java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Dialog
      - javax.swing.JDialog
        
        gov.nih.mipav.view.dialogs.JDialogBase
        
        gov.nih.mipav.view.dialogs.JDialogScriptableBase
        
        gov.nih.mipav.view.dialogs.JDialogExtractBrain

All Implemented Interfaces:

AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, ActionDiscovery, java.awt.event.ActionListener, java.awt.event.FocusListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants
```
public class JDialogExtractBrain
extends JDialogScriptableBase
implements AlgorithmInterface, ActionDiscovery, ScriptableActionInterface
```
DOCUMENT ME!

Version:

1.0 July 17, 2000

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase
  JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction
- Nested classes/interfaces inherited from class javax.swing.JDialog
  javax.swing.JDialog.AccessibleJDialog
- Nested classes/interfaces inherited from class java.awt.Dialog
  java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType
- Nested classes/interfaces inherited from class java.awt.Window
  java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  java.awt.Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field	Description
`private float`	`aboveMedian`	The factor above which second stage edge erosion occurs.
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`centerOfMass`	The volume's center of mass computed from `computeCenter(ModelImage, int, boolean)`
`private int`	`depth`	The maximum depth within the brain's surface to sample image intensities, by default set to 5.
`private javax.swing.JTextField`	`depthTF`	Field for entering the maximum depth.
`private javax.swing.JLabel`	`erosionLabel`	Label for the percentage entered for second stage edge erosion.
`private javax.swing.JTextField`	`erosionTF`	Defines the allowable percentage for edge intensity values ub second stage edge erosion, default is 50 percent.
`private AlgorithmBrainExtractor`	`extractBrainAlgo`	Algorithm used for brain extraction.
`private boolean`	`extractToPaint`	When true, mask of extracted brain is painted over the source image.
`private javax.swing.JCheckBox`	`extractToPaintCheckBox`	When checked, mask of extracted brain is painted over the source image.
`private ModelImage`	`image`	Source image for extracting brain, default image is `null`.
`private float`	`imageRatio`	Image influence ratio for controlling the sampling depth used to calculate intensity extrema, by default set to .1.
`private javax.swing.JTextField`	`imageRatioTF`	Field for entering the image influence ratio.
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`initCenterPoint`	Either the volume's center of mass or a user indicated point depending on the value of `useCenterOfMass`.
`private float`	`initCenterX`	Used to denote the brain's center of mass y-coordinate.
`private javax.swing.JLabel`	`initCenterXLabel`	Label for the x-coordinate of the user-defined center.
`private javax.swing.JTextField`	`initCenterXTF`	An optional field for denoting a desired initial x-corrdinate for the mesh.
`private float`	`initCenterY`	Used to denote the brain's center of mass y-coordinate.
`private javax.swing.JLabel`	`initCenterYLabel`	Label for the y-coordinate of the user-defined center.
`private javax.swing.JTextField`	`initCenterYTF`	An optional field for denoting a desired initial y-corrdinate for the mesh.
`private float`	`initCenterZ`	Used to denote the brain's center of mass y-coordinate.
`private javax.swing.JLabel`	`initCenterZLabel`	Label for the z-coordinate of the user-defined center.
`private javax.swing.JTextField`	`initCenterZTF`	An optional field for denoting a desired initial z-corrdinate for the mesh.
`private boolean`	`justEllipse`	When true, image mask is set to the initial ellipsoid approximation of the brain calculated from the volume's center of mass.
`private javax.swing.JCheckBox`	`justInitEllipsoidCheckbox`	When checked, `justEllipse` is set to true.
`private int`	`nIterations`	Number of surface evolutions to perform, by default set to 500.
`private javax.swing.JTextField`	`nIterationsTF`	Field for inputting the number of surface evolutions to perform.
`private int`	`orientation`	Orientation value corresponding to not the value of `AlgorithmBrainExtractor.SAT_COR`
`private javax.swing.JCheckBox`	`orientCheckbox`	When checked, denotes that the images orientation does not correspond to `AlgorithmBrainExtractor.SAT_COR`
`private javax.swing.JCheckBox`	`secondStageCheckBox`	Initially unchecked, determined whether this algorithm performs `secondStageErosion`
`private boolean`	`secondStageErosion`	When true, sets edge values which are greater than the median intensity by a user-defined factor of `aboveMedian` to zero.
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private float`	`stiffness`	Allows for variable motion of the mesh in the surface normal direction, default value of .15
`private javax.swing.JTextField`	`stiffnessTF`	Field for specifing stiffness of the mesh.
`private java.lang.String[]`	`titles`	DOCUMENT ME!
`private boolean`	`useCenterOfMass`	By default true, parameter indicates that the center position of the brain should be calculated using `JDialogExtractBrain.computeCenter(ModelImage, int, boolean)`
`private javax.swing.JCheckBox`	`useCenterOfMassCheckBox`	By default checked, yields a `true` value for `useCenterOfMass`
`private ViewUserInterface`	`userInterface`	The user interface for this dialog box.
`private boolean`	`useSphere`	When true estimates that boundary of the VOI by a sphere.
`private javax.swing.JCheckBox`	`useSphereCheckbox`	Initially not checked, estimates the boundary by a sphere rather than an ellipse.

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase
displayInNewFrame, isComplete, scriptParameters

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase
applyButton, bar, cancelButton, cancelFlag, closeButton, HELP, helpButton, mainDialogPanel, NEW, OKButton, parentFrame, progressBar, REPLACE, runInSeparateThread, runningScriptFlag, runQuiet, serif12, serif12B, voiManager

Fields inherited from class javax.swing.JDialog
accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog
DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Constructor Summary

Constructors
Constructor	Description
`JDialogExtractBrain()`	Empty constructor needed for dynamic instantiation (used during scripting).
`JDialogExtractBrain(java.awt.Frame theParentFrame, ModelImage im)`	Sets the appropriate variables.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Presently only the script function calls this method.
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	This method is required if the AlgorithmPerformed interface is implemented.
`protected void`	`callAlgorithm()`	Calls the algorithm.
`static WildMagic.LibFoundation.Mathematics.Vector3f`	`computeCenter(ModelImage img, int orientation, boolean sphereFlag)`	Calculate the center of the sphere / ellipsoid.
`ParameterTable`	`createInputParameters()`	Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in `setGUIFromParams()`).
`ParameterTable`	`createOutputParameters()`	Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
`ActionMetadata`	`getActionMetadata()`	Return meta-information about this discoverable action for categorization and labeling purposes.
`java.lang.String`	`getOutputImageName(java.lang.String imageParamName)`	Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).
`static int`	`histogramAnalysis(int[] imgBuffer)`	Analyze the histogram of the 10-bit binned 3D MRI.
`private void`	`init()`	Makes the GUI elements of the dialog.
`boolean`	`isActionComplete()`	Returns whether the action has successfully completed its execution.
`void`	`itemStateChanged(java.awt.event.ItemEvent event)`	Initial center position checkbox listener.
`void`	`setAboveMedian(float aboveMedian)`	Set the factor above the median at which second stage erosion occurs.
`void`	`setExtractToPaint(boolean extractToPaint)`	Sets whether or not to stop segmentation at paint.
`protected void`	`setGUIFromParams()`	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
`void`	`setImageRatio(float ratio)`	Sets the image influence ratio.
`void`	`setIterations(int nIter)`	Sets the number of iterations.
`void`	`setJustEllipse(boolean justEllipse)`	Accessor that sets whether of not initial ellipsoid result is displayed.
`void`	`setMaxDepth(int iMaxDepth)`	Set the maximum depth that is part of the image term in the surface evolution.
`void`	`setOrientation(int orient)`	Accessor that sets the orientation flag.
`void`	`setSecondStageErosion(boolean secondStageErosion)`	Sets whether or not the second stage performing edge erosion occurs.
`void`	`setStiffness(float fStiffness)`	Set the stiffness of the mesh that is part of the surface normal term in the surface evolution.
`void`	`setUseSphere(boolean useSphere)`	Sets whether or not to use only an estimate of sphere to nitialize the boundary evolution.
`private boolean`	`setVariables()`	Use the GUI results to set up the variables needed to run the algorithm.
`protected void`	`storeParamsFromGUI()`	Record the parameters just used to run this algorithm in a script.

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase
doPostAlgorithmActions, getDialogActionString, insertScriptLine, isComplete, scriptRun, setComplete

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase
buildApplyButton, buildButtons, buildCancelButton, buildCancelButton, buildCloseButton, buildHelpButton, buildImageComboBox, buildOKButton, buildOKButton, buildOKCancelButtons, buildTitledBorder, buildTitledBorder, createLabel, createProgressBar, createProgressBar, createTextField, focusGained, focusLost, getDialogName, isCancelled, isQuietRunning, isRunInSeparateThread, isScriptRunning, loadDefaults, loadDefaults, makeImageName, makeString, openNewFrame, saveDefaults, saveDefaults, setLeftHandSystem, setQuietRunning, setScriptRunning, setSeparateThread, setVisible, setVisible, setVisibleMenuBar, setVisibleStandard, setVOIManager, setWCSystem, testParameter, testParameterMin, updateFFTFileInfo, updateFileInfo, updateFileInfoOtherModality, updateFileInfoStatic, updateFileInfoStatic, updateFileTypeInfo, updateFileTypeInfo, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class javax.swing.JDialog
addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Dialog
addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface gov.nih.mipav.view.dialogs.ActionDiscovery
scriptRun

Methods inherited from interface gov.nih.mipav.model.scripting.ScriptableActionInterface
insertScriptLine, scriptRun

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - aboveMedian
```
private float aboveMedian
```
    The factor above which second stage edge erosion occurs.
  - centerOfMass
```
private WildMagic.LibFoundation.Mathematics.Vector3f centerOfMass
```
    The volume's center of mass computed from computeCenter(ModelImage, int, boolean)
  - depth
```
private int depth
```
    The maximum depth within the brain's surface to sample image intensities, by default set to 5.
  - depthTF
```
private javax.swing.JTextField depthTF
```
    Field for entering the maximum depth. The dialog box suggests a value between 3 - 19 and requires a value from 3 - 33.
  - erosionLabel
```
private javax.swing.JLabel erosionLabel
```
    Label for the percentage entered for second stage edge erosion.
  - erosionTF
```
private javax.swing.JTextField erosionTF
```
    Defines the allowable percentage for edge intensity values ub second stage edge erosion, default is 50 percent.
  - extractBrainAlgo
```
private AlgorithmBrainExtractor extractBrainAlgo
```
    Algorithm used for brain extraction.
  - extractToPaint
```
private boolean extractToPaint
```
    When true, mask of extracted brain is painted over the source image.
  - extractToPaintCheckBox
```
private javax.swing.JCheckBox extractToPaintCheckBox
```
    When checked, mask of extracted brain is painted over the source image.
  - image
```
private ModelImage image
```
    Source image for extracting brain, default image is null.
  - imageRatio
```
private float imageRatio
```
    Image influence ratio for controlling the sampling depth used to calculate intensity extrema, by default set to .1.
  - imageRatioTF
```
private javax.swing.JTextField imageRatioTF
```
    Field for entering the image influence ratio. The dialog box requires that a value from .01 - .51 be entered.
  - initCenterPoint
```
private WildMagic.LibFoundation.Mathematics.Vector3f initCenterPoint
```
    Either the volume's center of mass or a user indicated point depending on the value of useCenterOfMass.
  - initCenterX
```
private float initCenterX
```
    Used to denote the brain's center of mass y-coordinate. By default set to zero.
  - initCenterXLabel
```
private javax.swing.JLabel initCenterXLabel
```
    Label for the x-coordinate of the user-defined center.
  - initCenterXTF
```
private javax.swing.JTextField initCenterXTF
```
    An optional field for denoting a desired initial x-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false
  - initCenterY
```
private float initCenterY
```
    Used to denote the brain's center of mass y-coordinate. By default set to zero.
  - initCenterYLabel
```
private javax.swing.JLabel initCenterYLabel
```
    Label for the y-coordinate of the user-defined center.
  - initCenterYTF
```
private javax.swing.JTextField initCenterYTF
```
    An optional field for denoting a desired initial y-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false
  - initCenterZ
```
private float initCenterZ
```
    Used to denote the brain's center of mass y-coordinate. By default set to zero.
  - initCenterZLabel
```
private javax.swing.JLabel initCenterZLabel
```
    Label for the z-coordinate of the user-defined center.
  - initCenterZTF
```
private javax.swing.JTextField initCenterZTF
```
    An optional field for denoting a desired initial z-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false
  - justEllipse
```
private boolean justEllipse
```
    When true, image mask is set to the initial ellipsoid approximation of the brain calculated from the volume's center of mass.
  - justInitEllipsoidCheckbox
```
private javax.swing.JCheckBox justInitEllipsoidCheckbox
```
    When checked, justEllipse is set to true.
  - nIterations
```
private int nIterations
```
    Number of surface evolutions to perform, by default set to 500.
  - nIterationsTF
```
private javax.swing.JTextField nIterationsTF
```
    Field for inputting the number of surface evolutions to perform. This requests, but does not require, a value from 100 - 2000
  - orientation
```
private int orientation
```
    Orientation value corresponding to not the value of AlgorithmBrainExtractor.SAT_COR
  - orientCheckbox
```
private javax.swing.JCheckBox orientCheckbox
```
    When checked, denotes that the images orientation does not correspond to AlgorithmBrainExtractor.SAT_COR
  - secondStageCheckBox
```
private javax.swing.JCheckBox secondStageCheckBox
```
    Initially unchecked, determined whether this algorithm performs secondStageErosion
  - secondStageErosion
```
private boolean secondStageErosion
```
    When true, sets edge values which are greater than the median intensity by a user-defined factor of aboveMedian to zero.
  - stiffness
```
private float stiffness
```
    Allows for variable motion of the mesh in the surface normal direction, default value of .15
  - stiffnessTF
```
private javax.swing.JTextField stiffnessTF
```
    Field for specifing stiffness of the mesh. The dialog box suggests, but does not require that a value between .01 and .5 entered.
  - titles
```
private java.lang.String[] titles
```
    DOCUMENT ME!
  - useCenterOfMass
```
private boolean useCenterOfMass
```
    By default true, parameter indicates that the center position of the brain should be calculated using JDialogExtractBrain.computeCenter(ModelImage, int, boolean)
  - useCenterOfMassCheckBox
```
private javax.swing.JCheckBox useCenterOfMassCheckBox
```
    By default checked, yields a true value for useCenterOfMass
  - userInterface
```
private ViewUserInterface userInterface
```
    The user interface for this dialog box.
  - useSphere
```
private boolean useSphere
```
    When true estimates that boundary of the VOI by a sphere.
  - useSphereCheckbox
```
private javax.swing.JCheckBox useSphereCheckbox
```
    Initially not checked, estimates the boundary by a sphere rather than an ellipse.
- Constructor Detail
  - JDialogExtractBrain
```
public JDialogExtractBrain()
```
    Empty constructor needed for dynamic instantiation (used during scripting).
  - JDialogExtractBrain
```
public JDialogExtractBrain(java.awt.Frame theParentFrame,
                           ModelImage im)
```
    Sets the appropriate variables. Does not actually create a dialog that is visible because no user input is necessary at present.
    
    Parameters:
    
    theParentFrame - Parent frame.
    
    im - Source image.
- Method Detail
  - computeCenter
```
public static final WildMagic.LibFoundation.Mathematics.Vector3f computeCenter(ModelImage img,
                                                                               int orientation,
                                                                               boolean sphereFlag)
```
    Calculate the center of the sphere / ellipsoid.
    
    Parameters:
    
    img - the image to get the center of
    
    orientation - the orientation of the image
    
    sphereFlag - whether to find the center for a sphere or an ellipsoid
    
    Returns:
    
    the starting center point
  - histogramAnalysis
```
public static final int histogramAnalysis(int[] imgBuffer)
```
    Analyze the histogram of the 10-bit binned 3D MRI. The function computes a minimum threshold, a maximum threshold, and a background threshold that are used in the image term of the surface evolution. A brightness threshold is also computed that is used for determining the initial ellipsoid that approximates the brain surface.
    
    Parameters:
    
    imgBuffer - image data buffer normalized to 0 - 1023
    
    Returns:
    
    the current background threshold, which may have been changed during the histogram analysis
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Presently only the script function calls this method. When the script sends this dialog the action command, this method calls run.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Overrides:
    
    actionPerformed in class JDialogBase
    
    Parameters:
    
    event - event that triggers function
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    This method is required if the AlgorithmPerformed interface is implemented. It is called by the algorithms when it has completed or failed to to complete, so that the dialog can display the result image and/or clean up.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - Algorithm that caused the event.
  - itemStateChanged
```
public void itemStateChanged(java.awt.event.ItemEvent event)
```
    Initial center position checkbox listener.
    
    Specified by:
    
    itemStateChanged in interface java.awt.event.ItemListener
    
    Overrides:
    
    itemStateChanged in class JDialogBase
    
    Parameters:
    
    event - checkbox event
  - setAboveMedian
```
public void setAboveMedian(float aboveMedian)
```
    Set the factor above the median at which second stage erosion occurs.
    
    Parameters:
    
    aboveMedian - DOCUMENT ME!
  - setExtractToPaint
```
public void setExtractToPaint(boolean extractToPaint)
```
    Sets whether or not to stop segmentation at paint.
    
    Parameters:
    
    extractToPaint - .
  - setImageRatio
```
public void setImageRatio(float ratio)
```
    Sets the image influence ratio.
    
    Parameters:
    
    ratio - the image influence ratio
  - setIterations
```
public void setIterations(int nIter)
```
    Sets the number of iterations.
    
    Parameters:
    
    nIter - the number of iterations to do
  - setJustEllipse
```
public void setJustEllipse(boolean justEllipse)
```
    Accessor that sets whether of not initial ellipsoid result is displayed.
    
    Parameters:
    
    justEllipse - DOCUMENT ME!
  - setMaxDepth
```
public void setMaxDepth(int iMaxDepth)
```
    Set the maximum depth that is part of the image term in the surface evolution.
    
    Parameters:
    
    iMaxDepth - the new maximum depth
  - setOrientation
```
public void setOrientation(int orient)
```
    Accessor that sets the orientation flag.
    
    Parameters:
    
    orient - DOCUMENT ME!
  - setSecondStageErosion
```
public void setSecondStageErosion(boolean secondStageErosion)
```
    Sets whether or not the second stage performing edge erosion occurs.
    
    Parameters:
    
    secondStageErosion - if true erode boundary to clean up some.
  - setStiffness
```
public void setStiffness(float fStiffness)
```
    Set the stiffness of the mesh that is part of the surface normal term in the surface evolution.
    
    Parameters:
    
    fStiffness - the new stiffness
  - setUseSphere
```
public void setUseSphere(boolean useSphere)
```
    Sets whether or not to use only an estimate of sphere to nitialize the boundary evolution.
    
    Parameters:
    
    useSphere - if true estimate boundary using sphere model. If false the initial boundary is estimated using an ellipsoid, which is more difficult and error prone.
  - callAlgorithm
```
protected void callAlgorithm()
```
    Calls the algorithm.
    
    Specified by:
    
    callAlgorithm in class JDialogScriptableBase
  - setGUIFromParams
```
protected void setGUIFromParams()
```
    Set the dialog GUI using the script parameters while running this algorithm as part of a script.
    
    Specified by:
    
    setGUIFromParams in class JDialogScriptableBase
  - storeParamsFromGUI
```
protected void storeParamsFromGUI()
                           throws ParserException
```
    Record the parameters just used to run this algorithm in a script.
    
    Specified by:
    
    storeParamsFromGUI in class JDialogScriptableBase
    
    Throws:
    
    ParserException - If there is a problem creating/recording the new parameters.
  - init
```
private void init()
```
    Makes the GUI elements of the dialog. Not called at present because it is not necessary.
  - setVariables
```
private boolean setVariables()
```
    Use the GUI results to set up the variables needed to run the algorithm.
    
    Returns:
    
    true if parameters set successfully, false otherwise.
  - getActionMetadata
```
public ActionMetadata getActionMetadata()
```
    Return meta-information about this discoverable action for categorization and labeling purposes.
    
    Specified by:
    
    getActionMetadata in interface ActionDiscovery
    
    Returns:
    
    Metadata for this action.
  - createInputParameters
```
public ParameterTable createInputParameters()
```
    Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in setGUIFromParams()).
    
    Specified by:
    
    createInputParameters in interface ActionDiscovery
    
    Returns:
    
    A parameter table listing the inputs of this algorithm.
  - createOutputParameters
```
public ParameterTable createOutputParameters()
```
    Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
    
    Specified by:
    
    createOutputParameters in interface ActionDiscovery
    
    Returns:
    
    A parameter table listing the outputs of this algorithm.
  - getOutputImageName
```
public java.lang.String getOutputImageName(java.lang.String imageParamName)
```
    Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).
    
    Specified by:
    
    getOutputImageName in interface ActionDiscovery
    
    Parameters:
    
    imageParamName - The output image parameter label for which to get the image name.
    
    Returns:
    
    The image name of the requested output image parameter label.
  - isActionComplete
```
public boolean isActionComplete()
```
    Returns whether the action has successfully completed its execution.
    
    Specified by:
    
    isActionComplete in interface ActionDiscovery
    
    Returns:
    
    True, if the action is complete. False, if the action failed or is still running.

Class JDialogExtractBrain

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Nested classes/interfaces inherited from class javax.swing.JDialog

Nested classes/interfaces inherited from class java.awt.Dialog

Nested classes/interfaces inherited from class java.awt.Window

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Fields inherited from class javax.swing.JDialog

Fields inherited from class java.awt.Dialog

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface javax.swing.WindowConstants

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Methods inherited from class javax.swing.JDialog

Methods inherited from class java.awt.Dialog

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface gov.nih.mipav.view.dialogs.ActionDiscovery

Methods inherited from interface gov.nih.mipav.model.scripting.ScriptableActionInterface

Field Detail

serialVersionUID

aboveMedian

centerOfMass

depth

depthTF

erosionLabel

erosionTF

extractBrainAlgo

extractToPaint

extractToPaintCheckBox

image

imageRatio

imageRatioTF

initCenterPoint

initCenterX

initCenterXLabel

initCenterXTF

initCenterY

initCenterYLabel

initCenterYTF

initCenterZ

initCenterZLabel

initCenterZTF

justEllipse

justInitEllipsoidCheckbox

nIterations

nIterationsTF

orientation

orientCheckbox

secondStageCheckBox

secondStageErosion

stiffness

stiffnessTF

titles

useCenterOfMass

useCenterOfMassCheckBox

userInterface

useSphere

useSphereCheckbox

Constructor Detail

JDialogExtractBrain

JDialogExtractBrain

Method Detail

computeCenter

histogramAnalysis

actionPerformed

algorithmPerformed

itemStateChanged

setAboveMedian

setExtractToPaint

setImageRatio