	The kernel.
`private int`	`kernelShape`	user-selectable shape of the region for neighbor-selection.
`private int`	`kernelSize`	dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
`private int`	`numberOfSlices`	Used for 3D loop control.
`private boolean`	`sliceFiltering`	do all filtering slice-by-slice, rather than as a volume.
`static int`	`SQUARE_KERNEL`	square kernel (2D only).
`(package private) int`	`srcBufferDepth`	Source buffer number of slices.
`(package private) int`	`srcBufferHeight`	Source buffer number of rows.
`(package private) int`	`srcBufferWidth`	Source buffer number of columns.
`static int`	`VERT_KERNEL`	vertical (2D only).
`static int`	`X_KERNEL`	X-shaped kernel, from 1 corner to opposite corner.

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
`AlgorithmMode(ModelImage srcImg, int kSize, int kShape, boolean maskFlag)`	Constructor for 2D images in which changes are returned to the source image.
`AlgorithmMode(ModelImage srcImg, int kSize, int kShape, boolean sliceBySlice, boolean maskFlag)`	Constructor for 3D images in which changes are returned to the source image.
`AlgorithmMode(ModelImage destImg, ModelImage srcImg, int kSize, int kShape, boolean maskFlag)`	Constructor for 2D images in which changes are placed in a predetermined destination image.
`AlgorithmMode(ModelImage destImg, ModelImage srcImg, int kSize, int kShape, boolean sliceBySlice, boolean maskFlag)`	Constructor for 3D images in which changes are placed in a predetermined destination image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcInPlaceBorder2D()`	Mode filters the 2D source image.
`private void`	`calcInPlaceBorder3D()`	Mode filters the 3D source image and replaces it with the mode filtered image.
`private void`	`calcStoreInDestBorder2D()`	This function produces a new image that has been mode filtered and places filtered image in the destination image.
`private void`	`calcStoreInDestBorder3D()`	Mode filters the 3D source image and makes a new image for the mode filtered image.
`private void`	`copy2DSrcBufferToBdrBuffer(int[] srcBuffer, int[] bdrBuffer, int srcBufferOffsetIndex, int bdrBufferOffsetIndex)`	Method copies the data in srcBuffer centered in the border buffer That is, the src image is completely surrounded by a border.
`private void`	`copy3DSrcBufferToBdrBuffer(int[] srcBuffer, int[] bdrBuffer)`	Method copies the data in srcBuffer centered in the border buffer That is, the src image is completely surrounded by a border.
`void`	`finalize()`	Prepares this class for destruction.
`private int[]`	`getBorderBufferNeighborList(int i, int[] data, boolean is2D)`	Compiles a list of the values neighboring the desired pixel, that are defined in the kernel.
`private void`	`makeKernel()`	Forms kernel.
`private void`	`makeKernelMask()`	Makes the kernel mask.
`private int`	`mode(int[] list, int val)`	Finds the mode value of the list.
`void`	`runAlgorithm()`	Starts the algorithm.
`private void`	`setKernel()`	Fill in the mask for which pixels are used in filtering.
`private void`	`sliceFilterBorder(int[] srcBdrBuffer, int[] destBuffer, int srcBufferStartingPoint, int destBufferStartingPoint)`	Performs mode filtering on a single slice with a 2D or 3D buffer.
`private void`	`volumeFilterBorder(int[] srcBdrBuffer, int[] destBuffer)`	Assumes a monochrome image of type BYTE, SHORT, INTEGER, UBYTE, USHORT, UINTEGER.

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
  - SQUARE_KERNEL
```
public static final int SQUARE_KERNEL
```
    square kernel (2D only).
    
    See Also:
    
    Constant Field Values
  - CUBE_KERNEL
```
public static final int CUBE_KERNEL
```
    (3D only).
    
    See Also:
    
    Constant Field Values
  - CROSS_KERNEL
```
public static final int CROSS_KERNEL
```
    cross (2D only).
    
    See Also:
    
    Constant Field Values
  - AXIAL_KERNEL
```
public static final int AXIAL_KERNEL
```
    (3D only).
    
    See Also:
    
    Constant Field Values
  - X_KERNEL
```
public static final int X_KERNEL
```
    X-shaped kernel, from 1 corner to opposite corner.
    
    See Also:
    
    Constant Field Values
  - HORZ_KERNEL
```
public static final int HORZ_KERNEL
```
    horizontal (2D only).
    
    See Also:
    
    Constant Field Values
  - VERT_KERNEL
```
public static final int VERT_KERNEL
```
    vertical (2D only).
    
    See Also:
    
    Constant Field Values
  - bdrBufferDepth
```
int bdrBufferDepth
```
    Border buffer number of slices.
  - bdrBufferHeight
```
int bdrBufferHeight
```
    Border buffer number of rows.
  - bdrBufferWidth
```
int bdrBufferWidth
```
    Border buffer number of columns.
  - srcBufferDepth
```
int srcBufferDepth
```
    Source buffer number of slices.
  - srcBufferHeight
```
int srcBufferHeight
```
    Source buffer number of rows.
  - srcBufferWidth
```
int srcBufferWidth
```
    Source buffer number of columns.
  - currentSlice
```
private int currentSlice
```
    Used for 3D loop control.
  - entireImage
```
private boolean entireImage
```
    true means apply to entire image, false only region.
  - halfK
```
private int halfK
```
    The kernel radius.
  - kernel
```
private byte[] kernel
```
    mask to determine the region of pixels used in the mode filter.
  - kernelCenter
```
private int kernelCenter
```
    The index of the kernel center.
  - kernelMask
```
private int[] kernelMask
```
    The kernel.
  - kernelShape
```
private int kernelShape
```
    user-selectable shape of the region for neighbor-selection.
  - kernelSize
```
private int kernelSize
```
    dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
  - numberOfSlices
```
private int numberOfSlices
```
    Used for 3D loop control.
  - sliceFiltering
```
private boolean sliceFiltering
```
    do all filtering slice-by-slice, rather than as a volume.
- Constructor Detail
  - AlgorithmMode
```
public AlgorithmMode(ModelImage srcImg,
                     int kSize,
                     int kShape,
                     boolean maskFlag)
```
    Constructor for 2D images in which changes are returned to the source image.
    
    Parameters:
    
    srcImg - Source image model.
    
    kSize - Kernel size: dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
    
    kShape - Kernel shape: element neighbors to include when finding the mode.
    
    maskFlag - Flag that indicates that the mode filtering will be performed for the whole image if equal to true.
  - AlgorithmMode
```
public AlgorithmMode(ModelImage destImg,
                     ModelImage srcImg,
                     int kSize,
                     int kShape,
                     boolean maskFlag)
```
    Constructor for 2D images in which changes are placed in a predetermined destination image.
    
    Parameters:
    
    destImg - Image model where result image is stored.
    
    srcImg - Source image model.
    
    kSize - Kernel size: dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
    
    kShape - Kernel shape: element neighbors to include when finding the mode.
    
    maskFlag - Flag that indicates that the mode filtering will be performed for the whole image if equal to true.
  - AlgorithmMode
```
public AlgorithmMode(ModelImage srcImg,
                     int kSize,
                     int kShape,
                     boolean sliceBySlice,
                     boolean maskFlag)
```
    Constructor for 3D images in which changes are returned to the source image.
    
    Parameters:
    
    srcImg - Source image model.
    
    kSize - Kernel size: dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
    
    kShape - Kernel shape: element neighbors to include when finding the mode.
    
    sliceBySlice - Each slice in a volume image is to be filtered separately (when true), else the volume will use a kernel with 3 dimensions.
    
    maskFlag - Flag that indicates that the mode filtering will be performed for the whole image if equal to true.
  - AlgorithmMode
```
public AlgorithmMode(ModelImage destImg,
                     ModelImage srcImg,
                     int kSize,
                     int kShape,
                     boolean sliceBySlice,
                     boolean maskFlag)
```
    Constructor for 3D images in which changes are placed in a predetermined destination image.
    
    Parameters:
    
    destImg - Image model where result image is stored.
    
    srcImg - Source image model.
    
    kSize - Kernel size: dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
    
    kShape - Kernel shape: element neighbors to include when finding the mode.
    
    sliceBySlice - Each slice in a volume image is filtered separately (when true), else the volume will use a kernel with 3 dimensions.
    
    maskFlag - Flag that indicates that the mode filtering will be performed for the whole image if equal to true.
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - calcInPlaceBorder2D
```
private void calcInPlaceBorder2D()
```
    Mode filters the 2D source image. Replaces the original image with the filtered image.
  - calcInPlaceBorder3D
```
private void calcInPlaceBorder3D()
```
    Mode filters the 3D source image and replaces it with the mode filtered image.
  - calcStoreInDestBorder2D
```
private void calcStoreInDestBorder2D()
```
    This function produces a new image that has been mode filtered and places filtered image in the destination image.
  - calcStoreInDestBorder3D
```
private void calcStoreInDestBorder3D()
```
    Mode filters the 3D source image and makes a new image for the mode filtered image.
  - copy2DSrcBufferToBdrBuffer
```
private void copy2DSrcBufferToBdrBuffer(int[] srcBuffer,
                                        int[] bdrBuffer,
                                        int srcBufferOffsetIndex,
                                        int bdrBufferOffsetIndex)
```
    Method copies the data in srcBuffer centered in the border buffer That is, the src image is completely surrounded by a border. The values in the border locations are copies of nearby srcBuffer values.
    
    Parameters:
    
    srcBuffer - int[] the source image buffer
    
    bdrBuffer - int[] the border image buffer
    
    srcBufferOffsetIndex - offset into srcBuffer
    
    bdrBufferOffsetIndex - offset into bdrBuffer
  - copy3DSrcBufferToBdrBuffer
```
private void copy3DSrcBufferToBdrBuffer(int[] srcBuffer,
                                        int[] bdrBuffer)
```
    Method copies the data in srcBuffer centered in the border buffer That is, the src image is completely surrounded by a border. The values in the border locations are copies of nearby srcBuffer values.
    
    Parameters:
    
    srcBuffer - int[] the source image buffer
    
    bdrBuffer - int[] the border image buffer
  - getBorderBufferNeighborList
```
private int[] getBorderBufferNeighborList(int i,
                                          int[] data,
                                          boolean is2D)
```
    Compiles a list of the values neighboring the desired pixel, that are defined in the kernel.
    
    Parameters:
    
    i - The central pixel to find neighbors for.
    
    data - Image data
    
    is2D - True indicates that the neighbors are found along a 2D slice (or 2D image) instead of neighbors in a 3D volume.
    
    Returns:
    
    The neighboring pixel list corresponds to the kernel chosen.
  - makeKernel
```
private void makeKernel()
```
    Forms kernel.
  - makeKernelMask
```
private void makeKernelMask()
```
    Makes the kernel mask. The kernel mask is the list of values pulled from the image which will be used to find the mode of the central pixel. Its length is (number of pixels to be used to determine mode).
    Thus the kernel center (decided here), has the value of the location of the central pixel shown in the window. The value of the kernel center is the number of pixels picked up to mode sort.
    
    Note that for symmetric masks always have kernelCenter = count/2 and maskCenter = count/2.
  - mode
```
private int mode(int[] list,
                 int val)
```
    Finds the mode value of the list. If the numbers in the list are unique, return the value of the second parameter. This method assumes the parameter list is sorted, and counts consecutive array elements containing the same value.
    
    Parameters:
    
    list - int[] List of numbers
    
    val - Value to return if all list elements are unique
    
    Returns:
    
    the mode of the values in the list
  - setKernel
```
private void setKernel()
```
    Fill in the mask for which pixels are used in filtering.
  - sliceFilterBorder
```
private void sliceFilterBorder(int[] srcBdrBuffer,
                               int[] destBuffer,
                               int srcBufferStartingPoint,
                               int destBufferStartingPoint)
```
    Performs mode filtering on a single slice with a 2D or 3D buffer.
    
    Parameters:
    
    srcBdrBuffer - Source buffer.
    
    destBuffer - Destination Buffer.
    
    srcBufferStartingPoint - Index of the first pixel in the source buffer
    
    destBufferStartingPoint - Index of the first pixel for the slice to be filtered in the destination buffer.
  - volumeFilterBorder
```
private void volumeFilterBorder(int[] srcBdrBuffer,
                                int[] destBuffer)
```
    Assumes a monochrome image of type BYTE, SHORT, INTEGER, UBYTE, USHORT, UINTEGER.
    
    Parameters:
    
    srcBdrBuffer - int[] the border buffer containing the source image data
    
    destBuffer - int[] the destination buffer

Class AlgorithmMode

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

SQUARE_KERNEL

CUBE_KERNEL

CROSS_KERNEL

AXIAL_KERNEL

X_KERNEL

HORZ_KERNEL

VERT_KERNEL

bdrBufferDepth

bdrBufferHeight

bdrBufferWidth

srcBufferDepth

srcBufferHeight

srcBufferWidth

currentSlice

entireImage

halfK

kernel

kernelCenter

kernelMask

kernelShape

kernelSize

numberOfSlices

sliceFiltering

Constructor Detail

AlgorithmMode

AlgorithmMode

AlgorithmMode

AlgorithmMode

Method Detail

finalize

runAlgorithm

calcInPlaceBorder2D

calcInPlaceBorder3D

calcStoreInDestBorder2D

calcStoreInDestBorder3D

copy2DSrcBufferToBdrBuffer

copy3DSrcBufferToBdrBuffer

getBorderBufferNeighborList

makeKernel

makeKernelMask

mode

setKernel

sliceFilterBorder

volumeFilterBorder