Package gov.nih.mipav.model.algorithms

Class AlgorithmExtractSurface

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmExtractSurface

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmExtractSurface
extends AlgorithmBase

Extracts a surface using Tetrahedron Extraction. Triangle decimation can be invoked to reduce triangle count. The decimation algorithm produces a continious level of detail (clod) structure that can be used to optimize the the visualization of the surface. The input to this algorithm is typically a mask image where 0 = background and 100 = object (i.e. interior to a VOI). The mask image is then blurred slightly and the level (50) is extracted. A greyscale image may also be input and a surface is extracted given a level. The steps are:

1. Build mask image of VOI (i.e. all point interior to VOI are set to 100. All points exterior are = 0.
2. Blur mask image if not greyscale
3. Extract level surface at 50 or user defined level
4. Save surface ( ".sur")
5. If decimate then decimate surface and save (".sur")

Version:

0.1 June, 2001

Author:

Matthew J. McAuliffe, Ph.D., David H. Eberly, Ph.D. wrote all the extraction and decimation code found in the SurfaceExtraction, SurfaceDecimation and associated classes, with a little input from Matt with speed and memory optimizations

See Also:

• ModelSurfaceExtractor
• ModelSurfaceDecimator

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 final boolean	blurFlag	If true then the input image is blurred slightly.
private float	blurSigma	The amount to blur to smooth surface.
private final boolean	decimateFlag	If true then the extracted surface is decimated into a continuous level of detail surface (clod).
private final float	level	Indicates level surface to be extracted.
static final int	LEVEL_MODE	Extract surface based on intensity level.
static final int	MASK_MODE	Extract surface from mask image.
private ModelImage	maskImage	Mask image to extract surface from.
private final int	mode	Indicates mode - VOI, LEVELSET, or MASK.
private float[]	surfaceArea
private String	surfaceFileName	Path and name of extracted surface file. ".sur" will be appended if necessary.
static final int	VOI_MODE	Extract surface from VOI.

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
AlgorithmExtractSurface(ModelImage image, float level, int mode, boolean decFlag, boolean blurFlag, float sigma, String fileName, float[] surfaceArea)	Creates a new AlgorithmExtractSurface object.

Method Summary

Modifier and Type	Method	Description
float	ComputeSurfaceArea(WildMagic.LibGraphics.SceneGraph.TriMesh m_kMesh)	Calculate the surface mesh area.
private void	extractSurface()	Extracts a surface, in the form of triangles, from an image.
void	finalize()	Prepares this class for destruction.
private void	init()	DOCUMENT ME!
void	runAlgorithm()	Starts the program.

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

VOI_MODE

public static final int VOI_MODE

Extract surface from VOI.

See Also:

• Constant Field Values

MASK_MODE

public static final int MASK_MODE

Extract surface from mask image.

See Also:

• Constant Field Values

LEVEL_MODE

public static final int LEVEL_MODE

Extract surface based on intensity level.

See Also:

• Constant Field Values

blurFlag

private final boolean blurFlag

If true then the input image is blurred slightly.

blurSigma

private float blurSigma

The amount to blur to smooth surface.

decimateFlag

private final boolean decimateFlag

If true then the extracted surface is decimated into a continuous level of detail surface (clod).

level

private final float level

Indicates level surface to be extracted.

maskImage

private ModelImage maskImage

Mask image to extract surface from.

mode

private final int mode

Indicates mode - VOI, LEVELSET, or MASK.

surfaceFileName

private String surfaceFileName

Path and name of extracted surface file. ".sur" will be appended if necessary.

surfaceArea

private float[] surfaceArea

Constructor Details

AlgorithmExtractSurface

public AlgorithmExtractSurface(ModelImage image,
 float level,
 int mode,
 boolean decFlag,
 boolean blurFlag,
 float sigma,
 String fileName,
 float[] surfaceArea)

Creates a new AlgorithmExtractSurface object.

Parameters:

image - mask image or grayscale where a level surface is to be extracted

level - indicates level surface to be extraced

mode - Indicates mode - VOI, LEVELSET, or MASK.

decFlag - indicates whether or not the decimation into a CLOD should take place.

blurFlag - if true then the input image is blurred slightly

sigma - the amount to blur the image

fileName - path and name of extracted surface file. ".sur" will be appended if necessary.

surfaceArea - If not null the computed surface area will be returned

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

extractSurface

private void extractSurface()

Extracts a surface, in the form of triangles, from an image.

init

private void init()

DOCUMENT ME!

ComputeSurfaceArea

public float ComputeSurfaceArea(WildMagic.LibGraphics.SceneGraph.TriMesh m_kMesh)

Calculate the surface mesh area. Each surface mesh is composed of triangles. Calculate the surface area from the summation of the each triangle area. Based on the Area by Stokes' Theorem. Area(S) = 1/2 * Normal dot ( Sum from i = 0 to n-1 of ( V1 cross V2) ) ==> Area(S) = 1/2 * ( Sum from i = 0 to n-1 of ( Normal dot ( V1 cross V2) ) )

Returns:

float