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.JDialogRegistrationOAR35D

All Implemented Interfaces:

AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, 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 JDialogRegistrationOAR35D
extends JDialogScriptableBase
implements AlgorithmInterface
```
Dialog to get user input, then call AlgorithmRegOAR35D. Internal registration is performed within one 4D image. In adjacent mode the first volume above the reference volume is registered to the reference volume, then the second volume above the reference volume is registered to the first volume above the reference volume, and so on until the last volume is registered the next to last volume. Then, the first volume below the reference volume is registered to the reference volume, the second volume below the reference volume is registered to first volume below the reference volume, and so on unitl the first volume is registered to the second volume. In reference mode every volume is simply registered to the reference volume. In average mode every volume is registered to the average of all volumes.

Author:

Neva Cherniavsky

See Also:

AlgorithmCostFunctions, AlgorithmRegOAR35D, 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 javax.swing.JRadioButton`	`adjacentImageRButton`	DOCUMENT ME!
`private javax.swing.JDialog`	`advancedDialog`	Variables for Advanced Settings dialog.
`private javax.swing.JRadioButton`	`averageImageRButton`	DOCUMENT ME!
`private javax.swing.JButton`	`buttonWeightInput`	DOCUMENT ME!
`private float`	`coarseRate`	DOCUMENT ME!
`private javax.swing.JTextField`	`coarseRateText`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxCostFunct`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxDOF`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxInterp`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxInterp2`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxSearchAlgo`
`private int`	`cost`	DOCUMENT ME!
`private java.lang.String`	`directoryWInput`	DOCUMENT ME!
`private boolean`	`doColor`	DOCUMENT ME!
`private int`	`DOF`	DOCUMENT ME!
`(package private) boolean`	`doGraph`	DOCUMENT ME!
`private boolean`	`doJTEM`	When true, the full version of JTEM Powell search is used in the registration algorithm.
`private boolean`	`doSubsample`	DOCUMENT ME!
`private int`	`ELSUNC`
`private boolean`	`fastMode`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`fastModeCheckbox`	DOCUMENT ME!
`private java.lang.String`	`fileNameWInput`	DOCUMENT ME!
`private float`	`fineRate`	DOCUMENT ME!
`private javax.swing.JTextField`	`fineRateText`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`graphCheckBox`	DOCUMENT ME!
`private ModelImage`	`inputWeightImage`	DOCUMENT ME!
`private int`	`interp`	DOCUMENT ME!
`private int`	`interp2`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`jtemCheckbox`	Turns on the JTEM full version of Powell's algorithm on or off
`private javax.swing.JLabel`	`labelInterp2`	DOCUMENT ME!
`private int`	`LEVENBERG_MARQUARDT`
`private ModelImage`	`matchImage`	DOCUMENT ME!
`private int`	`maxIterations`	DOCUMENT ME!
`private int`	`maxIterations_def`	DOCUMENT ME!
`private javax.swing.JTextField`	`maxIterationsText`	DOCUMENT ME!
`private int`	`NL2SOL`
`private javax.swing.JRadioButton`	`noneRadio`	DOCUMENT ME!
`private int`	`numMinima`	DOCUMENT ME!
`private int`	`numMinima_def`	DOCUMENT ME!
`private javax.swing.JTextField`	`numMinText`	DOCUMENT ME!
`private int`	`POWELL`
`private int`	`refImageNum`	DOCUMENT ME!
`private javax.swing.JTextField`	`refImageNumText`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`refImageRButton`	DOCUMENT ME!
`private ModelImage`	`refVolume`	DOCUMENT ME!
`private AlgorithmRegOAR35D`	`reg35`	DOCUMENT ME!
`private AlgorithmRegELSUNCOAR35D`	`reg35E`
`private int`	`registerTo`	DOCUMENT ME!
`private float`	`rotateBegin`	DOCUMENT ME!
`private javax.swing.JTextField`	`rotateBeginText`	DOCUMENT ME!
`private float`	`rotateEnd`	DOCUMENT ME!
`private javax.swing.JTextField`	`rotateEndText`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`sampleCheckBox`	DOCUMENT ME!
`private int`	`searchAlgorithm`
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private javax.swing.JTextField`	`textInput`	DOCUMENT ME!
`private ViewUserInterface`	`UI`	DOCUMENT ME!
`private boolean`	`useOutsideReferenceVolume`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`voiRadio`	DOCUMENT ME!
`private boolean`	`voisOnly`	DOCUMENT ME!
`private boolean`	`weighted`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`weightRadio`	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
`JDialogRegistrationOAR35D()`	Empty constructor needed for dynamic instantiation (used during scripting).
`JDialogRegistrationOAR35D(java.awt.Frame theParentFrame, ModelImage im)`	Creates new dialog for user to choose variables for internal registration.

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, sets the variables, and calls the algorithm.
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	This method is required if the AlgorithmPerformed interface is implemented.
`private javax.swing.JDialog`	`buildAdvancedDialog(int maxIter, int numMinima)`	Build advanced settings dialog.
`protected void`	`callAlgorithm()`	Calls the algorithm with the set-up parameters.
`private void`	`init()`	Initializes the GUI components and displays the dialog.
`void`	`itemStateChanged(java.awt.event.ItemEvent event)`	Changes the interpolation box to enabled or disabled depending on if the transform box is checked or not.
`void`	`setCoarseBegin(float x)`	Accessor to set the coarse sample begin.
`void`	`setCoarseEnd(float x)`	Accessor to set the coarse sample end.
`void`	`setCoarseRate(float x)`	Accessor to set the coarse sample rate.
`void`	`setCostChoice(int x)`	Accessor to set the choice of cost function.
`void`	`setDOF(int x)`	Accessor to set the degrees of freedom.
`void`	`setFastMode(boolean flag)`	Accessor to set whether or not to execute the fast mode (skip sub sample and goto last final optimization).
`void`	`setFineRate(float x)`	Accessor to set the fine sample rate.
`void`	`setGraphCheckBox(boolean doGraph)`	Accessor to set graphCheckBox.
`protected void`	`setGUIFromParams()`	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
`void`	`setInputWeightImage(ModelImage im)`	Accessor to set the input weight image.
`void`	`setInterp(int x)`	Accessor to set the initial interpolation.
`void`	`setInterp2(int x)`	Accessor to set the final interpolation.
`void`	`setMaxIterations(int maxIterations)`	Accessor to set maxIterations.
`void`	`setNumMinima(int numMinima)`	Accessor to set numMinima.
`void`	`setOutsideReferenceVolume(ModelImage refVolume)`	allows user to use an outside reference volume for registering.
`void`	`setRefImageNum(int refImageNumber)`	Accessor to set refImageNum.
`void`	`setRegisterTo(int registerTo)`	Accessor to set registerTo.
`void`	`setSearchAlgorithm(int searchAlgorithm)`
`void`	`setSubsample(boolean doSubsample)`	Accessor to set whether or not subsampling occurs.
`private boolean`	`setVariables()`	Sets the variables needed to call the registration algorithm based on the values entered in the dialog.
`void`	`setVoisOnly(boolean flag)`	Accessor to set the VOIs only flag.
`void`	`setWeighted(boolean flag)`	Accessor to set the weighted images flag.
`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

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - POWELL
```
private final int POWELL
```
    See Also:
    
    Constant Field Values
  - ELSUNC
```
private final int ELSUNC
```
    See Also:
    
    Constant Field Values
  - LEVENBERG_MARQUARDT
```
private final int LEVENBERG_MARQUARDT
```
    See Also:
    
    Constant Field Values
  - NL2SOL
```
private final int NL2SOL
```
    See Also:
    
    Constant Field Values
  - searchAlgorithm
```
private int searchAlgorithm
```
  - doGraph
```
boolean doGraph
```
    DOCUMENT ME!
  - adjacentImageRButton
```
private javax.swing.JRadioButton adjacentImageRButton
```
    DOCUMENT ME!
  - advancedDialog
```
private javax.swing.JDialog advancedDialog
```
    Variables for Advanced Settings dialog.
  - averageImageRButton
```
private javax.swing.JRadioButton averageImageRButton
```
    DOCUMENT ME!
  - maxIterationsText
```
private javax.swing.JTextField maxIterationsText
```
    DOCUMENT ME!
  - numMinText
```
private javax.swing.JTextField numMinText
```
    DOCUMENT ME!
  - doJTEM
```
private boolean doJTEM
```
    When true, the full version of JTEM Powell search is used in the registration algorithm.
  - jtemCheckbox
```
private javax.swing.JCheckBox jtemCheckbox
```
    Turns on the JTEM full version of Powell's algorithm on or off
  - buttonWeightInput
```
private javax.swing.JButton buttonWeightInput
```
    DOCUMENT ME!
  - coarseRateText
```
private javax.swing.JTextField coarseRateText
```
    DOCUMENT ME!
  - comboBoxCostFunct
```
private javax.swing.JComboBox comboBoxCostFunct
```
    DOCUMENT ME!
  - comboBoxSearchAlgo
```
private javax.swing.JComboBox comboBoxSearchAlgo
```
  - comboBoxDOF
```
private javax.swing.JComboBox comboBoxDOF
```
    DOCUMENT ME!
  - comboBoxInterp
```
private javax.swing.JComboBox comboBoxInterp
```
    DOCUMENT ME!
  - comboBoxInterp2
```
private javax.swing.JComboBox comboBoxInterp2
```
    DOCUMENT ME!
  - cost
```
private int cost
```
    DOCUMENT ME!
  - interp
```
private int interp
```
    DOCUMENT ME!
  - interp2
```
private int interp2
```
    DOCUMENT ME!
  - DOF
```
private int DOF
```
    DOCUMENT ME!
  - doColor
```
private boolean doColor
```
    DOCUMENT ME!
  - doSubsample
```
private boolean doSubsample
```
    DOCUMENT ME!
  - fastMode
```
private boolean fastMode
```
    DOCUMENT ME!
  - fastModeCheckbox
```
private javax.swing.JCheckBox fastModeCheckbox
```
    DOCUMENT ME!
  - fileNameWInput
```
private java.lang.String fileNameWInput
```
    DOCUMENT ME!
  - directoryWInput
```
private java.lang.String directoryWInput
```
    DOCUMENT ME!
  - fineRateText
```
private javax.swing.JTextField fineRateText
```
    DOCUMENT ME!
  - graphCheckBox
```
private javax.swing.JCheckBox graphCheckBox
```
    DOCUMENT ME!
  - inputWeightImage
```
private ModelImage inputWeightImage
```
    DOCUMENT ME!
  - labelInterp2
```
private javax.swing.JLabel labelInterp2
```
    DOCUMENT ME!
  - matchImage
```
private ModelImage matchImage
```
    DOCUMENT ME!
  - maxIterations_def
```
private int maxIterations_def
```
    DOCUMENT ME!
  - numMinima_def
```
private int numMinima_def
```
    DOCUMENT ME!
  - maxIterations
```
private int maxIterations
```
    DOCUMENT ME!
  - noneRadio
```
private javax.swing.JRadioButton noneRadio
```
    DOCUMENT ME!
  - numMinima
```
private int numMinima
```
    DOCUMENT ME!
  - refImageNum
```
private int refImageNum
```
    DOCUMENT ME!
  - refImageNumText
```
private javax.swing.JTextField refImageNumText
```
    DOCUMENT ME!
  - refImageRButton
```
private javax.swing.JRadioButton refImageRButton
```
    DOCUMENT ME!
  - refVolume
```
private ModelImage refVolume
```
    DOCUMENT ME!
  - reg35
```
private AlgorithmRegOAR35D reg35
```
    DOCUMENT ME!
  - reg35E
```
private AlgorithmRegELSUNCOAR35D reg35E
```
  - registerTo
```
private int registerTo
```
    DOCUMENT ME!
  - rotateBegin
```
private float rotateBegin
```
    DOCUMENT ME!
  - rotateEnd
```
private float rotateEnd
```
    DOCUMENT ME!
  - coarseRate
```
private float coarseRate
```
    DOCUMENT ME!
  - fineRate
```
private float fineRate
```
    DOCUMENT ME!
  - rotateBeginText
```
private javax.swing.JTextField rotateBeginText
```
    DOCUMENT ME!
  - rotateEndText
```
private javax.swing.JTextField rotateEndText
```
    DOCUMENT ME!
  - sampleCheckBox
```
private javax.swing.JCheckBox sampleCheckBox
```
    DOCUMENT ME!
  - textInput
```
private javax.swing.JTextField textInput
```
    DOCUMENT ME!
  - UI
```
private ViewUserInterface UI
```
    DOCUMENT ME!
  - useOutsideReferenceVolume
```
private boolean useOutsideReferenceVolume
```
    DOCUMENT ME!
  - voiRadio
```
private javax.swing.JRadioButton voiRadio
```
    DOCUMENT ME!
  - voisOnly
```
private boolean voisOnly
```
    DOCUMENT ME!
  - weighted
```
private boolean weighted
```
    DOCUMENT ME!
  - weightRadio
```
private javax.swing.JRadioButton weightRadio
```
    DOCUMENT ME!
- Constructor Detail
  - JDialogRegistrationOAR35D
```
public JDialogRegistrationOAR35D()
```
    Empty constructor needed for dynamic instantiation (used during scripting).
  - JDialogRegistrationOAR35D
```
public JDialogRegistrationOAR35D(java.awt.Frame theParentFrame,
                                 ModelImage im)
```
    Creates new dialog for user to choose variables for internal registration.
    
    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, sets the variables, 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 complete.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - Algorithm that caused the event.
  - itemStateChanged
```
public void itemStateChanged(java.awt.event.ItemEvent event)
```
    Changes the interpolation box to enabled or disabled depending on if the transform box is checked or not.
    
    Specified by:
    
    itemStateChanged in interface java.awt.event.ItemListener
    
    Overrides:
    
    itemStateChanged in class JDialogBase
    
    Parameters:
    
    event - Event that triggered this function.
  - setCoarseBegin
```
public void setCoarseBegin(float x)
```
    Accessor to set the coarse sample begin.
    
    Parameters:
    
    x - Coarse begin
  - setCoarseEnd
```
public void setCoarseEnd(float x)
```
    Accessor to set the coarse sample end.
    
    Parameters:
    
    x - Coarse end
  - setCoarseRate
```
public void setCoarseRate(float x)
```
    Accessor to set the coarse sample rate.
    
    Parameters:
    
    x - Coarse rate
  - setCostChoice
```
public void setCostChoice(int x)
```
    Accessor to set the choice of cost function.
    
    Parameters:
    
    x - Cost function.
  - setDOF
```
public void setDOF(int x)
```
    Accessor to set the degrees of freedom.
    
    Parameters:
    
    x - Degrees of freedom
  - setFastMode
```
public void setFastMode(boolean flag)
```
    Accessor to set whether or not to execute the fast mode (skip sub sample and goto last final optimization).
    
    Parameters:
    
    flag - true then skip to level one (last ) optimization.
  - setFineRate
```
public void setFineRate(float x)
```
    Accessor to set the fine sample rate.
    
    Parameters:
    
    x - Fine rate
  - setGraphCheckBox
```
public void setGraphCheckBox(boolean doGraph)
```
    Accessor to set graphCheckBox.
    
    Parameters:
    
    doGraph - if true output graphs of rotations and translations
  - setInputWeightImage
```
public void setInputWeightImage(ModelImage im)
```
    Accessor to set the input weight image.
    
    Parameters:
    
    im - Input weight image.
  - setInterp
```
public void setInterp(int x)
```
    Accessor to set the initial interpolation.
    
    Parameters:
    
    x - Interpolation
  - setInterp2
```
public void setInterp2(int x)
```
    Accessor to set the final interpolation.
    
    Parameters:
    
    x - Interpolation
  - setMaxIterations
```
public void setMaxIterations(int maxIterations)
```
    Accessor to set maxIterations.
    
    Parameters:
    
    maxIterations - DOCUMENT ME!
  - setNumMinima
```
public void setNumMinima(int numMinima)
```
    Accessor to set numMinima.
    
    Parameters:
    
    numMinima - DOCUMENT ME!
  - setOutsideReferenceVolume
```
public void setOutsideReferenceVolume(ModelImage refVolume)
```
    allows user to use an outside reference volume for registering.
    
    Parameters:
    
    refVolume - (3-Dim reference volume)
  - setRefImageNum
```
public void setRefImageNum(int refImageNumber)
```
    Accessor to set refImageNum.
    
    Parameters:
    
    refImageNumber - number of reference slice
  - setRegisterTo
```
public void setRegisterTo(int registerTo)
```
    Accessor to set registerTo.
    
    Parameters:
    
    registerTo - - 1 = adjacent, 2 = average, 3 = reference
  - setSearchAlgorithm
```
public void setSearchAlgorithm(int searchAlgorithm)
```
    Parameters:
    
    searchAlgorithm -
  - setSubsample
```
public void setSubsample(boolean doSubsample)
```
    Accessor to set whether or not subsampling occurs.
    
    Parameters:
    
    doSubsample - DOCUMENT ME!
  - setVoisOnly
```
public void setVoisOnly(boolean flag)
```
    Accessor to set the VOIs only flag.
    
    Parameters:
    
    flag - true then only register the parts of the images in the VOIs.
  - setWeighted
```
public void setWeighted(boolean flag)
```
    Accessor to set the weighted images flag.
    
    Parameters:
    
    flag - true means there are weighted images.
  - callAlgorithm
```
protected void callAlgorithm()
```
    Calls the algorithm with the set-up parameters.
    
    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.
  - buildAdvancedDialog
```
private javax.swing.JDialog buildAdvancedDialog(int maxIter,
                                                int numMinima)
```
    Build advanced settings dialog. Returns JDialog.
    
    Parameters:
    
    maxIter - DOCUMENT ME!
    
    numMinima - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - init
```
private void init()
```
    Initializes the GUI components and displays the dialog.
  - setVariables
```
private boolean setVariables()
```
    Sets the variables needed to call the registration algorithm based on the values entered in the dialog.
    
    Returns:
    
    true if the variables are properly set, false otherwise.

Class JDialogRegistrationOAR35D

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

Field Detail

serialVersionUID

POWELL

ELSUNC

LEVENBERG_MARQUARDT

NL2SOL

searchAlgorithm

doGraph

adjacentImageRButton

advancedDialog

averageImageRButton

maxIterationsText

numMinText

doJTEM

jtemCheckbox

buttonWeightInput

coarseRateText

comboBoxCostFunct

comboBoxSearchAlgo

comboBoxDOF

comboBoxInterp

comboBoxInterp2

cost

interp

interp2

DOF

doColor

doSubsample

fastMode

fastModeCheckbox

fileNameWInput

directoryWInput

fineRateText

graphCheckBox

inputWeightImage

labelInterp2

matchImage

maxIterations_def

numMinima_def

maxIterations

noneRadio

numMinima

refImageNum

refImageNumText

refImageRButton

refVolume

reg35

reg35E

registerTo

rotateBegin

rotateEnd

coarseRate

fineRate

rotateBeginText