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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmSnake
extends AlgorithmBase
```
Snake-like algorithm deriviative. The algorithm is supplied a polygon (VOI - contour) and that polygon is allowed to evolve to the 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 the 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, AlgorithmBSnake

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`	`ANY_DIR`	Indicates boundary can move in or out.
`private int`	`boundaryIterations`	Maximum number of snake iterations.
`private int`	`evolveDirection`	Indicates boundary how the VOI boundary can move - in and/or out.
`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.
`static int`	`IN_DIR`	Indicates boundary can move in.
`private int[]`	`kExtents`	Dimensionality of the kernel.
`static int`	`OUT_DIR`	Indicates boundary can move out.
`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 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 float`	`smoothness`	The maximum angle we want to have between points in the result VOI.
`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
`AlgorithmSnake(ModelImage _srcImg, float[] _sigmas, int _boundaryIterations, float _smoothness, VOI srcVOI, int boundDir)`	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.
`private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector2f>`	`cleanLine(float[] xPts, float[] yPts)`	Removes points (vectors) that form sharp angles (i.e. smoothes boudnary) Also adds points separated by some distance and removes adjacent points
`private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>`	`cleanLine(float[] xPts, float[] yPts, float[] zPts)`
`private double`	`distance(float x1, float x2, float y1, float y2)`	Calculates the euclidian distance between two points.
`private double`	`distance(int x1, int x2, int y1, int y2)`	Calculates the euclidian distance between two points.
`void`	`finalize()`	Prepares this class for destruction.
`VOI`	`getResultVOI()`	Returns the resultant VOI.
`private void`	`makeKernels2D()`	Makes derivative kernels to be used in the calculation of the gradient magnitude.
`private void`	`makeKernels3D()`	Makes 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()`	run - starts the snake algorithm.
`private float`	`runSnake(float[] xPoints, float[] yPoints, float[] zPoints, float[] image, VOIBase contour)`
`private float`	`runSnake(float[] xPoints, float[] yPoints, float[] image, java.awt.Polygon resultGon)`	Actual function that evolves the boundary by moving normal to the boundary.
`private void`	`setPoints(float[] xPoints, float[] yPoints, float[] zPoints, VOIBase contour)`
`private void`	`setPoints(float[] xPoints, float[] yPoints, java.awt.Polygon gon)`	Takes the polygon and forms two special arrays for use in runSnake.
`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 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
  - ANY_DIR
```
public static final int ANY_DIR
```
    Indicates boundary can move in or out.
    
    See Also:
    
    Constant Field Values
  - IN_DIR
```
public static final int IN_DIR
```
    Indicates boundary can move in.
    
    See Also:
    
    Constant Field Values
  - OUT_DIR
```
public static final int OUT_DIR
```
    Indicates boundary can move out.
    
    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.
  - evolveDirection
```
private int evolveDirection
```
    Indicates boundary how the VOI boundary can move - in and/or out.
  - 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.
  - smoothness
```
private float smoothness
```
    The maximum angle we want to have between points in the result VOI.
  - srcImage
```
private ModelImage srcImage
```
    Source image.
  - srcVOI
```
private VOI srcVOI
```
    The initial VOI to initialize the evolution process.
- Constructor Detail
  - AlgorithmSnake
```
public AlgorithmSnake(ModelImage _srcImg,
                      float[] _sigmas,
                      int _boundaryIterations,
                      float _smoothness,
                      VOI srcVOI,
                      int boundDir)
```
    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
    
    _smoothness - the boundary smoothness parameter
    
    srcVOI - VOI that is to be evolved
    
    boundDir - indicates the boundary direction (in and/or out)
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultVOI
```
public VOI getResultVOI()
```
    Returns the resultant VOI.
    
    Returns:
    
    resultant VOI that has localized to the boundaries of the object
  - runAlgorithm
```
public void runAlgorithm()
```
    run - 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 orginal 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.
  - cleanLine
```
private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector2f> cleanLine(float[] xPts,
                                                                                 float[] yPts)
```
    Removes points (vectors) that form sharp angles (i.e. smoothes boudnary) Also adds points separated by some distance and removes adjacent points
    
    Parameters:
    
    xPts - x coords of points that define a contour
    
    yPts - y coords of points that define a contour
    
    Returns:
    
    an ordered list of the points along the cleaned-up line
  - cleanLine
```
private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> cleanLine(float[] xPts,
                                                                                 float[] yPts,
                                                                                 float[] zPts)
```
  - distance
```
private double distance(int x1,
                        int x2,
                        int y1,
                        int y2)
```
    Calculates the euclidian distance between two points.
    
    Parameters:
    
    x1 - first x coord.
    
    x2 - seconde x coord.
    
    y1 - first y1 coord.
    
    y2 - seconde y2 coord.
    
    Returns:
    
    the distance between the points (x1,y1) and (x2,y2)
  - distance
```
private double distance(float x1,
                        float x2,
                        float y1,
                        float y2)
```
    Calculates the euclidian distance between two points.
    
    Parameters:
    
    x1 - first x coord.
    
    x2 - seconde x coord.
    
    y1 - first y1 coord.
    
    y2 - seconde y2 coord.
    
    Returns:
    
    the distance between the points (x1,y1) and (x2,y2)
  - makeKernels2D
```
private void makeKernels2D()
```
    Makes derivative kernels to be used in the calculation of the gradient magnitude.
  - makeKernels3D
```
private void makeKernels3D()
```
    Makes derivative kernels to be used in the calculation of the gradient magnitude.
  - runSnake
```
private float runSnake(float[] xPoints,
                       float[] yPoints,
                       float[] image,
                       java.awt.Polygon resultGon)
```
    Actual function that evolves the boundary by moving normal to 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 contour)
```
  - propDown
```
private void propDown(VOIContour resultContour,
                      VOI resultVOI,
                      float baseEnergy,
                      int baseNPts)
```
  - propUp
```
private void propUp(VOIContour resultContour,
                    VOI resultVOI,
                    float baseEnergy,
                    int baseNPts)
```
  - setPoints
```
private void setPoints(float[] xPoints,
                       float[] yPoints,
                       java.awt.Polygon gon)
```
    Takes the polygon and forms two special arrays for use in runSnake.
    
    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)
```

Class AlgorithmSnake

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

ANY_DIR

IN_DIR

OUT_DIR

PROP_THRESHOLD

boundaryIterations

evolveDirection

GxData

GyData

GzData

kExtents

propagationType

resultVOI

sigmas

smoothness

srcImage

srcVOI

Constructor Detail

AlgorithmSnake

Method Detail

finalize

getResultVOI

runAlgorithm

setPropagation

calc2D

calc3D

cleanLine

cleanLine

distance

distance

makeKernels2D

makeKernels3D

runSnake

runSnake

propDown

propUp

setPoints

setPoints