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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmFloodFill
extends AlgorithmBase
```
Stack based flood-fill for 2D and 3D images. The input is a binary (BitSet) object and produces a BitSet or short mask. A short mask allows for different label values for disconnected objects in a BitSet image. For example, in a binarized image of cells, each cell could be labeled(filled) with a separate value. However, a short mask uses 16X more memory than does the BitSet mask.

Version:

0.1 Jan 5, 1998

Author:

Matthew J. McAuliffe, Ph.D.

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 short`	`BITSET`	DOCUMENT ME!
`private int[]`	`dims`	Dimensionality of the data.
`private short`	`floodValue`	Flood value.
`private java.util.BitSet`	`mask`	DOCUMENT ME!
`private int`	`mode`	Indicates the type of result mask: BITSET or SHORT.
`private int`	`nDims`	The number of dimensions.
`private java.util.BitSet`	`newMask`	DOCUMENT ME!
`private short[]`	`newShortMask`	Reference to short mask.
`private java.awt.Point`	`seed2DPt`	Seed point for 2D datasets.
`private Point3D`	`seed3DPt`	Seed point for 3D datasets.
`static short`	`SHORT`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, 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
`AlgorithmFloodFill(java.util.BitSet mask, int[] dims, int mode, Point3D pt)`	Stack based flood-fill for 2D and 3D images.
`AlgorithmFloodFill(java.util.BitSet mask, int[] dims, int mode, java.awt.Point pt)`	Stack based flood-fill for 2D and 3D images.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for destruction.
`java.util.BitSet`	`floodFill2DBitSet()`	2D flood fill that forms a binary(BitSet) mask.
`short[]`	`floodFill2DShort()`	2D flood fill that forms a short mask.
`java.util.BitSet`	`floodFill3DBitSet()`	3D flood fill that forms a binary(BitSet) mask.
`short[]`	`floodFill3DShort()`	3D flood fill that forms a short mask.
`java.util.BitSet`	`getBitSetMask()`	Gets the Mask image returned as a Java Bitset object.
`short[]`	`getShortMask()`	Gets the mask image (array of short values).
`void`	`runAlgorithm()`	Starts the program.
`void`	`setBitSetMask(java.util.BitSet mask)`	Sets this classes BitSet mask to new mask.
`void`	`setFloodValue(short floodValue)`	Sets the value to be placed in the flood region.
`void`	`setSeed2DPt(java.awt.Point seedPt)`	Sets the seed point for the flood fill for a 2D image region grow.
`void`	`setSeed3DPt(Point3D seedPt)`	Sets the point at which a the flood filling begins.
`void`	`setShortMask(short[] mask)`	Sets this classes short mask to the new mask.

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
  - BITSET
```
public static final short BITSET
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - SHORT
```
public static final short SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - dims
```
private int[] dims
```
    Dimensionality of the data.
  - floodValue
```
private short floodValue
```
    Flood value. Default in 1.
  - mask
```
private java.util.BitSet mask
```
    DOCUMENT ME!
  - mode
```
private int mode
```
    Indicates the type of result mask: BITSET or SHORT.
  - nDims
```
private int nDims
```
    The number of dimensions.
  - newMask
```
private java.util.BitSet newMask
```
    DOCUMENT ME!
  - newShortMask
```
private short[] newShortMask
```
    Reference to short mask.
  - seed2DPt
```
private java.awt.Point seed2DPt
```
    Seed point for 2D datasets.
  - seed3DPt
```
private Point3D seed3DPt
```
    Seed point for 3D datasets.
- Constructor Detail
  - AlgorithmFloodFill
```
public AlgorithmFloodFill(java.util.BitSet mask,
                          int[] dims,
                          int mode,
                          java.awt.Point pt)
```
    Stack based flood-fill for 2D and 3D images.
    
    Parameters:
    
    mask - BitSet object that has the binary object(s) that needs to be filled
    
    dims - dimensionality of mask
    
    mode - BITSET or SHORT mode for result mask
    
    pt - seed point for the flood fill to begin for 2D image
  - AlgorithmFloodFill
```
public AlgorithmFloodFill(java.util.BitSet mask,
                          int[] dims,
                          int mode,
                          Point3D pt)
```
    Stack based flood-fill for 2D and 3D images.
    
    Parameters:
    
    mask - BitSet object that has the binary object(s) that needs to be filled
    
    dims - dimensionality of mask
    
    mode - BITSET or SHORT mode for result mask
    
    pt - seed point for the flood fill to begin for 3D image
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - floodFill2DBitSet
```
public java.util.BitSet floodFill2DBitSet()
```
    2D flood fill that forms a binary(BitSet) mask.
    
    Returns:
    
    mask of flooded image
  - floodFill2DShort
```
public short[] floodFill2DShort()
```
    2D flood fill that forms a short mask.
    
    Returns:
    
    mask of flooded image
  - floodFill3DBitSet
```
public java.util.BitSet floodFill3DBitSet()
```
    3D flood fill that forms a binary(BitSet) mask.
    
    Returns:
    
    mask of flooded image
  - floodFill3DShort
```
public short[] floodFill3DShort()
```
    3D flood fill that forms a short mask.
    
    Returns:
    
    mask of flooded image
  - getBitSetMask
```
public java.util.BitSet getBitSetMask()
```
    Gets the Mask image returned as a Java Bitset object.
    
    Returns:
    
    BitSet mask of flooded image
  - getShortMask
```
public short[] getShortMask()
```
    Gets the mask image (array of short values).
    
    Returns:
    
    short mask of flooded image
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setBitSetMask
```
public void setBitSetMask(java.util.BitSet mask)
```
    Sets this classes BitSet mask to new mask.
    
    Parameters:
    
    mask - sets BitSet mask
  - setFloodValue
```
public void setFloodValue(short floodValue)
```
    Sets the value to be placed in the flood region.
    
    Parameters:
    
    floodValue - sets the flood-fill value used when generating a short type mask
  - setSeed2DPt
```
public void setSeed2DPt(java.awt.Point seedPt)
```
    Sets the seed point for the flood fill for a 2D image region grow.
    
    Parameters:
    
    seedPt - sets 2D seed point for beginning of flood fill
  - setSeed3DPt
```
public void setSeed3DPt(Point3D seedPt)
```
    Sets the point at which a the flood filling begins.
    
    Parameters:
    
    seedPt - sets 3D seed point for beginning of flood fill
  - setShortMask
```
public void setShortMask(short[] mask)
```
    Sets this classes short mask to the new mask.
    
    Parameters:
    
    mask - sets short mask

Class AlgorithmFloodFill

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

BITSET

SHORT

dims

floodValue

mask

mode

nDims

newMask

newShortMask

seed2DPt

seed3DPt

Constructor Detail

AlgorithmFloodFill

AlgorithmFloodFill

Method Detail

finalize

floodFill2DBitSet

floodFill2DShort

floodFill3DBitSet

floodFill3DShort

getBitSetMask

getShortMask

runAlgorithm

setBitSetMask

setFloodValue

setSeed2DPt

setSeed3DPt

setShortMask