gov.nih.mipav.model.algorithms.AlgorithmSnake

All Implemented Interfaces:: ActionListener, WindowListener, Runnable, 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:

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread
Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler
Field Summary

Fields

Modifier and Type

Field

Description

static final 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 final int

IN_DIR

Indicates boundary can move in.

private int[]

kExtents

Dimensionality of the kernel.

static final int

OUT_DIR

Indicates boundary can move out.

static final int

PROP_ALL

Propagate the source VOI to slices above and below its current slice.

static final int

PROP_NEXT

Propagate the source VOI to slices above its current slice in the volume.

static final int

PROP_PREV

Propagate the source VOI to slices below its current slice in the volume.

static final int

PROP_SINGLE

Do not propagate the VOI to any slices (2D).

private static final 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

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 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 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, 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, 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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details
- 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 Details
- 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 Details
- 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 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 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, 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, 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 Details

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 Details

AlgorithmSnake

Method Details

finalize

getResultVOI

runAlgorithm

setPropagation

calc2D

calc3D

cleanLine

cleanLine

distance

distance

makeKernels2D

makeKernels3D

runSnake

runSnake

propDown

propUp

setPoints

setPoints