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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmExtractSurfaceCubes
extends AlgorithmBase
```
Extracts a surface using Marching Cube Extraction. Triangle decimation can be invoked to reduce triangle count. The decimation algorithm produces a continuous 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 grey-scale
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
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`ADJ_MODE`	Use adjacency model to perform triangle consistency.
`private boolean`	`blurFlag`	If true then the input image is blurred slightly.
`private float`	`blurSigma`	The amount to blur to smooth surface.
`private boolean`	`decimateFlag`	If true then the extracted surface is decimated into a continuous level of detail surface (clod).
`private int`	`level`	Indicates level surface to be extracted.
`static int`	`LEVEL_MODE`	Extract surface based on intensity level.
`static int`	`MASK_MODE`	Extract surface from mask image.
`private ModelImage`	`maskImage`	Mask image to extract surface from.
`private int`	`mode`	Indicates mode - VOI, LEVELSET, or MASK.
`static int`	`NONE_MODE`	Do not perform triangle consistency checking - all counter clockwise or all clockwise.
`static int`	`SMOOTH_MODE`	Use smoothing model to perform triangle consistency.
`private java.lang.String`	`surfaceFileName`	Path and name of extracted surface file. ".sur" will be appended if necessary.
`static 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
`AlgorithmExtractSurfaceCubes(ModelImage image, int level, int mode, boolean decFlag, boolean blurFlag, float sigma, java.lang.String fileName)`	Creates a new AlgorithmExtractSurfaceCubes object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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, 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
  - 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
  - NONE_MODE
```
public static final int NONE_MODE
```
    Do not perform triangle consistency checking - all counter clockwise or all clockwise.
    
    See Also:
    
    Constant Field Values
  - ADJ_MODE
```
public static final int ADJ_MODE
```
    Use adjacency model to perform triangle consistency.
    
    See Also:
    
    Constant Field Values
  - SMOOTH_MODE
```
public static final int SMOOTH_MODE
```
    Use smoothing model to perform triangle consistency. Smooths normals.
    
    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 int 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 java.lang.String surfaceFileName
```
    Path and name of extracted surface file. ".sur" will be appended if necessary.
- Constructor Detail
  - AlgorithmExtractSurfaceCubes
```
public AlgorithmExtractSurfaceCubes(ModelImage image,
                                    int level,
                                    int mode,
                                    boolean decFlag,
                                    boolean blurFlag,
                                    float sigma,
                                    java.lang.String fileName)
```
    Creates a new AlgorithmExtractSurfaceCubes object.
    
    Parameters:
    
    image - mask image or gray-scale where a level surface is to be extracted
    
    level - indicates level surface to be extracted
    
    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.
    
    smoothFlag - whether the generated mesh should have smoothing applied to it
- Method Detail
  - 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!

Class AlgorithmExtractSurfaceCubes

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

VOI_MODE

MASK_MODE

LEVEL_MODE

NONE_MODE

ADJ_MODE

SMOOTH_MODE

blurFlag

blurSigma

decimateFlag

level

maskImage

mode

surfaceFileName

Constructor Detail

AlgorithmExtractSurfaceCubes

Method Detail

finalize

runAlgorithm

extractSurface

init