Package gov.nih.mipav.model.algorithms

Class AlgorithmFaceAnonymizerBET

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmFaceAnonymizerBET

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmFaceAnonymizerBET
extends AlgorithmBase

Anonymize an image of a patient's head by removing the face.

This version of of the de-facer uses BET to find the brain, the brain's location is then used to calculate a plane. This plane is then used to remove the patient's face from the image.

Author:

mccreedy

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmFaceAnonymizerBET.BitSetUtility	Private utility class for operations on BitSets

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	estimateWithSphereBET	Parameter for brain extraction by default set to false
private int	faceOrientation	The orientation of an image.
static final int	FACING_DOWN	For indicating the axial image is facing down.
static final int	FACING_INTO_SCREEN	For indicating the coronal image is facing into the screen.
static final int	FACING_LEFT	For indicating the sagittal image is facing left.
static final int	FACING_OUT_OF_SCREEN	For indicating the coronal image is facing out of the screen.
static final int	FACING_RIGHT	For indicating the sagittal image is facing right.
static final int	FACING_UP	For indicating the axial image is facing up.
private float	imageInfluenceBET	Parameter for brain extraction by default set to .1
static final int	MIN_RADIUS	May no longer be necessary.
private int	mmToPad	Length to buffer brain by in millimeters.
static final int	REMOVED_INTENSITY	Eventually won't be necessary.
private final int	sliceSize	Computed as xDim*yDim
private float	stiffnessBET	Parameter for brain extraction by default set to .15
private final int	volumeSize	Computed as xDim*yDim*zDim
private final int	xDim	Length of the x dimension in pixels.
private final int	yDim	Length of the y dimension in pixels.
private final int	zDim	Length of the z dimension in pixels.

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
AlgorithmFaceAnonymizerBET(ModelImage srcImg, int faceDirection, int extraMMsToPad)	Construct the face anonymizer, but do not run it yet.

Method Summary

Modifier and Type	Method	Description
private void	anonymizeFace()	Executes the de-facing algorithm.
private BitSet	bufferBrain(BitSet brainMaskTemp, int mmToPad)	Appends the given brainMaskTemp by mmToPad in pixels in all directions.
private BitSet	defineInitialRegion(BitSet interestRegion)	Defines an initial region for face de-identification.
private BitSet	defineInterestRegion()	Defines the bounding region for face de-identification.
private BitSet	extractBrain()	Performs the BET brain extraction using parameters specified from JDialogFaceAnonymizer.
private BitSet	extractFace(BitSet interestRegion, BitSet initialRegion, BitSet brainMask)	Performs the face de-identification within the bounding area by approximating the given shape using a geometry suitable for the given shape.
void	finalize()	Clean up memory used by the algorithm.
void	runAlgorithm()	Run the de-facing algorithm.
void	setBETParameters(boolean estimateWithSphere, float imageInfluence, float stiffness)	Changes the BET algorithm parameters from their defaults (which we choose).
private BitSet	smoothFace(BitSet removeRegion)	Connects near neighbors of set values in removeRegion.

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

REMOVED_INTENSITY

public static final int REMOVED_INTENSITY

Eventually won't be necessary.

See Also:

• Constant Field Values

MIN_RADIUS

public static final int MIN_RADIUS

May no longer be necessary.

See Also:

• Constant Field Values

FACING_RIGHT

public static final int FACING_RIGHT

For indicating the sagittal image is facing right.

See Also:

• Constant Field Values

FACING_LEFT

public static final int FACING_LEFT

For indicating the sagittal image is facing left.

See Also:

• Constant Field Values

FACING_DOWN

public static final int FACING_DOWN

For indicating the axial image is facing down.

See Also:

• Constant Field Values

FACING_UP

public static final int FACING_UP

For indicating the axial image is facing up.

See Also:

• Constant Field Values

FACING_INTO_SCREEN

public static final int FACING_INTO_SCREEN

For indicating the coronal image is facing into the screen.

See Also:

• Constant Field Values

FACING_OUT_OF_SCREEN

public static final int FACING_OUT_OF_SCREEN

For indicating the coronal image is facing out of the screen.

See Also:

• Constant Field Values

mmToPad

private int mmToPad

Length to buffer brain by in millimeters.

faceOrientation

private int faceOrientation

The orientation of an image.

estimateWithSphereBET

private boolean estimateWithSphereBET

Parameter for brain extraction by default set to false

imageInfluenceBET

private float imageInfluenceBET

Parameter for brain extraction by default set to .1

stiffnessBET

private float stiffnessBET

Parameter for brain extraction by default set to .15

sliceSize

private final int sliceSize

Computed as xDim*yDim

volumeSize

private final int volumeSize

Computed as xDim*yDim*zDim

xDim

private final int xDim

Length of the x dimension in pixels.

yDim

private final int yDim

Length of the y dimension in pixels.

zDim

private final int zDim

Length of the z dimension in pixels.

Constructor Details

AlgorithmFaceAnonymizerBET

public AlgorithmFaceAnonymizerBET(ModelImage srcImg,
 int faceDirection,
 int extraMMsToPad)

Construct the face anonymizer, but do not run it yet.

Parameters:

srcImg - The image to de-face

faceDirection - the orientation of the patient's face, as determined by the dialog

extraMMsToPad - the number of millimeters to buffer brain by after extraction

Method Details

finalize

public void finalize()

Clean up memory used by the algorithm.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Run the de-facing algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

setBETParameters

public void setBETParameters(boolean estimateWithSphere,
 float imageInfluence,
 float stiffness)

Changes the BET algorithm parameters from their defaults (which we choose).

Parameters:

estimateWithSphere - whether to estimate the brain with a sphere initially

imageInfluence - the image influence ratio

stiffness - the mesh stiffness

anonymizeFace

private void anonymizeFace()

Executes the de-facing algorithm.

extractBrain

private BitSet extractBrain()

Performs the BET brain extraction using parameters specified from JDialogFaceAnonymizer.

Returns:

A BitSet of size srcImage.getSize() where set values are the location of brain.

bufferBrain

private BitSet bufferBrain(BitSet brainMaskTemp,
 int mmToPad)

Appends the given brainMaskTemp by mmToPad in pixels in all directions. TODO: Use Algorithms -> Morphological -> Dilate

Parameters:

brainMaskTemp - The BitSet returned by this.extractBrain().

mmToPad - Length in millimeters that the brain's BitSet should be extended.

Returns:

The original BitSet with mmToPad in pixels appended to this BitSet

defineInterestRegion

private BitSet defineInterestRegion()

Defines the bounding region for face de-identification.

Returns:

A BitSet of size srcImage.getSize() where set values are the inital shape's location.

defineInitialRegion

private BitSet defineInitialRegion(BitSet interestRegion)

Defines an initial region for face de-identification.

Parameters:

interestRegion - The bounding area of the face de-identification.

Returns:

A BitSet of size srcImage.getSize() where set values are the inital shape's location.

extractFace

private BitSet extractFace(BitSet interestRegion,
 BitSet initialRegion,
 BitSet brainMask)

Performs the face de-identification within the bounding area by approximating the given shape using a geometry suitable for the given shape. For example, the approximation of a quarter cylinder is performed using spheres with centers on the boundary points of the initialRegion with further iterations on the boundary points of the resulting shape.

Parameters:

interestRegion - The bounding area for face de-identification.

initialRegion - Initial area.

brainMask - Brain extraction derived from BET and apended by this.bufferBrain(BitSet, int)

Returns:

A BitSet of size srcImage.getSize() where set values denote face de-identification may be performed.

smoothFace

private BitSet smoothFace(BitSet removeRegion)

Connects near neighbors of set values in removeRegion. Near neighbors are those values which are set and are within five percent of the image resolution.

Parameters:

removeRegion - The original BitSet for face de-identification.

interestRegion - The bounding region.

brainMask - The location of the brain in this image.

Returns:

A BitSet of size srcImage.getSize() where set values denote face de-identification may be performed.