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

All Implemented Interfaces:

AlgorithmInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmObjectExtractor
extends AlgorithmBase
implements AlgorithmInterface
```
A class for segmenting objects. The algorithm is partially based on the paper:
```
     BET: Brain Extraction Tool

     Stephen M. Smith

     FMRIB Technical Report TR00SMS2

     Oxford Centre for Functional Magnetic Resonance Imaging of the Brain

 
```
See the document BrainExtraction.pdf for a detailed description of the algorithm as implemented in this class. A few modifications to the original algorithm were made.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`protected class`	`AlgorithmObjectExtractor.Edge`	A representation of an edge for the vertex-edge-triangle table.
`private class`	`AlgorithmObjectExtractor.UnorderedSetInt`	An unordered set of 'int' stored in an array.

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[]`	`box`	DOCUMENT ME!
`protected float`	`c1Factor`	DOCUMENT ME!
`protected float`	`c3Factor`	DOCUMENT ME!
`private int[]`	`direction`	DOCUMENT ME!
`private float[]`	`gvfBuffer`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`private int`	`iSubdivisions`	DOCUMENT ME!
`protected float[]`	`m_afCurvature`	DOCUMENT ME!
`protected float[]`	`m_afImage`	The 3D MRI image stored as a 1D array.
`protected float[]`	`m_afLength`	DOCUMENT ME!
`protected int[]`	`m_aiConnect`	DOCUMENT ME!
`protected byte[]`	`m_aiMask`	object mask creation.
`protected AlgorithmObjectExtractor.UnorderedSetInt[]`	`m_akAdjacent`	DOCUMENT ME!
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akSNormal`	DOCUMENT ME!
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akSTangent`	DOCUMENT ME!
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akVertex`	DOCUMENT ME!
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akVMean`	DOCUMENT ME!
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akVNormal`	DOCUMENT ME!
`protected float`	`m_fEParam`	DOCUMENT ME!
`protected float`	`m_fFParam`	DOCUMENT ME!
`protected float`	`m_fMeanEdgeLength`	update parameters.
`protected float`	`m_fRayDelta`	DOCUMENT ME!
`protected float`	`m_fReductionX`	DOCUMENT ME!
`protected float`	`m_fReductionY`	DOCUMENT ME!
`protected float`	`m_fReductionZ`	DOCUMENT ME!
`protected float`	`m_fStiffness`	DOCUMENT ME!
`protected float`	`m_fXDelta`	The size of a voxel, in voxel units.
`protected float`	`m_fYDelta`	The size of a voxel, in voxel units.
`protected float`	`m_fZDelta`	The size of a voxel, in voxel units.
`protected int`	`m_iDMax`	DOCUMENT ME!
`protected int`	`m_iEQuantity`	DOCUMENT ME!
`protected int`	`m_iMedianIntensity`	DOCUMENT ME!
`protected int`	`m_iQuantity`	The MRI image bounds and quantity of voxels.
`protected int`	`m_iTQuantity`	DOCUMENT ME!
`protected int`	`m_iVQuantity`	mesh data.
`protected int`	`m_iXBound`	The MRI image bounds and quantity of voxels.
`protected int`	`m_iYBound`	The MRI image bounds and quantity of voxels.
`protected int`	`m_iZBound`	The MRI image bounds and quantity of voxels.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`m_kCenter`	initial ellipsoid parameters.
`protected java.util.HashMap<AlgorithmObjectExtractor.Edge,java.lang.Integer>`	`m_kEMap`	DOCUMENT ME!
`protected WildMagic.LibFoundation.Mathematics.Matrix3f`	`m_kRotate`	DOCUMENT ME!
`private float`	`oldUVal`	DOCUMENT ME!
`private float`	`oldVVal`	DOCUMENT ME!
`private float`	`oldWVal`	DOCUMENT ME!
`private boolean`	`onlyInit`	DOCUMENT ME!
`private float[]`	`outputBuffer`
`private boolean`	`saveGVF`	DOCUMENT ME!
`private float[]`	`startLocation`	DOCUMENT ME!
`protected WildMagic.LibGraphics.SceneGraph.TriMesh`	`triMesh`	DOCUMENT ME!
`private float[]`	`uVal`	DOCUMENT ME!
`private VOI`	`voi`	DOCUMENT ME!
`private float[]`	`vVal`	DOCUMENT ME!
`private float[]`	`wVal`	DOCUMENT ME!

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
`AlgorithmObjectExtractor(ModelImage srcImg, VOI voi, boolean justInit, boolean saveGVF, WildMagic.LibGraphics.SceneGraph.TriMesh triMesh, float[] uVal, float[] vVal, float[] wVal)`	Create an extractor for segmenting an object from an image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
`private void`	`calcGradMag()`	DOCUMENT ME!
`private void`	`calcGVF3D()`	Calculate GVF from 3D image buffer.
`protected void`	`computeMeanEdgeLength()`	Compute the average length of all the edges in the triangle mesh.
`protected void`	`computeVertexInformation()`	Let V[i] be a vertex in the triangle mesh.
`protected void`	`computeVertexNormals()`	Compute the vertex normals of the triangle mesh.
`protected void`	`estimateEllipsoid()`	Approximate the brain surface by an ellipsoid.
`void`	`extractObject()`	The segmentation function.
`void`	`finalize()`	Prepares this class for destruction.
`protected void`	`floodFill(int iX, int iY, int iZ)`	Identify voxels enclosed by the brain surface by using a flood fill.
`protected void`	`generateEllipsoidMesh()`	Tessellate a unit sphere centered at the origin.
`int`	`getDilationSize()`	Get the dilation size for dilating the voxelized object surface obtained by rasterizing the triangle mesh.
`protected int`	`getIndex(int iX, int iY, int iZ)`	A convenience function for mapping the 3D voxel position (iX,iY,iZ) to a 1D array index.
`protected void`	`getInsideVoxels()`	Identify all voxels that are inside or on the mesh that represents the brain surface.
`protected int`	`getIntersectX(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f kV2, int iY, int iZ)`	Compute the point of intersection between a line (0,iY,iZ)+t(1,0,0) and the triangle defined by the three input points.
`protected int`	`getIntersectY(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f kV2, int iX, int iZ)`	Compute the point of intersection between a line (iX,0,iZ)+t(0,1,0) and the triangle defined by the three input points.
`protected int`	`getIntersectZ(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f kV2, int iX, int iY)`	Compute the point of intersection between a line (iX,iY,0)+t(0,0,1) and the triangle defined by the three input points.
`byte[]`	`getObjectMask()`	Get the 3D image that represents the extracted object.
`float`	`getRayDelta()`	Get the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`float`	`getReductionX()`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`float`	`getReductionY()`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`float`	`getReductionZ()`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`float`	`getStiffness()`	Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution.
`float`	`getTriLinear(float x, float y, float z, float[] buffer)`	DOCUMENT ME!
`void`	`runAlgorithm()`	Starts the program.
`protected void`	`saveMesh(boolean flip)`	Internal support to write vertices, normals, and connectivity indices to the file.
`void`	`setDilationSize(int iDMax)`	Set the dilation size for dilating the voxelized object surface obtained by rasterizing the triangle mesh.
`void`	`setJustIntial(boolean flag)`	Indicates if surface evolution should be skipped.
`void`	`setRayDelta(float fRayDelta)`	Set the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`void`	`setReductionX(float fReduction)`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`void`	`setReductionY(float fReduction)`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`void`	`setReductionZ(float fReduction)`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`void`	`setStiffness(float fStiffness)`	Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution.
`protected float`	`update2(int i)`	Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction.
`protected void`	`update3(int i)`	Compute the coefficient of the vertex normal for the update of the mesh vertex V[i] in the VNormal[i] direction.
`void`	`updateMesh()`	The heart of the segmentation.

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
  - c1Factor
```
protected float c1Factor
```
    DOCUMENT ME!
  - c3Factor
```
protected float c3Factor
```
    DOCUMENT ME!
  - m_afCurvature
```
protected float[] m_afCurvature
```
    DOCUMENT ME!
  - m_afImage
```
protected float[] m_afImage
```
    The 3D MRI image stored as a 1D array. The mapping from (x,y,z) to 1D is: index = x + xbound*(y + ybound*z).
  - m_afLength
```
protected float[] m_afLength
```
    DOCUMENT ME!
  - m_aiConnect
```
protected int[] m_aiConnect
```
    DOCUMENT ME!
  - m_aiMask
```
protected byte[] m_aiMask
```
    object mask creation.
  - m_akAdjacent
```
protected AlgorithmObjectExtractor.UnorderedSetInt[] m_akAdjacent
```
    DOCUMENT ME!
  - m_akSNormal
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akSNormal
```
    DOCUMENT ME!
  - m_akSTangent
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akSTangent
```
    DOCUMENT ME!
  - m_akVertex
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akVertex
```
    DOCUMENT ME!
  - m_akVMean
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akVMean
```
    DOCUMENT ME!
  - m_akVNormal
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akVNormal
```
    DOCUMENT ME!
  - m_fEParam
```
protected float m_fEParam
```
    DOCUMENT ME!
  - m_fFParam
```
protected float m_fFParam
```
    DOCUMENT ME!
  - m_fMeanEdgeLength
```
protected float m_fMeanEdgeLength
```
    update parameters.
  - m_fRayDelta
```
protected float m_fRayDelta
```
    DOCUMENT ME!
  - m_fReductionX
```
protected float m_fReductionX
```
    DOCUMENT ME!
  - m_fReductionY
```
protected float m_fReductionY
```
    DOCUMENT ME!
  - m_fReductionZ
```
protected float m_fReductionZ
```
    DOCUMENT ME!
  - m_fStiffness
```
protected float m_fStiffness
```
    DOCUMENT ME!
  - m_fXDelta
```
protected float m_fXDelta
```
    The size of a voxel, in voxel units.
  - m_fYDelta
```
protected float m_fYDelta
```
    The size of a voxel, in voxel units.
  - m_fZDelta
```
protected float m_fZDelta
```
    The size of a voxel, in voxel units.
  - m_iDMax
```
protected int m_iDMax
```
    DOCUMENT ME!
  - m_iEQuantity
```
protected int m_iEQuantity
```
    DOCUMENT ME!
  - m_iMedianIntensity
```
protected int m_iMedianIntensity
```
    DOCUMENT ME!
  - m_iTQuantity
```
protected int m_iTQuantity
```
    DOCUMENT ME!
  - m_iVQuantity
```
protected int m_iVQuantity
```
    mesh data.
  - m_iXBound
```
protected int m_iXBound
```
    The MRI image bounds and quantity of voxels.
  - m_iYBound
```
protected int m_iYBound
```
    The MRI image bounds and quantity of voxels.
  - m_iZBound
```
protected int m_iZBound
```
    The MRI image bounds and quantity of voxels.
  - m_iQuantity
```
protected int m_iQuantity
```
    The MRI image bounds and quantity of voxels.
  - m_kCenter
```
protected WildMagic.LibFoundation.Mathematics.Vector3f m_kCenter
```
    initial ellipsoid parameters.
  - m_kEMap
```
protected java.util.HashMap<AlgorithmObjectExtractor.Edge,java.lang.Integer> m_kEMap
```
    DOCUMENT ME!
  - m_kRotate
```
protected WildMagic.LibFoundation.Mathematics.Matrix3f m_kRotate
```
    DOCUMENT ME!
  - triMesh
```
protected WildMagic.LibGraphics.SceneGraph.TriMesh triMesh
```
    DOCUMENT ME!
  - box
```
private float[] box
```
    DOCUMENT ME!
  - direction
```
private int[] direction
```
    DOCUMENT ME!
  - gvfBuffer
```
private float[] gvfBuffer
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - iSubdivisions
```
private int iSubdivisions
```
    DOCUMENT ME!
  - oldUVal
```
private float oldUVal
```
    DOCUMENT ME!
  - oldVVal
```
private float oldVVal
```
    DOCUMENT ME!
  - oldWVal
```
private float oldWVal
```
    DOCUMENT ME!
  - onlyInit
```
private boolean onlyInit
```
    DOCUMENT ME!
  - saveGVF
```
private boolean saveGVF
```
    DOCUMENT ME!
  - startLocation
```
private float[] startLocation
```
    DOCUMENT ME!
  - uVal
```
private float[] uVal
```
    DOCUMENT ME!
  - voi
```
private VOI voi
```
    DOCUMENT ME!
  - vVal
```
private float[] vVal
```
    DOCUMENT ME!
  - wVal
```
private float[] wVal
```
    DOCUMENT ME!
  - outputBuffer
```
private float[] outputBuffer
```
- Constructor Detail
  - AlgorithmObjectExtractor
```
public AlgorithmObjectExtractor(ModelImage srcImg,
                                VOI voi,
                                boolean justInit,
                                boolean saveGVF,
                                WildMagic.LibGraphics.SceneGraph.TriMesh triMesh,
                                float[] uVal,
                                float[] vVal,
                                float[] wVal)
```
    Create an extractor for segmenting an object from an image.
    
    Parameters:
    
    srcImg - the source image.
    
    voi - initial voi used to estimate the inital ellipsoid
    
    justInit - if true just perform one iteration
    
    saveGVF - if true save uvf, vvf, and wvf files
    
    triMesh - if not null use mesh instead of voi
    
    uVal - x component of GVF field
    
    vVal - y component of GVF field
    
    wVal - z component of GVF field
- Method Detail
  - extractObject
```
public void extractObject()
```
    The segmentation function. Various parameters may be modified, if necessary, before the call.
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getDilationSize
```
public final int getDilationSize()
```
    Get the dilation size for dilating the voxelized object surface obtained by rasterizing the triangle mesh. The rasterization is designed so that the voxel surface has no holes, thereby allowing it to be flood-filled. But just in case numerical round-off errors cause a few holes, this parameter is exposed for public use. The default value is 0 (no dilation). If the value is D > 0, the dilation mask is a cube of size (2*D+1)x(2*D+1)x(2*D+1).
    
    Returns:
    
    the current dilation size
  - getObjectMask
```
public final byte[] getObjectMask()
```
    Get the 3D image that represents the extracted object. The image is ternary and has the same dimensions as the input MRI. A voxel value of 0 indicates background. A voxel value of 1 indicates object surface. A voxel value of 2 indicates a voxel inside the object surface.
    
    Returns:
    
    the image that represents the extracted object
  - getRayDelta
```
public final float getRayDelta()
```
    Get the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 1.0.
    
    Returns:
    
    the current spacing
  - getReductionX
```
public final float getReductionX()
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.75.
    
    Returns:
    
    the current reduction factor
  - getReductionY
```
public final float getReductionY()
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.75.
    
    Returns:
    
    the current reduction factor
  - getReductionZ
```
public final float getReductionZ()
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.75.
    
    Returns:
    
    the current reduction factor
  - getStiffness
```
public final float getStiffness()
```
    Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution. The default value is 0.1.
    
    Returns:
    
    the current stiffness
  - getTriLinear
```
public final float getTriLinear(float x,
                                float y,
                                float z,
                                float[] buffer)
```
    DOCUMENT ME!
    
    Parameters:
    
    x - DOCUMENT ME!
    
    y - DOCUMENT ME!
    
    z - DOCUMENT ME!
    
    buffer - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setDilationSize
```
public final void setDilationSize(int iDMax)
```
    Set the dilation size for dilating the voxelized object surface obtained by rasterizing the triangle mesh. The rasterization is designed so that the voxel surface has no holes, thereby allowing it to be flood-filled. But just in case numerical round-off errors cause a few holes, this parameter is exposed for public use. The default value is 0 (no dilation). If the value is D > 0, the dilation mask is a cube of size (2*D+1)x(2*D+1)x(2*D+1).
    
    Parameters:
    
    iDMax - the new dilation size
  - setJustIntial
```
public final void setJustIntial(boolean flag)
```
    Indicates if surface evolution should be skipped. This is helpful when determining if the initial ellipsoid is a good estimate.
    
    Parameters:
    
    flag - whether the surface evolution should be skipped
  - setRayDelta
```
public final void setRayDelta(float fRayDelta)
```
    Set the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 1.0.
    
    Parameters:
    
    fRayDelta - the new spacing along the vertex normal rays
  - setReductionX
```
public final void setReductionX(float fReduction)
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.6.
    
    Parameters:
    
    fReduction - the amount to reduce the axis of the ellipsoid.
  - setReductionY
```
public final void setReductionY(float fReduction)
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.5.
    
    Parameters:
    
    fReduction - the amount to reduce the axis of the ellipsoid.
  - setReductionZ
```
public final void setReductionZ(float fReduction)
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.6.
    
    Parameters:
    
    fReduction - the amount to reduce the axis of the ellipsoid.
  - setStiffness
```
public final void setStiffness(float fStiffness)
```
    Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution. The default value is 0.1.
    
    Parameters:
    
    fStiffness - the new stiffness
  - updateMesh
```
public void updateMesh()
```
    The heart of the segmentation. This function is responsible for the evolution of the triangle mesh that approximates the object surface. The update has a tangential component, a surface normal component, and a vertex normal component for each vertex in the mesh. The first two components control the geometry of the mesh. The last component is based on the MRI data itself. See BrainExtraction.pdf for a detailed description of the update terms.
  - computeMeanEdgeLength
```
protected void computeMeanEdgeLength()
```
    Compute the average length of all the edges in the triangle mesh.
  - computeVertexInformation
```
protected void computeVertexInformation()
```
    Let V[i] be a vertex in the triangle mesh. This function computes VMean[i], the average of the immediate neighbors of V[i]. Define S[i] = VMean[i] - V[i]. The function also computes a surface normal SNormal[i], the component of S[i] in the vertex normal direction. STangent[i] = S[i] - SNormal[i] is computed as an approximation to a tangent to the surface. Finally, Curvature[i] is an approximation of the surface curvature at V[i].
  - computeVertexNormals
```
protected void computeVertexNormals()
```
    Compute the vertex normals of the triangle mesh. Each vertex normal is the unitized average of the non-unit triangle normals for those triangles sharing the vertex.
  - estimateEllipsoid
```
protected void estimateEllipsoid()
```
    Approximate the brain surface by an ellipsoid. The approximation is based on locating all voxels of intensity larger than a brightness threshold and that are part of the upper-half of the head. The idea is that the scalp voxels in the upper-half form lie approximately on an ellipsoidal surface.
    
    NOTE. The assumption is that the traversal from bottom to top of head is in the y-direction of the 3D image. It does not matter if the top of the head has y-values smaller/larger than those for the bottom of the head. If this assumption is not met, the image should be permuted OR this code must be modified to attempt to recognize the orientation of the head
  - floodFill
```
protected void floodFill(int iX,
                         int iY,
                         int iZ)
```
    Identify voxels enclosed by the brain surface by using a flood fill. The flood fill is nonrecursive to avoid overflowing the program stack.
    
    Parameters:
    
    iX - the x-value of the seed point for the fill
    
    iY - the y-value of the seed point for the fill
    
    iZ - the z-value of the seed point for the fill
  - generateEllipsoidMesh
```
protected void generateEllipsoidMesh()
```
    Tessellate a unit sphere centered at the origin. Start with an octahedron and subdivide. The final mesh is then affinely mapped to the initial ellipsoid produced by estimateEllipsoid(). The subdivision scheme is described in BrainExtraction.pdf.
  - getIndex
```
protected final int getIndex(int iX,
                             int iY,
                             int iZ)
```
    A convenience function for mapping the 3D voxel position (iX,iY,iZ) to a 1D array index. The images are stored as 1D arrays, so this function is used frequently.
    
    Parameters:
    
    iX - the x-value of the voxel position
    
    iY - the y-value of the voxel position
    
    iZ - the z-value of the voxel position
    
    Returns:
    
    the 1D array index corresponding to (iX,iY,iZ)
  - getInsideVoxels
```
protected void getInsideVoxels()
```
    Identify all voxels that are inside or on the mesh that represents the brain surface. The surface voxels are constructed by rasterizing the triangles of the mesh in 3D. The centroid of these voxels is used as a seed point for a flood fill of the region enclosed by the surface.
  - getIntersectX
```
protected int getIntersectX(WildMagic.LibFoundation.Mathematics.Vector3f kV0,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV1,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV2,
                            int iY,
                            int iZ)
```
    Compute the point of intersection between a line (0,iY,iZ)+t(1,0,0) and the triangle defined by the three input points. All calculations are in voxel coordinates and the x-value of the intersection point is truncated to an integer.
    
    Parameters:
    
    kV0 - a 3D vertex of the triangle
    
    kV1 - a 3D vertex of the triangle
    
    kV2 - a 3D vertex of the triangle
    
    iY - the y-value of the origin of the line
    
    iZ - the z-value of the origin of the line
    
    Returns:
    
    the x-value of the intersection
  - getIntersectY
```
protected int getIntersectY(WildMagic.LibFoundation.Mathematics.Vector3f kV0,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV1,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV2,
                            int iX,
                            int iZ)
```
    Compute the point of intersection between a line (iX,0,iZ)+t(0,1,0) and the triangle defined by the three input points. All calculations are in voxel coordinates and the y-value of the intersection point is truncated to an integer.
    
    Parameters:
    
    kV0 - a 3D vertex of the triangle
    
    kV1 - a 3D vertex of the triangle
    
    kV2 - a 3D vertex of the triangle
    
    iX - the x-value of the origin of the line
    
    iZ - the z-value of the origin of the line
    
    Returns:
    
    the y-value of the intersection
  - getIntersectZ
```
protected int getIntersectZ(WildMagic.LibFoundation.Mathematics.Vector3f kV0,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV1,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV2,
                            int iX,
                            int iY)
```
    Compute the point of intersection between a line (iX,iY,0)+t(0,0,1) and the triangle defined by the three input points. All calculations are in voxel coordinates and the z-value of the intersection point is truncated to an integer.
    
    Parameters:
    
    kV0 - a 3D vertex of the triangle
    
    kV1 - a 3D vertex of the triangle
    
    kV2 - a 3D vertex of the triangle
    
    iX - the x-value of the origin of the line
    
    iY - the y-value of the origin of the line
    
    Returns:
    
    the z-value of the intersection
  - saveMesh
```
protected void saveMesh(boolean flip)
                 throws java.io.IOException
```
    Internal support to write vertices, normals, and connectivity indices to the file.
    
    Parameters:
    
    flip - if the y axis should be inverted - true for extract, false for from another surface
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - update2
```
protected float update2(int i)
```
    Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction. See BrainExtraction.pdf for a description of the update.
    
    Parameters:
    
    i - the index of the vertex to update
    
    Returns:
    
    the coefficient of SNormal[i] for the update
  - update3
```
protected void update3(int i)
```
    Compute the coefficient of the vertex normal for the update of the mesh vertex V[i] in the VNormal[i] direction. See BrainExtraction.pdf for a description of the update.
    
    Parameters:
    
    i - the index of the vertex to update
  - calcGradMag
```
private void calcGradMag()
```
    DOCUMENT ME!
  - calcGVF3D
```
private void calcGVF3D()
```
    Calculate GVF from 3D image buffer.
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    Description copied from interface: AlgorithmInterface
    
    Called after an algorithm this listener is registered to exits (maybe successfully, maybe not). If the algorithm is run in a separate thread, this call will be made within that thread. If not, this call will be made from that same, shared thread.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - the algorithm which has just completed

Class AlgorithmObjectExtractor

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

c1Factor

c3Factor

m_afCurvature

m_afImage

m_afLength

m_aiConnect

m_aiMask

m_akAdjacent

m_akSNormal

m_akSTangent

m_akVertex

m_akVMean

m_akVNormal

m_fEParam

m_fFParam

m_fMeanEdgeLength

m_fRayDelta

m_fReductionX

m_fReductionY

m_fReductionZ

m_fStiffness

m_fXDelta

m_fYDelta

m_fZDelta

m_iDMax

m_iEQuantity

m_iMedianIntensity

m_iTQuantity

m_iVQuantity

m_iXBound

m_iYBound

m_iZBound

m_iQuantity

m_kCenter

m_kEMap

m_kRotate

triMesh

box

direction

gvfBuffer

image

iSubdivisions

oldUVal

oldVVal

oldWVal

onlyInit

saveGVF

startLocation

uVal

voi

vVal

wVal

outputBuffer

Constructor Detail

AlgorithmObjectExtractor

Method Detail

extractObject

finalize

getDilationSize

getObjectMask

getRayDelta

getReductionX

getReductionY

getReductionZ

getStiffness

getTriLinear

runAlgorithm

setDilationSize