gov.nih.mipav.model.algorithms.AlgorithmBSnake

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

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

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 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 source 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 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

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, 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, 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, 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 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 Details
- 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 Details
- 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, 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, 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 Details

PROP_SINGLE

PROP_NEXT

PROP_PREV

PROP_ALL

PROP_THRESHOLD

boundaryIterations

GxData

GyData

GzData

kExtents

propagationType

resultVOI

sigmas

srcImage

srcVOI

Constructor Details

AlgorithmBSnake

Method Details

finalize

getResultVOI

runAlgorithm

setPropagation

calc2D

calc3D

makeKernels2D

makeKernels3D

propDown

propUp

runSnake

runSnake

setPoints

setPoints