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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.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 int`	`FACING_DOWN`	For indicating the axial image is facing down.
`static int`	`FACING_INTO_SCREEN`	For indicating the coronal image is facing into the screen.
`static int`	`FACING_LEFT`	For indicating the sagittal image is facing left.
`static int`	`FACING_OUT_OF_SCREEN`	For indicating the coronal image is facing out of the screen.
`static int`	`FACING_RIGHT`	For indicating the sagittal image is facing right.
`static int`	`FACING_UP`	For indicating the axial image is facing up.
`private float`	`imageInfluenceBET`	Parameter for brain extraction by default set to .1
`static int`	`MIN_RADIUS`	May no longer be necessary.
`private int`	`mmToPad`	Length to buffer brain by in millimeters.
`static int`	`REMOVED_INTENSITY`	Eventually won't be necessary.
`private int`	`sliceSize`	Computed as xDim*yDim
`private float`	`stiffnessBET`	Parameter for brain extraction by default set to .15
`private int`	`volumeSize`	Computed as xDimyDimzDim
`private int`	`xDim`	Length of the x dimension in pixels.
`private int`	`yDim`	Length of the y dimension in pixels.
`private 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`anonymizeFace()`	Executes the de-facing algorithm.
`private java.util.BitSet`	`bufferBrain(java.util.BitSet brainMaskTemp, int mmToPad)`	Appends the given `brainMaskTemp` by `mmToPad` in pixels in all directions.
`private java.util.BitSet`	`defineInitialRegion(java.util.BitSet interestRegion)`	Defines an initial region for face de-identification.
`private java.util.BitSet`	`defineInterestRegion()`	Defines the bounding region for face de-identification.
`private java.util.BitSet`	`extractBrain()`	Performs the BET brain extraction using parameters specified from JDialogFaceAnonymizer.
`private java.util.BitSet`	`extractFace(java.util.BitSet interestRegion, java.util.BitSet initialRegion, java.util.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 java.util.BitSet`	`smoothFace(java.util.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, 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
  - 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 Detail
  - 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 Detail
  - 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 java.util.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 java.util.BitSet bufferBrain(java.util.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 java.util.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 java.util.BitSet defineInitialRegion(java.util.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 java.util.BitSet extractFace(java.util.BitSet interestRegion,
                                     java.util.BitSet initialRegion,
                                     java.util.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 java.util.BitSet smoothFace(java.util.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.

Class AlgorithmFaceAnonymizerBET

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

REMOVED_INTENSITY

MIN_RADIUS

FACING_RIGHT

FACING_LEFT

FACING_DOWN

FACING_UP

FACING_INTO_SCREEN

FACING_OUT_OF_SCREEN

mmToPad

faceOrientation

estimateWithSphereBET

imageInfluenceBET

stiffnessBET

sliceSize

volumeSize

xDim

yDim

zDim

Constructor Detail

AlgorithmFaceAnonymizerBET

Method Detail

finalize

runAlgorithm

setBETParameters

anonymizeFace

extractBrain

bufferBrain

defineInterestRegion

defineInitialRegion

extractFace

smoothFace