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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmBSnake
extends AlgorithmBase
```
Snake-like algorithm derivative using BSplines. The algorithm is supplied a polygon (VOI - contour) and that polygon is allowed to evolve to edge of the object generated by calculating the gradient magnitude (i.e. the energy function) at scale define by the user. The user/programmer supplies the sigmas (scales) at which to calculate the gradient magnitude. A large scale slows the snake and causes the snake to conform to large scale structure. A small sigma value causes the snake to conform to the small scale structure is therefore more sensitive to noise. The three-dimensional version is really a two-and-half dimensional algorithm where resultant contour in a slice is projected into the adjacent slice and is used as an initialization to the evolution in the new slice.

Version:

0.1 Feb 11, 1998

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

AlgorithmBSpline, GenerateGaussian, AlgorithmVOISimplexOpt, AlgorithmSnake

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 int`	`boundaryIterations`	Maximum number of snake iterations.
`private float[]`	`GxData`	Storage location of the first derivative of the Gaussian in the X direction.
`private float[]`	`GyData`	Storage location of the first derivative of the Gaussian in the Y direction.
`private float[]`	`GzData`	Storage location of the first derivative of the Gaussian in the Z direction.
`private int[]`	`kExtents`	Dimensionality of the kernel.
`static int`	`PROP_ALL`	Propagate the source VOI to slices above and below its current slice.
`static int`	`PROP_NEXT`	Propagate the source VOI to slices above its current slice in the volume.
`static int`	`PROP_PREV`	Propagate the source VOI to slices below its current slice in the volume.
`static int`	`PROP_SINGLE`	Do not propagate the source VOI to any slices (2D).
`private static float`	`PROP_THRESHOLD`	The maximum ratio of change in the energy under the VOI after propagation.
`private int`	`propagationType`	The VOI propagation mode to use.
`private VOI`	`resultVOI`	The resultant polygon and the evolution has completed.
`private float[]`	`sigmas`	Standard deviations of the Gaussian used to calculate the kernels.
`private ModelImage`	`srcImage`	Source image.
`private VOI`	`srcVOI`	The initial VOI to initialize the evolution process.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmBSnake(ModelImage srcImg, float[] sigmas, int boundaryIterations, VOI srcVOI)`	Set up the snake algorithm so that it can be run.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calc2D()`	Prepares the data and runs the algorithm for a 2D image.
`private void`	`calc3D()`	Prepares the data and runs the algorithm for a 3D image.
`void`	`finalize()`	Prepares this class for destruction.
`VOI`	`getResultVOI()`	Accessor that returns the resultant VOI.
`private void`	`makeKernels2D()`	Makes 2D derivative kernels to be used in the calculation of the gradient magnitude.
`private void`	`makeKernels3D()`	Makes 3D derivative kernels to be used in the calculation of the gradient magnitude.
`private void`	`propDown(VOIContour resultContour, VOI resultVOI, float baseEnergy, int baseNPts)`
`private void`	`propUp(VOIContour resultContour, VOI resultVOI, float baseEnergy, int baseNPts)`
`void`	`runAlgorithm()`	Starts the snake algorithm.
`private float`	`runSnake(float[] xPoints, float[] yPoints, float[] zPoints, float[] image, VOIBase result)`	Actual function that evolves the boundary.
`private float`	`runSnake(float[] xPoints, float[] yPoints, float[] image, java.awt.Polygon resultGon)`	Actual function that evolves the boundary.
`private void`	`setPoints(float[] xPoints, float[] yPoints, float[] zPoints, VOIBase contour)`	Takes the polygon and forms two special arrays for use in the Bspline.
`private void`	`setPoints(float[] xPoints, float[] yPoints, java.awt.Polygon gon)`	Takes the polygon and forms two special arrays for use in the Bspline.
`void`	`setPropagation(int type)`	Sets the propagation type.

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
  - PROP_SINGLE
```
public static final int PROP_SINGLE
```
    Do not propagate the source VOI to any slices (2D).
    
    See Also:
    
    Constant Field Values
  - PROP_NEXT
```
public static final int PROP_NEXT
```
    Propagate the source VOI to slices above its current slice in the volume.
    
    See Also:
    
    Constant Field Values
  - PROP_PREV
```
public static final int PROP_PREV
```
    Propagate the source VOI to slices below its current slice in the volume.
    
    See Also:
    
    Constant Field Values
  - PROP_ALL
```
public static final int PROP_ALL
```
    Propagate the source VOI to slices above and below its current slice.
    
    See Also:
    
    Constant Field Values
  - PROP_THRESHOLD
```
private static final float PROP_THRESHOLD
```
    The maximum ratio of change in the energy under the VOI after propagation.
    
    See Also:
    
    Constant Field Values
  - boundaryIterations
```
private int boundaryIterations
```
    Maximum number of snake iterations.
  - GxData
```
private float[] GxData
```
    Storage location of the first derivative of the Gaussian in the X direction.
  - GyData
```
private float[] GyData
```
    Storage location of the first derivative of the Gaussian in the Y direction.
  - GzData
```
private float[] GzData
```
    Storage location of the first derivative of the Gaussian in the Z direction.
  - kExtents
```
private int[] kExtents
```
    Dimensionality of the kernel.
  - propagationType
```
private int propagationType
```
    The VOI propagation mode to use.
  - resultVOI
```
private VOI resultVOI
```
    The resultant polygon and the evolution has completed.
  - sigmas
```
private float[] sigmas
```
    Standard deviations of the Gaussian used to calculate the kernels.
  - srcImage
```
private ModelImage srcImage
```
    Source image.
  - srcVOI
```
private VOI srcVOI
```
    The initial VOI to initialize the evolution process.
- Constructor Detail
  - AlgorithmBSnake
```
public AlgorithmBSnake(ModelImage srcImg,
                       float[] sigmas,
                       int boundaryIterations,
                       VOI srcVOI)
```
    Set up the snake algorithm so that it can be run.
    
    Parameters:
    
    srcImg - 2D or 3D source image
    
    sigmas - describe the scale of the Gaussian in each dimension
    
    boundaryIterations - maximum number of snake iterations
    
    srcVOI - VOI that is to be evolved
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultVOI
```
public VOI getResultVOI()
```
    Accessor that returns the resultant VOI.
    
    Returns:
    
    resultant VOI that has localized to the boundaries of the object
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the snake algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setPropagation
```
public void setPropagation(int type)
```
    Sets the propagation type.
    
    Parameters:
    
    type - if PROP_ALL, result contour from a slice is propagated to the adjacent slice and used to initialize the snake algorithm for that slice. If PROP_NEXT, result contour from the original slice is propagated to the next slice and used to initialize the snake algorithm for that slice. If PROP_PREV, result contour from the original slice is propagated to the previous slice. If PROP_SINGLE, the snake algorithm stops after optimizing the boundary in the present slice.
  - calc2D
```
private void calc2D()
```
    Prepares the data and runs the algorithm for a 2D image.
  - calc3D
```
private void calc3D()
```
    Prepares the data and runs the algorithm for a 3D image.
  - makeKernels2D
```
private void makeKernels2D()
```
    Makes 2D derivative kernels to be used in the calculation of the gradient magnitude.
  - makeKernels3D
```
private void makeKernels3D()
```
    Makes 3D derivative kernels to be used in the calculation of the gradient magnitude.
  - propDown
```
private void propDown(VOIContour resultContour,
                      VOI resultVOI,
                      float baseEnergy,
                      int baseNPts)
```
  - propUp
```
private void propUp(VOIContour resultContour,
                    VOI resultVOI,
                    float baseEnergy,
                    int baseNPts)
```
  - runSnake
```
private float runSnake(float[] xPoints,
                       float[] yPoints,
                       float[] image,
                       java.awt.Polygon resultGon)
```
    Actual function that evolves the boundary.
    
    Parameters:
    
    xPoints - x coordinates that describe the contour
    
    yPoints - y coordinates that describe the contour
    
    image - image data
    
    resultGon - resultant polygon
    
    Returns:
    
    the sum of the energy along the boundary of the resultGon
  - runSnake
```
private float runSnake(float[] xPoints,
                       float[] yPoints,
                       float[] zPoints,
                       float[] image,
                       VOIBase result)
```
    Actual function that evolves the boundary.
    
    Parameters:
    
    xPoints - x coordinates that describe the contour
    
    yPoints - y coordinates that describe the contour
    
    image - image data
    
    resultGon - resultant polygon
    
    Returns:
    
    the sum of the energy along the boundary of the resultGon
  - setPoints
```
private void setPoints(float[] xPoints,
                       float[] yPoints,
                       java.awt.Polygon gon)
```
    Takes the polygon and forms two special arrays for use in the Bspline.
    
    Parameters:
    
    xPoints - storage location of array of x coord. points
    
    yPoints - storage location array of y coord. points
    
    gon - initial polygon
  - setPoints
```
private void setPoints(float[] xPoints,
                       float[] yPoints,
                       float[] zPoints,
                       VOIBase contour)
```
    Takes the polygon and forms two special arrays for use in the Bspline.
    
    Parameters:
    
    xPoints - storage location of array of x coord. points
    
    yPoints - storage location array of y coord. points
    
    gon - initial polygon

Class AlgorithmBSnake

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

PROP_SINGLE

PROP_NEXT

PROP_PREV

PROP_ALL

PROP_THRESHOLD

boundaryIterations

GxData

GyData

GzData

kExtents

propagationType

resultVOI

sigmas

srcImage

srcVOI

Constructor Detail

AlgorithmBSnake

Method Detail

finalize

getResultVOI

runAlgorithm

setPropagation

calc2D

calc3D

makeKernels2D

makeKernels3D

propDown

propUp

runSnake

runSnake

setPoints

setPoints