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, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private float[]`	`m_afX`	Previous snake results (X-position):.
`private float[]`	`m_afY`	Previous snake results (Y-position):.
`private boolean`	`m_bDilate`	whether or not to dilate the cell contour before solving for the cell on the next frame (dilation helps capture cells that are moving fast).
`private boolean`	`m_bUseVelocity`	boolean when true, use the velocity vector:.
`private float`	`m_fDilationFactor`	Amount to dilate the cell (multiple of the cell radius).
`private float`	`m_fK`	expected cell radius:.
`private float`	`m_fLambda1`	Constraint factor for the cell shape:.
`private float`	`m_fLambda2`	Constraint factor for the cell size:.
`private float`	`m_fLambda3`	Constraint factor for sampling:.
`private float`	`m_fTolerance`	tolerance factor for snake evolution:.
`private Jama.Matrix`	`m_kC`	Cos matrix: = cos( 2pii/n).
`private Jama.Matrix`	`m_kG`	G Matrix, equation 19:.
`private Jama.Matrix`	`m_kH`	H Matrix, equation 19:.
`private java.awt.Polygon`	`m_kPreviousSnake`	Previous snake polygon:.
`private Jama.Matrix`	`m_kQ`	Q Matrix, equation 24 (inverse calculated once per image sequence on the inital frame):.
`private Jama.Matrix`	`m_kS`	Sin matrix: = sin( 2pii/n).
`private WildMagic.LibFoundation.Mathematics.Vector2f`	`m_kVelocity`	Velocity vector (either the initial user-defined guess, or the calculated velocity (new snake center - previous snake center):.

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, separable, srcImage, threadStopped

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

Constructor Summary

Constructors
Constructor	Description
`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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for destruction.
`private void`	`initSnakeConstants(int iNPoints)`	Initializes the H, G, and Q matrices once per image sequence on the first frame.
`protected void`	`runSnake(float[] xPoints, float[] yPoints, float[] u, float[] v, java.awt.Polygon resultGon)`	Actual function that evolves the boundary.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmAGVF
algorithmPerformed, cleanLine, cleanup, getBilinear, getResultVOI, runAlgorithm, runSnake, setPropagation

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
  - m_afX
```
private float[] m_afX
```
    Previous snake results (X-position):.
  - m_afY
```
private float[] m_afY
```
    Previous snake results (Y-position):.
  - m_bDilate
```
private boolean m_bDilate
```
    whether or not to dilate the cell contour before solving for the cell on the next frame (dilation helps capture cells that are moving fast).
  - m_bUseVelocity
```
private boolean m_bUseVelocity
```
    boolean when true, use the velocity vector:.
  - m_fDilationFactor
```
private float m_fDilationFactor
```
    Amount to dilate the cell (multiple of the cell radius).
  - m_fK
```
private float m_fK
```
    expected cell radius:.
  - m_fLambda1
```
private float m_fLambda1
```
    Constraint factor for the cell shape:.
  - m_fLambda2
```
private float m_fLambda2
```
    Constraint factor for the cell size:.
  - m_fLambda3
```
private float m_fLambda3
```
    Constraint factor for sampling:.
  - m_fTolerance
```
private float m_fTolerance
```
    tolerance factor for snake evolution:.
  - m_kC
```
private Jama.Matrix m_kC
```
    Cos matrix: = cos( 2*pi*i/n).
  - m_kG
```
private Jama.Matrix m_kG
```
    G Matrix, equation 19:.
  - m_kH
```
private Jama.Matrix m_kH
```
    H Matrix, equation 19:.
  - m_kPreviousSnake
```
private java.awt.Polygon m_kPreviousSnake
```
    Previous snake polygon:.
  - m_kQ
```
private Jama.Matrix m_kQ
```
    Q Matrix, equation 24 (inverse calculated once per image sequence on the inital frame):.
  - m_kS
```
private Jama.Matrix m_kS
```
    Sin matrix: = sin( 2*pi*i/n).
  - m_kVelocity
```
private WildMagic.LibFoundation.Mathematics.Vector2f m_kVelocity
```
    Velocity vector (either the initial user-defined guess, or the calculated velocity (new snake center - previous snake center):.
- 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,
                        java.awt.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
  - initSnakeConstants
```
private void initSnakeConstants(int iNPoints)
```
    Initializes the H, G, and Q matrices once per image sequence on the first frame. The matrix inverse only has to be computed once.
    
    Parameters:
    
    iNPoints - the number of points in the initial VOI (snake)

Class AlgorithmCellTrackingAGVF

Nested Class Summary

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

Field Summary

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

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.AlgorithmAGVF

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

m_afX

m_afY

m_bDilate

m_bUseVelocity

m_fDilationFactor

m_fK

m_fLambda1

m_fLambda2

m_fLambda3

m_fTolerance

m_kC

m_kG

m_kH

m_kPreviousSnake

m_kQ

m_kS

m_kVelocity

Constructor Detail

AlgorithmCellTrackingAGVF

Method Detail

finalize

runSnake

initSnakeConstants