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

All Implemented Interfaces:

AlgorithmInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmNMSuppression
extends AlgorithmBase
implements AlgorithmInterface
```
Calculates the non-maximum suppression of an image at a scale defined by the user Edges are defined as the union of points for which the gradient magnitude assumes a maximum in the gradient direction. Introduce a local orthonormal coordinate system (u,v) at any point P0, where the v-axis is parallel to the gradient direction at P0, and the u-axis is perpindicular. Iu = sin(a)*Ix - cos(a)*Iy Iv = cos(a)*Ix + sin(a)*Iy cos(a) = Ix/(sqrt(Ix*Ix + Iy*Iy)) evaluated at P0 sin(a) = Iy/(sqrt(Ix*Ix + Iy*Iy)) evaluated at P0 Iu = (Ix*Iy - Ix*Iy)/(sqrt(Ix*Ix + Iy*Iy)) = 0 Iv = (Ix*Ix + Iy*Iy)/(sqrt(Ix*Ix + Iy*Iy)) = sqrt(Ix*Ix + Iy*Iy) Iv*Iv = Ix*Ix + Iy*Iy Ivv = (cos(a)*Ix + sin(a)*Iy)(cos(a)*Ix + sin(a)*Iy) = cos(a)*cos(a)*Ixx + 2*cos(a)*sin(a)*Ixy + sin(a)*sin(a)*Iyy = (Ix*Ix*Ixx + 2*Ix*Iy*Ixy + Iy*Iy*Iyy)/(Ix*Ix + Iy*Iy) Iv*Iv*Ivv = Ix*Ix*Ixx + 2*Ix*Iy*Ixy + Iy*Iy*Iyy Ivvv = (cos(a)*cos(a)*Ixx + 2*cos(a)*sin(a)*Ixy + sin(a)*sin(a)*Iyy)(cos(a)*Ix + sin(a)*Iy) = cos(a)*cos(a)*cos(a)*Ixxx + 3*cos(a)*cos(a)*sin(a)*Ixxy + 3*cos(a)*sin(a)*sin(a)*Ixyy + sin(a)*sin(a)*sin(a)*Iyyy = (Ix*Ix*Ix*Ixxx + 3*Ix*Ix*Iy*Ixxy + 3*Ix*Iy*Iy*Ixyy + Iy*Iy*Iy*Iyyy)/((Ix*Ix + Iy*Iy)**3/2) Iv*Iv*Iv*Ivvv = Ix*Ix*Ix*Ixxx + 3*Ix*Ix*Iy*Ixxy + 3*Ix*Iy*Iy*Ixyy + Iy*Iy*Iy*Iyyy Assuming that the second and third-order directional derivatives of I in the v-direction are not simultaneously zero, a necessary and sufficient condition for P0 to be a gradient maximum in the gradient direction may be stated as: Ivv = 0, Ivvv For 3D a similar derivation: Iv = cos(a)*sin(b)*Ix + sin(a)*sin(b)*Iy + cos(b)*Iz where spherical coordinates are being used cos(a) = Ix/(sqrt(Ix*Ix + Iy*Iy)) evaluated at P0 sin(a) = Iy/(sqrt(Ix*Ix + Iy*Iy)) evaluated at P0 cos(b) = Iz/(sqrt(Ix*Ix + Iy*Iy + Iz*Iz)) evaluated at P0 sin(b) = sqrt(Ix*Ix + Iy*Iy)/(sqrt(Ix*Ix + Iy*Iy + Iz*Iz)) evaluated at P0 Iv = (Ix*Ix + Iy*Iy + Iz*Iz)/(sqrt(Ix*Ix + Iy*Iy + Iz*Iz)) = sqrt(Ix*Ix + Iy*Iy + Iz*Iz) Iv*Iv = Ix*Ix + Iy*Iy + Iz*Iz Ivv = (cos(a)*sin(b)*Ix + sin(a)*sin(b)*Iy + cos(b)*Iz)(cos(a)*sin(b)*Ix + sin(a)*sin(b)*Iy + cos(b)*Iz) = cos(a)*cos(a)*sin(b)*sin(b)*Ixx + 2*cos(a)*sin(a)*sin(b)*sin(b)*Ixy + 2*cos(a)*cos(b)*sin(b)*Ixz + sin(a)*sin(a)*sin(b)*sin(b)*Iyy + 2*sin(a)*cos(b)*sin(b)*Iyz + cos(b)*cos(b)*Izz = (Ix*Ix*Ixx + 2*Ix*Iy*Ixy + 2*Ix*Iz*Ixz + Iy*Iy*Iyy + 2*Iy*Iz*Iyz + Iz*Iz*Izz)/ (Ix*Ix + Iy*Iy + Iz*Iz) Iv*Iv*Ivv = Ix*Ix*Ixx + 2*Ix*Iy*Ixy + 2*Ix*Iz*Ixz + Iy*Iy*Iyy + 2*Iy*Iz*Iyz + Iz*Iz*Izz Ivvv = (cos(a)*cos(a)*sin(b)*sin(b)*Ixx + 2*cos(a)*sin(a)*sin(b)*sin(b)*Ixy + 2*cos(a)*cos(b)*sin(b)*Ixz + sin(a)*sin(a)*sin(b)*sin(b)*Iyy + 2*sin(a)*cos(b)*sin(b)*Iyz + cos(b)*cos(b)*Izz)(cos(a)*sin(b)*Ix + sin(a)*sin(b)*Iy + cos(b)*Iz) = cos(a)*cos(a)*cos(a)*sin(b)*sin(b)*sin(b)*Ixxx + 3*cos(a)*cos(a)*sin(a)*sin(b)*sin(b)*sin(b)*Ixxy + 3*cos(a)*cos(a)*cos(b)*sin(b)*sin(b)*Ixxz + 3*cos(a)*sin(a)*sin(a)*sin(b)*sin(b)*sin(b)*Ixyy + 6*cos(a)*sin(a)*cos(b)*sin(b)*sin(b)*Ixyz + 3*cos(a)*cos(b)*cos(b)*sin(b)*Ixzz + sin(a)*sin(a)*sin(a)*sin(b)*sin(b)*sin(b)*Iyyy + 3*sin(a)*sin(a)*cos(b)*sin(b)*sin(b)*Iyyz + 3*sin(a)*cos(b)*cos(b)*sin(b)*Iyzz + cos(b)*cos(b)*cos(b)*Izzz = (Ix*Ix*Ix*Ixxx + 3*Ix*Ix*Iy*Ixxy + 3*Ix*Ix*Iz*Ixxz + 3*Ix*Iy*Iy*Ixyy + 6*Ix*Iy*Iz*Ixyz + 3*Ix*Iz*Iz*Ixzz + Iy*Iy*Iy*Iyyy + 3*Iy*Iy*Iz*Iyyz + 3*Iy*Iz*Iz*Iyzz + Iz*Iz*Iz*Izzz)/ ((Ix*Ix + Iy*Iy + Iz*Iz)**1.5) Iv*Iv*Iv*Ivvv = Ix*Ix*Ix*Ixxx + 3*Ix*Ix*Iy*Ixxy + 3*Ix*Ix*Iz*Ixxz + 3*Ix*Iy*Iy*Ixyy + 6*Ix*Iy*Iz*Ixyz + 3*Ix*Iz*Iz*Ixzz + Iy*Iy*Iy*Iyyy + 3*Iy*Iy*Iz*Iyyz + 3*Iy*Iz*Iz*Iyzz + Iz*Iz*Iz*Izzz

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 boolean`	`edgeImage`	DOCUMENT ME!
`private boolean`	`entireImage`	DOCUMENT ME!
`private float[]`	`GxData`	DOCUMENT ME!
`private float[]`	`GxxData`	DOCUMENT ME!
`private float[]`	`GxxxData`	DOCUMENT ME!
`private float[]`	`GxxyData`	DOCUMENT ME!
`private float[]`	`GxyData`	DOCUMENT ME!
`private float[]`	`GxyyData`	DOCUMENT ME!
`private float[]`	`GxzData`	DOCUMENT ME!
`private float[]`	`GyData`	DOCUMENT ME!
`private float[]`	`GyyData`	DOCUMENT ME!
`private float[]`	`GyyyData`	DOCUMENT ME!
`private float[]`	`GyzData`	DOCUMENT ME!
`private float[]`	`GzData`	DOCUMENT ME!
`private float[]`	`GzzData`	DOCUMENT ME!
`private float`	`hiThres`	DOCUMENT ME!
`private int[]`	`kExtents`	DOCUMENT ME!
`private float`	`loThres`	DOCUMENT ME!
`private float[]`	`outputBuffer`
`private float[]`	`sigmas`	DOCUMENT ME!
`private ModelImage`	`zXMask`	DOCUMENT ME!

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
`AlgorithmNMSuppression(ModelImage srcImg, float[] sigmas, boolean maskFlag, boolean img25D)`	AlgorithmNMSuppression - Constructor.
`AlgorithmNMSuppression(ModelImage destImg, ModelImage srcImg, float[] sigmas, boolean maskFlag, boolean img25D)`	AlgorithmNMSuppression - Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
`private void`	`calcInPlace2D(int nImages)`	Calculates the non-maximum suppression image and replaces the source image with the new image.
`private void`	`calcInPlace3D()`	Calculates the non-maximum suppression and replaces the source image with the new image.
`private void`	`calcStoreInDest2D(int nImages)`	This function produces the non-maximum suppression of input image.
`private void`	`calcStoreInDest3D()`	This function produces the Non-maximum suppression of input image.
`void`	`finalize()`	Prepares this class for destruction.
`static void`	`genLevelMask(int xDim, int yDim, float[] buffer, java.util.BitSet edgeImage, float level)`	Generates a zero crossing mask for a 2D function sets a Bitset object to 1 is a zero crossing is detected.
`void`	`genZeroXMask(float[] buffer, float[] buffer2)`	Generates a zero crossing mask for a 2D function sets a ModelImage to 1 if a zero crossing is detected.
`ModelImage`	`getZeroXMask()`	Accessor to return mask indicating zero crossings.
`private void`	`makeKernels2D()`	Creates 2D Gaussian derivative kernels.
`private void`	`makeKernels3D()`	Creates 3D Gaussian derivative kernels.
`void`	`runAlgorithm()`	Starts the program.
`void`	`setEdgeOptions(float loThres, float hiThres)`	Call from dialog if you wish to produce edge image.

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
  - edgeImage
```
private boolean edgeImage
```
    DOCUMENT ME!
  - entireImage
```
private boolean entireImage
```
    DOCUMENT ME!
  - GxData
```
private float[] GxData
```
    DOCUMENT ME!
  - GxxData
```
private float[] GxxData
```
    DOCUMENT ME!
  - GxxxData
```
private float[] GxxxData
```
    DOCUMENT ME!
  - GxxyData
```
private float[] GxxyData
```
    DOCUMENT ME!
  - GxyData
```
private float[] GxyData
```
    DOCUMENT ME!
  - GxyyData
```
private float[] GxyyData
```
    DOCUMENT ME!
  - GxzData
```
private float[] GxzData
```
    DOCUMENT ME!
  - GyData
```
private float[] GyData
```
    DOCUMENT ME!
  - GyyData
```
private float[] GyyData
```
    DOCUMENT ME!
  - GyyyData
```
private float[] GyyyData
```
    DOCUMENT ME!
  - GyzData
```
private float[] GyzData
```
    DOCUMENT ME!
  - GzData
```
private float[] GzData
```
    DOCUMENT ME!
  - GzzData
```
private float[] GzzData
```
    DOCUMENT ME!
  - kExtents
```
private int[] kExtents
```
    DOCUMENT ME!
  - loThres
```
private float loThres
```
    DOCUMENT ME!
  - hiThres
```
private float hiThres
```
    DOCUMENT ME!
  - sigmas
```
private float[] sigmas
```
    DOCUMENT ME!
  - zXMask
```
private ModelImage zXMask
```
    DOCUMENT ME!
  - outputBuffer
```
private float[] outputBuffer
```
- Constructor Detail
  - AlgorithmNMSuppression
```
public AlgorithmNMSuppression(ModelImage srcImg,
                              float[] sigmas,
                              boolean maskFlag,
                              boolean img25D)
```
    AlgorithmNMSuppression - Constructor.
    
    Parameters:
    
    srcImg - source image model
    
    sigmas - Gaussian's standard deviations in the each dimension
    
    maskFlag - Flag that indicates that the non-maximum suppression will be calculated for the whole image if equal to true
    
    img25D - Flag, if true, indicates that each slice of the 3D volume should be processed independently. 2D images disregard this flag.
  - AlgorithmNMSuppression
```
public AlgorithmNMSuppression(ModelImage destImg,
                              ModelImage srcImg,
                              float[] sigmas,
                              boolean maskFlag,
                              boolean img25D)
```
    AlgorithmNMSuppression - Constructor.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    sigmas - Gaussian's standard deviations in the each dimension
    
    maskFlag - Flag that indicates that the non-maximum suppression will be calculated for the whole image if equal to true
    
    img25D - Flag, if true, indicates that each slice of the 3D volume should be processed independently. 2D images disregard this flag.
- Method Detail
  - genLevelMask
```
public static void genLevelMask(int xDim,
                                int yDim,
                                float[] buffer,
                                java.util.BitSet edgeImage,
                                float level)
```
    Generates a zero crossing mask for a 2D function sets a Bitset object to 1 is a zero crossing is detected.
    
    Parameters:
    
    xDim - X dimension length
    
    yDim - Y dimension length
    
    buffer - array of data in which to find level crossing
    
    edgeImage - edge map of level crossings
    
    level - level of crossings to find (e.g. zero crossing of the non-maximum suppression)
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - genZeroXMask
```
public void genZeroXMask(float[] buffer,
                         float[] buffer2)
```
    Generates a zero crossing mask for a 2D function sets a ModelImage to 1 if a zero crossing is detected.
    
    Parameters:
    
    buffer - array in which to find zero crossing
    
    buffer2 - array which ensures that zero crossing is only counted if buffer2 value at that position is less than zero
  - getZeroXMask
```
public ModelImage getZeroXMask()
```
    Accessor to return mask indicating zero crossings.
    
    Returns:
    
    - ModelImage of zero crossings ( 2D function 1 = indicates zero crossing
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setEdgeOptions
```
public void setEdgeOptions(float loThres,
                           float hiThres)
```
    Call from dialog if you wish to produce edge image.
    
    Parameters:
    
    loThres - DOCUMENT ME!
    
    hiThres - DOCUMENT ME!
  - calcInPlace2D
```
private void calcInPlace2D(int nImages)
```
    Calculates the non-maximum suppression image and replaces the source image with the new image.
    
    Parameters:
    
    nImages - number of images to be blurred. If 2D image then nImage = 1, if 3D image where each image is to processed independently then nImages equals the number of images in the volume.
  - calcInPlace3D
```
private void calcInPlace3D()
```
    Calculates the non-maximum suppression and replaces the source image with the new image.
  - calcStoreInDest2D
```
private void calcStoreInDest2D(int nImages)
```
    This function produces the non-maximum suppression of input image.
    
    Parameters:
    
    nImages - number of images to be blurred. If 2D image then nImage = 1, if 3D image where each image is to processed independently then nImages equals the number of images in the volume.
  - calcStoreInDest3D
```
private void calcStoreInDest3D()
```
    This function produces the Non-maximum suppression of input image.
  - makeKernels2D
```
private void makeKernels2D()
```
    Creates 2D Gaussian derivative kernels.
  - makeKernels3D
```
private void makeKernels3D()
```
    Creates 3D Gaussian derivative kernels.
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    Description copied from interface: AlgorithmInterface
    
    Called after an algorithm this listener is registered to exits (maybe successfully, maybe not). If the algorithm is run in a separate thread, this call will be made within that thread. If not, this call will be made from that same, shared thread.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - the algorithm which has just completed

Class AlgorithmNMSuppression

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

edgeImage

entireImage

GxData

GxxData

GxxxData

GxxyData

GxyData

GxyyData

GxzData

GyData

GyyData

GyyyData

GyzData

GzData

GzzData

kExtents

loThres

hiThres

sigmas

zXMask

outputBuffer

Constructor Detail

AlgorithmNMSuppression

AlgorithmNMSuppression

Method Detail

genLevelMask

finalize

genZeroXMask

getZeroXMask

runAlgorithm

setEdgeOptions

calcInPlace2D

calcInPlace3D

calcStoreInDest2D

calcStoreInDest3D

makeKernels2D

makeKernels3D

algorithmPerformed