Package gov.nih.mipav.model.algorithms

Class AlgorithmMSER

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmMSER

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmMSER
extends AlgorithmBase

Author:

Andrea Vedaldi

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmMSER.VlMserExtrReg	Extremal regions (ER) are extracted from the region forest.
private class	AlgorithmMSER.VlMserFilt
private class	AlgorithmMSER.VlMserReg	Extremal regions and maximally stable extremal regions are instances of image regions.
private class	AlgorithmMSER.VlMserStats

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 boolean	bright_on_dark
private boolean	dark_on_bright
private short[]	data
private double	delta
private int[]	dims
private static int	ELLIPSES_ONLY
private double	max_area
private double	max_variation
private double	min_area
private double	min_diversity
private int	ndims
private int	outputVOIType
private static int	POINTS_AND_ELLIPSES
private static int	POINTS_ONLY
private int	sliceSize
private static int	VL_MSER_PIX_MAXVAL
private static int	VL_MSER_VOID_NODE

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
AlgorithmMSER(ModelImage srcImage, double delta, double max_area, double min_area, double max_variation, double min_diversity, boolean bright_on_dark, boolean dark_on_bright, int outputVOIType)

Method Summary

Modifier and Type	Method	Description
private void	adv(int ndims, int[] dims, int[] subs)	Advance N-dimensional subscript
private int	climb(AlgorithmMSER.VlMserReg[] r, int idx)	Climb the region forest to reach a root The function climbs the regions' forest r[] starting from the node idx to the corresponding root.
void	runAlgorithm()	Start algorithm.
private void	vl_mser_delete(AlgorithmMSER.VlMserFilt f)	Delete MSER filter This function releases the MSER filter and all its resources
private void	vl_mser_ell_fit(AlgorithmMSER.VlMserFilt f)
private AlgorithmMSER.VlMserFilt	vl_mser_new(int ndims, int[] dims)
private void	vl_mser_process(AlgorithmMSER.VlMserFilt f, short[] im)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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

VL_MSER_PIX_MAXVAL

private static final int VL_MSER_PIX_MAXVAL

See Also:

Constant Field Values

VL_MSER_VOID_NODE

private static final int VL_MSER_VOID_NODE

See Also:

Constant Field Values

POINTS_ONLY

private static final int POINTS_ONLY

See Also:

Constant Field Values

ELLIPSES_ONLY

private static final int ELLIPSES_ONLY

See Also:

Constant Field Values

POINTS_AND_ELLIPSES

private static final int POINTS_AND_ELLIPSES

See Also:

Constant Field Values

delta

private double delta

max_area

private double max_area

min_area

private double min_area

max_variation

private double max_variation

min_diversity

private double min_diversity

bright_on_dark

private boolean bright_on_dark

dark_on_bright

private boolean dark_on_bright

outputVOIType

private int outputVOIType

ndims

private int ndims

dims

private int[] dims

data

private short[] data

sliceSize

private int sliceSize

Constructor Detail

AlgorithmMSER

public AlgorithmMSER(ModelImage srcImage,
                     double delta,
                     double max_area,
                     double min_area,
                     double max_variation,
                     double min_diversity,
                     boolean bright_on_dark,
                     boolean dark_on_bright,
                     int outputVOIType)

Method Detail

runAlgorithm

public void runAlgorithm()

Start algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

vl_mser_ell_fit

private void vl_mser_ell_fit(AlgorithmMSER.VlMserFilt f)

vl_mser_delete

private void vl_mser_delete(AlgorithmMSER.VlMserFilt f)

Delete MSER filter This function releases the MSER filter and all its resources

Parameters:

f - MSER filter to be deleted

adv

private void adv(int ndims,
                 int[] dims,
                 int[] subs)

Advance N-dimensional subscript

Parameters:

ndims -

dims -

subs - subscript to advance

vl_mser_process

private void vl_mser_process(AlgorithmMSER.VlMserFilt f,
                             short[] im)

climb

private int climb(AlgorithmMSER.VlMserReg[] r,
                  int idx)

Climb the region forest to reach a root The function climbs the regions' forest r[] starting from the node idx to the corresponding root. To speed-up the operation, the function uses the VlMserReg::shortcut field to quickly jump to the root. After the root is reached, all the used shortcuts are updated.

Parameters:

r - regions' forest

idx - starting node

Returns:

index of the reached root.

vl_mser_new

private AlgorithmMSER.VlMserFilt vl_mser_new(int ndims,
                                             int[] dims)