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.JDialogN4MRIBiasFieldCorrection

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 JDialogN4MRIBiasFieldCorrection
extends JDialogScriptableBase
implements AlgorithmInterface, ActionDiscovery
```
Dialog to get user input, then call the algorithm.

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 boolean`	`autoThreshold`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`autoThresholdCheckbox`	DOCUMENT ME!
`private ModelImage`	`confidenceImage`
`private int`	`controlPoints`
`private float`	`convertTomm`	DOCUMENT ME!
`private boolean`	`createField`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`createFieldCheckbox`	DOCUMENT ME!
`private int[]`	`destExtents`	DOCUMENT ME!
`private double`	`endTol`	DOCUMENT ME!
`private float`	`fieldDistance`	DOCUMENT ME!
`private ModelImage`	`fieldImage`	DOCUMENT ME!
`private int`	`fittingLevels`
`private ModelImage`	`image`	DOCUMENT ME!
`private double`	`kernelfwhm`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelControlPoints`
`private javax.swing.JLabel`	`labelDistance`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelEndTol`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelFittingLevels`
`private javax.swing.JLabel`	`labelKernel`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelMaxIter`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelNoise`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelShrink`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelSignal`	DOCUMENT ME!
`private int`	`maxIter`	DOCUMENT ME!
`private AlgorithmN4MRIBiasFieldCorrectionFilter`	`N4Algo`	DOCUMENT ME!
`private double`	`noise`	DOCUMENT ME!
`private float[]`	`orgResol`	DOCUMENT ME!
`private boolean`	`regionFlag`	DOCUMENT ME!
`private ModelImage`	`resultImage`	DOCUMENT ME!
`private int`	`resXUnit`	DOCUMENT ME!
`private int`	`resYUnit`	DOCUMENT ME!
`private int`	`resZUnit`	DOCUMENT ME!
`private float`	`shrink`	DOCUMENT ME!
`private javax.swing.JTextField`	`textControlPoints`
`private javax.swing.JTextField`	`textDistance`	DOCUMENT ME!
`private javax.swing.JTextField`	`textEndTol`	DOCUMENT ME!
`private javax.swing.JTextField`	`textFittingLevels`
`private javax.swing.JTextField`	`textKernel`	DOCUMENT ME!
`private javax.swing.JTextField`	`textMaxIter`	DOCUMENT ME!
`private javax.swing.JTextField`	`textNoise`	DOCUMENT ME!
`private javax.swing.JTextField`	`textShrink`	DOCUMENT ME!
`private javax.swing.JTextField`	`textSignal`	DOCUMENT ME!
`private float`	`threshold`	DOCUMENT ME!
`private boolean`	`useScript`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`VOIRegions`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`wholeImage`	DOCUMENT ME!

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
`JDialogN4MRIBiasFieldCorrection()`	Empty constructor needed for dynamic instantiation (used during scripting).
`JDialogN4MRIBiasFieldCorrection(java.awt.Frame theParentFrame, ModelImage im)`	Create new dialog to set parameters for N4 MRI Bias Field Correction algorithm.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Closes dialog box when the OK button is pressed and calls the algorithm.
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	This method is required if the AlgorithmPerformed interface is implemented.
`protected void`	`callAlgorithm()`	Once all the necessary variables are set, call the N4 MRI Bias Field Correction algorithm.
`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).
`protected void`	`doPostAlgorithmActions()`	Store the result image in the script runner's image table now that the action execution is finished.
`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).
`ModelImage`	`getResultImage()`	Accessor that returns the image.
`private void`	`init()`	Sets up the GUI (panels, buttons, etc) and displays it on the screen.
`private void`	`initVars()`	Initializes the variables (resolutions) needed for the algorithm.
`boolean`	`isActionComplete()`	Returns whether the action has successfully completed its execution.
`void`	`setAutoFlag(boolean flag)`	Accessor that sets the auto threshold flag.
`void`	`setControlPoints(int controlPoints)`
`void`	`setCreateField(boolean flag)`	Accessor that sets the create field flag.
`void`	`setEndTol(double scale)`	Accessor that sets the end tol.
`void`	`setFieldDistance(float scale)`	Accessor that sets the field distance.
`void`	`setFittingLevels(int fittingLevels)`
`protected void`	`setGUIFromParams()`	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
`void`	`setKernel(double scale)`	Accessor that sets the kernel.
`void`	`setMaxIter(int max)`	Accessor that sets the max iterations.
`void`	`setNoise(double scale)`	Accessor that sets the noise.
`void`	`setRegionFlag(boolean flag)`	Accessor that sets the region flag.
`void`	`setShrink(float scale)`	Accessor that sets the shrink.
`void`	`setThreshold(float scale)`	Accessor that sets the threshold.
`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
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, itemStateChanged, 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

- Field Detail
  - autoThreshold
```
private boolean autoThreshold
```
    DOCUMENT ME!
  - autoThresholdCheckbox
```
private javax.swing.JCheckBox autoThresholdCheckbox
```
    DOCUMENT ME!
  - convertTomm
```
private float convertTomm
```
    DOCUMENT ME!
  - createField
```
private boolean createField
```
    DOCUMENT ME!
  - createFieldCheckbox
```
private javax.swing.JCheckBox createFieldCheckbox
```
    DOCUMENT ME!
  - destExtents
```
private int[] destExtents
```
    DOCUMENT ME!
  - endTol
```
private double endTol
```
    DOCUMENT ME!
  - fieldDistance
```
private float fieldDistance
```
    DOCUMENT ME!
  - fieldImage
```
private ModelImage fieldImage
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - kernelfwhm
```
private double kernelfwhm
```
    DOCUMENT ME!
  - labelDistance
```
private javax.swing.JLabel labelDistance
```
    DOCUMENT ME!
  - labelEndTol
```
private javax.swing.JLabel labelEndTol
```
    DOCUMENT ME!
  - labelKernel
```
private javax.swing.JLabel labelKernel
```
    DOCUMENT ME!
  - labelMaxIter
```
private javax.swing.JLabel labelMaxIter
```
    DOCUMENT ME!
  - labelNoise
```
private javax.swing.JLabel labelNoise
```
    DOCUMENT ME!
  - labelShrink
```
private javax.swing.JLabel labelShrink
```
    DOCUMENT ME!
  - labelSignal
```
private javax.swing.JLabel labelSignal
```
    DOCUMENT ME!
  - labelFittingLevels
```
private javax.swing.JLabel labelFittingLevels
```
  - labelControlPoints
```
private javax.swing.JLabel labelControlPoints
```
  - maxIter
```
private int maxIter
```
    DOCUMENT ME!
  - N4Algo
```
private AlgorithmN4MRIBiasFieldCorrectionFilter N4Algo
```
    DOCUMENT ME!
  - noise
```
private double noise
```
    DOCUMENT ME!
  - orgResol
```
private float[] orgResol
```
    DOCUMENT ME!
  - regionFlag
```
private boolean regionFlag
```
    DOCUMENT ME!
  - resultImage
```
private ModelImage resultImage
```
    DOCUMENT ME!
  - resXUnit
```
private int resXUnit
```
    DOCUMENT ME!
  - resYUnit
```
private int resYUnit
```
    DOCUMENT ME!
  - resZUnit
```
private int resZUnit
```
    DOCUMENT ME!
  - shrink
```
private float shrink
```
    DOCUMENT ME!
  - textDistance
```
private javax.swing.JTextField textDistance
```
    DOCUMENT ME!
  - textEndTol
```
private javax.swing.JTextField textEndTol
```
    DOCUMENT ME!
  - textKernel
```
private javax.swing.JTextField textKernel
```
    DOCUMENT ME!
  - textMaxIter
```
private javax.swing.JTextField textMaxIter
```
    DOCUMENT ME!
  - textNoise
```
private javax.swing.JTextField textNoise
```
    DOCUMENT ME!
  - textShrink
```
private javax.swing.JTextField textShrink
```
    DOCUMENT ME!
  - textSignal
```
private javax.swing.JTextField textSignal
```
    DOCUMENT ME!
  - textFittingLevels
```
private javax.swing.JTextField textFittingLevels
```
  - textControlPoints
```
private javax.swing.JTextField textControlPoints
```
  - fittingLevels
```
private int fittingLevels
```
  - controlPoints
```
private int controlPoints
```
  - threshold
```
private float threshold
```
    DOCUMENT ME!
  - confidenceImage
```
private ModelImage confidenceImage
```
  - useScript
```
private boolean useScript
```
    DOCUMENT ME!
  - VOIRegions
```
private javax.swing.JRadioButton VOIRegions
```
    DOCUMENT ME!
  - wholeImage
```
private javax.swing.JRadioButton wholeImage
```
    DOCUMENT ME!
- Constructor Detail
  - JDialogN4MRIBiasFieldCorrection
```
public JDialogN4MRIBiasFieldCorrection()
```
    Empty constructor needed for dynamic instantiation (used during scripting).
  - JDialogN4MRIBiasFieldCorrection
```
public JDialogN4MRIBiasFieldCorrection(java.awt.Frame theParentFrame,
                                       ModelImage im)
```
    Create new dialog to set parameters for N4 MRI Bias Field Correction algorithm.
    
    Parameters:
    
    theParentFrame - Parent frame.
    
    im - Source image.
- Method Detail
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Closes dialog box when the OK button is pressed and calls the algorithm.
    
    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 be display the result image and/or clean up.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - Algorithm that caused the event.
  - getResultImage
```
public ModelImage getResultImage()
```
    Accessor that returns the image.
    
    Returns:
    
    The result image.
  - setAutoFlag
```
public void setAutoFlag(boolean flag)
```
    Accessor that sets the auto threshold flag.
    
    Parameters:
    
    flag - true indicates auto threshold, false otherwise.
  - setCreateField
```
public void setCreateField(boolean flag)
```
    Accessor that sets the create field flag.
    
    Parameters:
    
    flag - true indicates create field image, false otherwise.
  - setEndTol
```
public void setEndTol(double scale)
```
    Accessor that sets the end tol.
    
    Parameters:
    
    scale - Value to set end tol to.
  - setFieldDistance
```
public void setFieldDistance(float scale)
```
    Accessor that sets the field distance.
    
    Parameters:
    
    scale - Value to set field distance to.
  - setKernel
```
public void setKernel(double scale)
```
    Accessor that sets the kernel.
    
    Parameters:
    
    scale - Value to set kernel to.
  - setMaxIter
```
public void setMaxIter(int max)
```
    Accessor that sets the max iterations.
    
    Parameters:
    
    max - The max iterations
  - setNoise
```
public void setNoise(double scale)
```
    Accessor that sets the noise.
    
    Parameters:
    
    scale - Value to set noise to.
  - setFittingLevels
```
public void setFittingLevels(int fittingLevels)
```
    Parameters:
    
    fittingLevels -
  - setControlPoints
```
public void setControlPoints(int controlPoints)
```
    Parameters:
    
    controlPoints -
  - setRegionFlag
```
public void setRegionFlag(boolean flag)
```
    Accessor that sets the region flag.
    
    Parameters:
    
    flag - true indicates the whole image is blurred, false indicates a region.
  - setShrink
```
public void setShrink(float scale)
```
    Accessor that sets the shrink.
    
    Parameters:
    
    scale - Value to set shrink to.
  - setThreshold
```
public void setThreshold(float scale)
```
    Accessor that sets the threshold.
    
    Parameters:
    
    scale - Value to set the threshold to.
  - callAlgorithm
```
protected void callAlgorithm()
```
    Once all the necessary variables are set, call the N4 MRI Bias Field Correction algorithm.
    
    Specified by:
    
    callAlgorithm in class JDialogScriptableBase
  - doPostAlgorithmActions
```
protected void doPostAlgorithmActions()
```
    Store the result image in the script runner's image table now that the action execution is finished.
    
    Overrides:
    
    doPostAlgorithmActions 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()
```
    Sets up the GUI (panels, buttons, etc) and displays it on the screen.
  - initVars
```
private void initVars()
```
    Initializes the variables (resolutions) needed for the algorithm.
  - 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 JDialogN4MRIBiasFieldCorrection

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

Field Detail

autoThreshold

autoThresholdCheckbox

convertTomm

createField

createFieldCheckbox

destExtents

endTol

fieldDistance

fieldImage

image

kernelfwhm

labelDistance

labelEndTol

labelKernel

labelMaxIter

labelNoise

labelShrink

labelSignal

labelFittingLevels

labelControlPoints

maxIter

N4Algo

noise

orgResol

regionFlag

resultImage

resXUnit

resYUnit

resZUnit

shrink

textDistance

textEndTol

textKernel

textMaxIter

textNoise

textShrink

textSignal

textFittingLevels

textControlPoints

fittingLevels

controlPoints

threshold

confidenceImage

useScript

VOIRegions

wholeImage

Constructor Detail

JDialogN4MRIBiasFieldCorrection

JDialogN4MRIBiasFieldCorrection

Method Detail

actionPerformed

algorithmPerformed