gov.nih.mipav.model.algorithms
Class AlgorithmCellTrackingAGVF

java.lang.Object
  java.lang.Thread
      gov.nih.mipav.model.algorithms.AlgorithmBase
          gov.nih.mipav.model.algorithms.AlgorithmAGVF
              gov.nih.mipav.model.algorithms.AlgorithmCellTrackingAGVF

All Implemented Interfaces:

AlgorithmInterface, ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmCellTrackingAGVF
extends AlgorithmAGVF

Active Contour class optimized for Cell Tacking, based on the following paper:

"Active Contours for Cell Tracking", by Nilanjan Ray and Scott T. Acton. 5th IEEE Southwest Symposium on Image Analysis and Interpretation (SSIAI'02), 2002.

Most functionality is inherited from AlgorithmAGVF, the runSnake function is optimized with the following constraints for cell-tracking:

1). Constrained Gradient Vector Flow: using a Dirichlet boundary condition, the gradient inside the initial user-defined snake is set to a user-defined velocity vector.

2). Shape-size constraint: the shape and size of the snake is constrained to be circular with a user-defined cell radius.

3). Implicit Resampling: the points along the snake curve are minimized such that they maintain an equal distance between points.

The gradient vector flow is calculated for each frame in the image sequence. Once the GVF is calculated, the points inside the initial snake (either the user-defined snake for frame 0, or the snake for the previous frame) are set to the velocity vector. runSnake then minimizes the shape-size and resampling constraints for the new GVF, based on the user-defined constraint contributions (see the Lambda member variable). The output snake is used as the initial guess for the next frame in the image sequence.

See Also:

AlgorithmAGVF, GenerateGaussian

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmAGVF

boundaryIterations, extents, xDim, yDim, zDim

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

AlgorithmCellTrackingAGVF(ModelImage resultImage, ModelImage srcImg, float[] sigmas, int gvfIterations, int boundaryIterations, float k, float smoothness, VOI srcVOI, boolean do25D, float radiusConstraint, float shapeConstraint, float sizeConstraint, float resamplingConstraint, boolean bDilate, float fDilation, float fDx, float fDy)
Creates a new AlgorithmCellTrackingAGVF object.

Method Summary

void	finalize() Prepares this class for destruction.
protected void	runSnake(float[] xPoints, float[] yPoints, float[] u, float[] v, Polygon resultGon) Actual function that evolves the boundary.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmAGVF

algorithmPerformed, cleanLine, cleanup, getBilinear, getResultVOI, runAlgorithm, setPropagation

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculatePrincipleAxis, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AlgorithmCellTrackingAGVF

public AlgorithmCellTrackingAGVF(ModelImage resultImage,
                                 ModelImage srcImg,
                                 float[] sigmas,
                                 int gvfIterations,
                                 int boundaryIterations,
                                 float k,
                                 float smoothness,
                                 VOI srcVOI,
                                 boolean do25D,
                                 float radiusConstraint,
                                 float shapeConstraint,
                                 float sizeConstraint,
                                 float resamplingConstraint,
                                 boolean bDilate,
                                 float fDilation,
                                 float fDx,
                                 float fDy)

Creates a new AlgorithmCellTrackingAGVF object.

Parameters:

resultImage - image of GVF field magnitude

srcImg - 2D or 3D source image

sigmas - describe the scale of the gaussian in each dimension

gvfIterations - iterations in calculating GVF field

boundaryIterations - iterations in calculating boundary

k - GVF constant

smoothness - factor for smoothing points on contour (see AlgorithmAGVF)

srcVOI - VOI that is to be evolved

do25D - only applies to 3D, if true do slice by slice

radiusConstraint - The user-defined cell radius

shapeConstraint - The contribution of the shape constraint in the minimization

sizeConstraint - The contribution of the size constraint in the minimization

resamplingConstraint - The contribution of the resampling constraint in the minimization

bDilate - Whether to dilate the cell radius before optimizing

fDilation - dilation factor (multiple of the cell radius)

fDx - The initial cell velocity (x-component)

fDy - The initial cell velocity (y-component)

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmAGVF

runSnake

protected void runSnake(float[] xPoints,
                        float[] yPoints,
                        float[] u,
                        float[] v,
                        Polygon resultGon)

Actual function that evolves the boundary.

Overrides:

runSnake in class AlgorithmAGVF

Parameters:

xPoints - x coordinates that describe the contour

yPoints - y coordinates that describe the contour

u - x component of the GVF

v - y component of the GVF

resultGon - resultant polygon