java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Frame
      - javax.swing.JFrame
        
        gov.nih.mipav.view.ViewJFrameBase
        
        gov.nih.mipav.view.ViewJFrameRegistrationTool

All Implemented Interfaces:

VOIManagerInterfaceListener, ViewImageUpdateInterface, java.awt.event.ActionListener, java.awt.event.ComponentListener, 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.event.ChangeListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants
```
public class ViewJFrameRegistrationTool
extends ViewJFrameBase
implements java.awt.event.ItemListener, javax.swing.event.ChangeListener, java.awt.event.FocusListener, java.awt.event.WindowListener, VOIManagerInterfaceListener
```
ViewJFrameRegistrationTool is called in ViewJFrameImage. ViewJFrameRegistrationTool calls ViewJComponentRegistration.
In ordinary image dragging you simply drag one image. Here the adjustable slice is moved while the reference slice stays fixed, and a bilinear transformation followed by an alpha blending of the 2 images occurs. Because g.drawImage in ViewJComponentBase draws the blended image, the movement cannot simply be performed by changing the parameters of g.drawImage.

The adjustable image slice moves are determined by floating point values fed into a transform routine that performs bilinear interpolation.

The file menu has 2 items, Show VOIs in blended window and Close registration. An alpha blending slider determines the percentages of the image produced by the reference slice(image R) and the adjusted slice(imageA). 2 tabs are present, blended and dual. On the blended tab 17 toolbar buttons are present:

1.) Display LUT table calls forth a display panel which allows the user to set separate histograms for the reference and adjusted slices.
2.) Create checkerboard pattern
3.) Magnify image 2.0X.
4.) Magnify image 0.5X.
5.) Window region of imageB
6.) Reset to return slice to original state and remove all markers
7.) Commit the slice to the image.
8.) Set the pixel increment for image translations and movements of the rotation center. Values can range from 0.01 to 2048.0. Movements of the rotation center will only be performed to the nearest integer. The default value is 1.0 pixels.
9.) Put in translate mode. In this mode the image can either be moved with the up, down, right, and left buttons or moved a distance and direction with mouse dragging. 10.) up button for image translation in translate mode.
11.) down button for image translation in translate mode.
12.) right button for image translation in translate mode.
13.) left button for image translation in translate mode.
14.) Set degree increment for image rotations. Values can range from 0.01 to 360.0 degrees. The default value is 1.0 degrees.
15.) Put in rotate mode for rotating the image. In this mode the image can be moved either with the cw and ccw buttons or moved an angle around the rotation center point as given by mouse dragging. The initial rotation point is the center, but a new rotation point can be set with a mouse press.
16.) cw button for rotating an image clockwise in rotate mode.
17.) ccw button for rotating an image counterclockwise in rotate mode.
On the dual tab 16 toolbar buttons are present:
*
1.) Display LUT table calls forth a display panel which allows the user to set separate histograms for the reference and adjusted slices.
2.) Magnify reference image 2.0X.
3.) Magnify reference image 0.5X.
4.) Magnify adjusted image 2.0X.
5.) Magnify adjusted image 0.5X.
6.) Apply least squares alignment.
7.) Apply thin plate spline alignment.
8.) Reset image to original state and remove all markers.
9.) Put in POINT_VOI mode for setting the location of reference slice markers. Red markers are used.
10.) Put in the POINT_VOI mode for setting the location of adjusted slice markers. Green markers are used.
11.) Delete selected reference slice markers.
12.) Delete selected adjusted slice markers.
13.) Copy reference markers to the adjusted image.
14.) Copy adjusted markers to the reference image.
15.) Return to default mode.
16.) Commit the slice to image.

Version:

1.0

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`ViewJFrameRegistrationTool.JDialogIncrement`	Class for the two dialogs for incrementing - the pixel increment dialog and the degree increment dialog.

Nested classes/interfaces inherited from class javax.swing.JFrame
javax.swing.JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame

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 int`	`adjMark`	DOCUMENT ME!
`static int`	`ADJMARK`	adjusted marker type.
`private javax.swing.JToggleButton`	`adjMarkButton`	DOCUMENT ME!
`private javax.swing.JButton`	`adjMarkMinusButton`	DOCUMENT ME!
`private AlgorithmCostFunctions2D`	`algoCost`
`private javax.swing.JSlider`	`alphaSlider`	DOCUMENT ME!
`private javax.swing.JPanel`	`bothPanel`	DOCUMENT ME!
`private int`	`bufferFactor`	DOCUMENT ME!
`private int`	`bufferSize`	DOCUMENT ME!
`private javax.swing.JButton[]`	`buttonArray`	DOCUMENT ME!
`private javax.swing.JButton`	`calculateCostButton`
`private javax.swing.JButton`	`ccwButton`	DOCUMENT ME!
`private ViewJComponentRegistration`	`componentImage`	for both images displayed together.
`private ViewJComponentSingleRegistration`	`componentImageA`	for images to be displayed separately.
`private ViewJComponentSingleRegistration`	`componentImageB`	DOCUMENT ME!
`private javax.swing.JPanel`	`controlPanel`	DOCUMENT ME!
`private ViewControlsImage`	`controls`	DOCUMENT ME!
`private javax.swing.JButton`	`copyAdjToRefButton`	DOCUMENT ME!
`private javax.swing.JButton`	`copyRefToAdjButton`	DOCUMENT ME!
`private javax.swing.JScrollPane`	`costFunctionScrollPane`	Scroll Pane for the Text Area
`private javax.swing.JTextArea`	`costFunctionTextArea`
`private java.awt.GridBagConstraints`	`cpGBC`	DOCUMENT ME!
`private java.awt.GridBagLayout`	`cpGBL`	DOCUMENT ME!
`private int`	`curAdjMark`	DOCUMENT ME!
`private int`	`curRefMark`	DOCUMENT ME!
`private javax.swing.JButton`	`cwButton`	DOCUMENT ME!
`private javax.swing.JToggleButton`	`defaultModeButton`	DOCUMENT ME!
`private float`	`degreeIncrement`	DOCUMENT ME!
`private javax.swing.JButton`	`degreeIncrementButton`	DOCUMENT ME!
`private boolean`	`doDrag`	DOCUMENT ME!
`private boolean`	`doneLeastSquares`	DOCUMENT ME!
`private boolean`	`doRegionB`	DOCUMENT ME!
`private javax.swing.JButton`	`downButton`	DOCUMENT ME!
`private javax.swing.border.Border`	`etchedBorder`	DOCUMENT ME!
`private int[]`	`extents`	DOCUMENT ME!
`private javax.swing.JMenu`	`fileMenu`	DOCUMENT ME!
`private boolean`	`firstDraw`	DOCUMENT ME!
`private java.awt.Font`	`font12`	DOCUMENT ME!
`private java.awt.GridBagConstraints`	`gbc`	DOCUMENT ME!
`private javax.swing.JMenu`	`helpMenu`	DOCUMENT ME!
`private int`	`i`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`private float[]`	`imageBufferA`	DOCUMENT ME!
`private float[]`	`imageBufferB`	DOCUMENT ME!
`private float[]`	`imageBufferOriginalB`	DOCUMENT ME!
`private int`	`imageSize`	DOCUMENT ME!
`private javax.swing.JMenuItem`	`itemClose`	DOCUMENT ME!
`private javax.swing.JMenuItem`	`itemHelp`	DOCUMENT ME!
`private int`	`j`	DOCUMENT ME!
`private javax.swing.JButton`	`leftButton`	DOCUMENT ME!
`private boolean`	`logMagDisplay`	DOCUMENT ME!
`private boolean`	`lsPerformed`	DOCUMENT ME!
`private int`	`mode`	DOCUMENT ME!
`private javax.swing.ButtonGroup`	`movementGroup`	DOCUMENT ME!
`private int`	`n`	DOCUMENT ME!
`private int`	`newAlphaBlend`	DOCUMENT ME!
`private int[]`	`newExtents`	DOCUMENT ME!
`private javax.swing.JMenuBar`	`openingMenuBar`	DOCUMENT ME!
`private int[]`	`pixBuffer`	DOCUMENT ME!
`private int[]`	`pixBufferB`	DOCUMENT ME!
`private int[]`	`pixBufferCompA`	DOCUMENT ME!
`private int[]`	`pixBufferCompB`	DOCUMENT ME!
`private float`	`pixelIncrement`	DOCUMENT ME!
`private javax.swing.JButton`	`pixelIncrementButton`	DOCUMENT ME!
`private double[][]`	`pointSetA`	DOCUMENT ME!
`private double[][]`	`pointSetB`	DOCUMENT ME!
`private double[][]`	`pointSetBT`	DOCUMENT ME!
`private int`	`refMark`	DOCUMENT ME!
`static int`	`REFMARK`	reference marker type.
`private javax.swing.JToggleButton`	`refMarkButton`	DOCUMENT ME!
`private javax.swing.JButton`	`refMarkMinusButton`	DOCUMENT ME!
`private javax.swing.JToggleButton`	`regButton`	DOCUMENT ME!
`private ModelRGB`	`RGBa`	DOCUMENT ME!
`private ModelRGB`	`RGBb`	DOCUMENT ME!
`private javax.swing.JButton`	`rightButton`	DOCUMENT ME!
`private javax.swing.JToggleButton`	`rotateButton`	DOCUMENT ME!
`static int`	`ROTATIONCENTER`	The 3 types of markers - rotation center, reference slice, and adjusted slice.
`private javax.swing.JScrollPane`	`scrollPane`	DOCUMENT ME!
`private javax.swing.JScrollPane`	`scrollPaneSeparateA`	DOCUMENT ME!
`private javax.swing.JScrollPane`	`scrollPaneSeparateB`	DOCUMENT ME!
`private int`	`scrollPaneSize`	DOCUMENT ME!
`private ModelImage`	`secondImage`	DOCUMENT ME!
`private javax.swing.JPanel`	`separatePanel`	DOCUMENT ME!
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`protected java.awt.Font`	`serif12`	DOCUMENT ME!
`private javax.swing.JCheckBoxMenuItem`	`showVOIs`	DOCUMENT ME!
`private ModelSimpleImage`	`simpleImg1`	Holds extents, other info about firstImage and SecondImage
`private ModelSimpleImage`	`simpleImg2`	Holds extents, other info about firstImage and SecondImage
`private javax.swing.JTabbedPane`	`tabbedPane`	DOCUMENT ME!
`private TransMatrix`	`tMatrix`	Identity matrix for testing cost
`javax.swing.JToggleButton[]`	`toggleArray`	DOCUMENT ME!
`private javax.swing.JToolBar`	`toolBar`	DOCUMENT ME!
`private javax.swing.JToolBar`	`toolBar2`	DOCUMENT ME!
`private javax.swing.JToolBar`	`toolBarSep`	DOCUMENT ME!
`private javax.swing.JPanel`	`topPanel`	DOCUMENT ME!
`private javax.swing.JToggleButton`	`translateButton`	DOCUMENT ME!
`private javax.swing.JButton`	`upButton`	DOCUMENT ME!
`private ViewUserInterface`	`userInterface`	DOCUMENT ME!
`private VOIManagerInterface`	`voiManager`
`private int[]`	`xCoords`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private TransMatrix`	`xfrm`	DOCUMENT ME!
`private TransMatrix`	`xfrmBA`	DOCUMENT ME!
`private TransMatrix`	`xfrmD`	DOCUMENT ME!
`private TransMatrix`	`xfrmH`	DOCUMENT ME!
`private int[]`	`xOrg`	DOCUMENT ME!
`private float`	`xRes`	DOCUMENT ME!
`private float`	`xRotation`	DOCUMENT ME!
`private int`	`xScreen`	DOCUMENT ME!
`private int[]`	`yCoords`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private int[]`	`yOrg`	DOCUMENT ME!
`private float`	`yRes`	DOCUMENT ME!
`private float`	`yRotation`	DOCUMENT ME!
`private int`	`yScreen`	DOCUMENT ME!
`private float`	`zoom`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.view.ViewJFrameBase
absoluteGoToButton, absoluteGoToPanel, absoluteLabel, absoluteLabelVals, absolutePanel, absoluteXLabel, absoluteXTextField, absoluteYLabel, absoluteYTextField, absoluteZLabel, absoluteZTextField, alphaBlend, defaultLUTa, defaultLUTb, displayMode, IMAGE_A, IMAGE_A_B, IMAGE_B, imageA, imageB, isClosing, linkedScrolling, linkFrame, linkTriFrame, LUTa, LUTb, progressBar, scannerLPS_APLabel, scannerLPS_APTextField, scannerLPS_GoToButton, scannerLPS_GoToPanel, scannerLPS_ISLabel, scannerLPS_ISTextField, scannerLPS_RLLabel, scannerLPS_RLTextField, scannerLPSLabel, scannerLPSLabelVals, scannerLPSPanel, scannerRAS_APLabel, scannerRAS_APTextField, scannerRAS_GoToButton, scannerRAS_GoToPanel, scannerRAS_ISLabel, scannerRAS_ISTextField, scannerRAS_RLLabel, scannerRAS_RLTextField, scannerRASLabel, scannerRASLabelVals, scannerRASPanel, scannerTabbedPane, talGoToButton, talGoToPanel, talXLabel, talXTextField, talYLabel, talYTextField, talZLabel, talZTextField, zoomMode

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

Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

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
`ViewJFrameRegistrationTool(ModelImage _image, ModelImage _image2, ModelStorageBase _LUT, ModelStorageBase _LUT2)`	Makes a frame of the manually registered image.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Calls various methods depending on the action.
`private void`	`addControlPanel(java.awt.Component c, java.awt.GridBagConstraints gbc, int x, int y, int w, int h)`	Adds a component to the control panel.
`void`	`addSphereVOIs(VOI annotations)`
`private void`	`addTopPanel(java.awt.Component c, java.awt.GridBagConstraints gbc, int x, int y, int w, int h)`	Adds a component to the top panel.
`private void`	`buildControlPanel()`	panel that sets the at rest frame number and the desired frames per second.
`private void`	`buildMenu()`	this method builds a menu which contains the options Save image as and Close Registration.
`private javax.swing.JToolBar`	`buildRegistrationToolBar(java.awt.event.ActionListener al, boolean both)`	builds the first registration toolbar.
`private void`	`buildScrollPanes()`	Make a scroll frame and puts an image component into it.
`private javax.swing.JToolBar`	`buildToolBar2(java.awt.event.ActionListener al)`	builds the second registration toolbar.
`TransMatrix`	`buildXfrm(double[] p1, double[] p2, Jama.Matrix R)`	Builds 4x4 transformation matrix from R and T T=p2-R*p1.
`private void`	`calculateCostFunctionValues()`
`void`	`calculateResiduals()`	Calculates the residuals of the least squares fit.
`void`	`close()`	Disposes of components and frame.
`void`	`componentResized(java.awt.event.ComponentEvent event)`	Resizes frame and all components.
`void`	`create3DVOI(boolean bIntersection)`
`double`	`euclideanDistance(double[] ptA, double[] ptB)`	Calculates the Euclidean distance.
`void`	`finalize()`	Finalizes and closes the window.
`void`	`focusGained(java.awt.event.FocusEvent event)`	Currently unused.
`void`	`focusLost(java.awt.event.FocusEvent event)`	Currently unused.
`ModelImage`	`getActiveImage()`
`ModelLUT`	`getActiveLUT()`
`ModelRGB`	`getActiveRGB()`
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getCenterPt()`
`ViewControlsImage`	`getControls()`	Gets control widgets for frame.
`javax.swing.JFrame`	`getFrame()`
`ModelImage`	`getImageA()`	Returns the reference to imageA.
`ModelImage`	`getImageB()`	Returns the reference to imageB.
`VOIManagerInterface`	`getVOIManager()`
`private void`	`init()`	Creates the GUI.
`private void`	`initVOI()`
`void`	`itemStateChanged(java.awt.event.ItemEvent event)`	sets the flags for the checkboxes.
`private boolean`	`leastSquares()`	This code comes from matchBtoA() and buildXfrm(double p1[],double p2[], Matrix R) in AlgorithmRegLeastSquares.
`private javax.swing.JButton`	`makeSeparator()`	makes a separator for the use in the toolbars.
`void`	`maskToPaint()`
`void`	`paintToShortMask()`
`void`	`paintToUbyteMask()`
`void`	`PointerActive(boolean bActive)`
`WildMagic.LibFoundation.Mathematics.Vector3f`	`PropDown(int iActive)`
`WildMagic.LibFoundation.Mathematics.Vector3f`	`PropUp(int iActive)`
`void`	`removeControls()`	Removes the menu and controls of the main frame so that a new frame can load the main frame with the proper controls.
`void`	`setActiveImage(int active)`	Sets the active image for drawing VOIs.
`void`	`setActiveImage(ModelImage kImage)`
`void`	`setAlphaBlend(int value)`	Sets the alpha blending of parameter for two image displaying.
`void`	`setCenter(WildMagic.LibFoundation.Mathematics.Vector3f kCenter)`
`void`	`setControls()`	Sets the menu and controls (i.e. toolbars) of the main frame!
`void`	`setCursor(java.awt.Cursor kCursor)`
`void`	`setDefaultMode()`	setDefaultMode.
`void`	`setEnabled(boolean flag)`	Controls whether or not the images/VOIs of the frame can be modified.
`void`	`setImageB(ModelImage _imageB)`	Sets the reference to imageB.
`void`	`setLUTa(ModelLUT LUT)`	Sets the model LUT for the imageA.
`void`	`setLUTb(ModelLUT LUT)`	setLUTb - accessor that sets the model LUTb for the imageB.
`void`	`setMode(int mode)`	sets mode.
`void`	`setModified()`
`void`	`setMove(float xStart, float yStart, float xFinish, float yFinish)`	If doDrag == false, this routine processes movements generated by mouse presses and releases.
`void`	`setPaintBitmapSwitch(boolean paintBitmapSwitch)`	When switching the active image, take the paintBitmap of the previous active image as the paintBitmap of the new active image.
`void`	`setPaintMask(java.util.BitSet mask)`
`void`	`setRGBTA(ModelRGB RGBT)`	Sets the RGB LUT table for ARGB image A.
`void`	`setRGBTB(ModelRGB RGBT)`	Sets the RGB LUT table for ARGB image B.
`void`	`setRotationCenter(float xRot, float yRot)`	Sets the coordinates of the point the will be the new image rotation center.
`void`	`setSlice(int slice)`	Not used.
`void`	`setTimeSlice(int slice)`	Not used.
`void`	`setTitle()`	sets the title of the frame with the image name and magnification.
`static double`	`SQR(double x)`	SQR = x^2.
`void`	`stateChanged(javax.swing.event.ChangeEvent e)`	sets values based on knob along slider and catches the tabbed pane switching events.
`private void`	`tpSpline()`	Thin-plate registration method.
`private void`	`transform()`	Transforms the image.
`private void`	`transformC()`	Transforms color image.
`void`	`updateData()`
`void`	`updateFrame(float sX, float sY)`	DOCUMENT ME!
`boolean`	`updateImageExtents()`	This methods calls the componentImage's REPAINT method to redraw the screen.
`boolean`	`updateImages()`	This methods calls the componentImage's update method to redraw the screen.
`boolean`	`updateImages(boolean forceShow)`	Calls the componentImage's update method to redraw the screen.
`boolean`	`updateImages(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow, int interpMode)`	This methods calls the componentImage's update method to redraw the screen.
`void`	`windowActivated(java.awt.event.WindowEvent event)`	unchanged.
`void`	`windowClosed(java.awt.event.WindowEvent event)`	unchanged.
`void`	`windowClosing(java.awt.event.WindowEvent event)`	Calls dispose.
`void`	`windowDeactivated(java.awt.event.WindowEvent event)`	unchanged.
`void`	`windowDeiconified(java.awt.event.WindowEvent event)`	unchanged.
`void`	`windowIconified(java.awt.event.WindowEvent event)`	unchanged.
`void`	`windowOpened(java.awt.event.WindowEvent event)`	Unchanged.

Methods inherited from class gov.nih.mipav.view.ViewJFrameBase
about, buildLabelPanel, canCloseImageBAfterLoad, close, closeImageB, componentHidden, componentMoved, componentShown, getAlphaBlend, getDefaultLUTa, getDefaultLUTb, getDisplayMode, getImageNameA, getImageNameB, getLastState, getLUTa, getLUTb, getRGBTA, getRGBTB, getTriImg, getUserInterface, handleMaskPopupMenu, handlePaintToMaskPopupMenu, handleZoomPopupMenu, initExtents, initImageBuffer, initLUT, initNumSlices, initPixelBuffer, initResFactor, initResolutions, initRGB, initSlicePositions, initUnits, initZoom, loadAllVOIs, loadAllVOIsFrom, loadImage, loadLUT, loadLUTandTransferFunctionFrom, loadLUTandTransferFunctionFrom, makeString, newFrameBeenCreated, openVOI, openVOI, pickImageFile, save, save, save, saveAllVOIs, saveAllVOIsTo, saveLabels, saveLUT, saveLUTandTransferFunction, saveLUTandTransferFunction, saveLUTAs, saveLUTAs, saveVOI, saveVOIAs, saveVOIAs, saveVOIIntensities, saveVOIIntensitiesTo, setAbsPositionLabels, setEnableCloseImageBAfterLoad, setImageA, setLastState, setLinkedFrame, setLinkedTriFrame, setLUTs, setMessageText, setOpacityInfo, setpaintBitmap, setScannerPosition

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

Methods inherited from class java.awt.Frame
addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

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, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, 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, 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, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

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

Methods inherited from interface java.awt.MenuContainer
getFont, postEvent

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - ROTATIONCENTER
```
public static final int ROTATIONCENTER
```
    The 3 types of markers - rotation center, reference slice, and adjusted slice.
    
    See Also:
    
    Constant Field Values
  - REFMARK
```
public static final int REFMARK
```
    reference marker type.
    
    See Also:
    
    Constant Field Values
  - ADJMARK
```
public static final int ADJMARK
```
    adjusted marker type.
    
    See Also:
    
    Constant Field Values
  - toggleArray
```
public javax.swing.JToggleButton[] toggleArray
```
    DOCUMENT ME!
  - serif12
```
protected java.awt.Font serif12
```
    DOCUMENT ME!
  - adjMark
```
private int adjMark
```
    DOCUMENT ME!
  - adjMarkButton
```
private javax.swing.JToggleButton adjMarkButton
```
    DOCUMENT ME!
  - adjMarkMinusButton
```
private javax.swing.JButton adjMarkMinusButton
```
    DOCUMENT ME!
  - alphaSlider
```
private javax.swing.JSlider alphaSlider
```
    DOCUMENT ME!
  - bothPanel
```
private javax.swing.JPanel bothPanel
```
    DOCUMENT ME!
  - bufferFactor
```
private int bufferFactor
```
    DOCUMENT ME!
  - bufferSize
```
private int bufferSize
```
    DOCUMENT ME!
  - buttonArray
```
private javax.swing.JButton[] buttonArray
```
    DOCUMENT ME!
  - ccwButton
```
private javax.swing.JButton ccwButton
```
    DOCUMENT ME!
  - componentImage
```
private ViewJComponentRegistration componentImage
```
    for both images displayed together.
  - componentImageA
```
private ViewJComponentSingleRegistration componentImageA
```
    for images to be displayed separately.
  - componentImageB
```
private ViewJComponentSingleRegistration componentImageB
```
    DOCUMENT ME!
  - controlPanel
```
private javax.swing.JPanel controlPanel
```
    DOCUMENT ME!
  - controls
```
private ViewControlsImage controls
```
    DOCUMENT ME!
  - copyAdjToRefButton
```
private javax.swing.JButton copyAdjToRefButton
```
    DOCUMENT ME!
  - copyRefToAdjButton
```
private javax.swing.JButton copyRefToAdjButton
```
    DOCUMENT ME!
  - cpGBC
```
private java.awt.GridBagConstraints cpGBC
```
    DOCUMENT ME!
  - cpGBL
```
private java.awt.GridBagLayout cpGBL
```
    DOCUMENT ME!
  - curAdjMark
```
private int curAdjMark
```
    DOCUMENT ME!
  - curRefMark
```
private int curRefMark
```
    DOCUMENT ME!
  - cwButton
```
private javax.swing.JButton cwButton
```
    DOCUMENT ME!
  - defaultModeButton
```
private javax.swing.JToggleButton defaultModeButton
```
    DOCUMENT ME!
  - degreeIncrement
```
private float degreeIncrement
```
    DOCUMENT ME!
  - degreeIncrementButton
```
private javax.swing.JButton degreeIncrementButton
```
    DOCUMENT ME!
  - doDrag
```
private boolean doDrag
```
    DOCUMENT ME!
  - doneLeastSquares
```
private boolean doneLeastSquares
```
    DOCUMENT ME!
  - doRegionB
```
private boolean doRegionB
```
    DOCUMENT ME!
  - downButton
```
private javax.swing.JButton downButton
```
    DOCUMENT ME!
  - etchedBorder
```
private javax.swing.border.Border etchedBorder
```
    DOCUMENT ME!
  - extents
```
private int[] extents
```
    DOCUMENT ME!
  - fileMenu
```
private javax.swing.JMenu fileMenu
```
    DOCUMENT ME!
  - firstDraw
```
private boolean firstDraw
```
    DOCUMENT ME!
  - font12
```
private java.awt.Font font12
```
    DOCUMENT ME!
  - gbc
```
private java.awt.GridBagConstraints gbc
```
    DOCUMENT ME!
  - helpMenu
```
private javax.swing.JMenu helpMenu
```
    DOCUMENT ME!
  - i
```
private int i
```
    DOCUMENT ME!
  - j
```
private int j
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imageBufferA
```
private float[] imageBufferA
```
    DOCUMENT ME!
  - imageBufferB
```
private float[] imageBufferB
```
    DOCUMENT ME!
  - imageBufferOriginalB
```
private float[] imageBufferOriginalB
```
    DOCUMENT ME!
  - imageSize
```
private int imageSize
```
    DOCUMENT ME!
  - itemClose
```
private javax.swing.JMenuItem itemClose
```
    DOCUMENT ME!
  - itemHelp
```
private javax.swing.JMenuItem itemHelp
```
    DOCUMENT ME!
  - leftButton
```
private javax.swing.JButton leftButton
```
    DOCUMENT ME!
  - logMagDisplay
```
private boolean logMagDisplay
```
    DOCUMENT ME!
  - lsPerformed
```
private boolean lsPerformed
```
    DOCUMENT ME!
  - mode
```
private int mode
```
    DOCUMENT ME!
  - movementGroup
```
private javax.swing.ButtonGroup movementGroup
```
    DOCUMENT ME!
  - n
```
private int n
```
    DOCUMENT ME!
  - newAlphaBlend
```
private int newAlphaBlend
```
    DOCUMENT ME!
  - newExtents
```
private int[] newExtents
```
    DOCUMENT ME!
  - openingMenuBar
```
private javax.swing.JMenuBar openingMenuBar
```
    DOCUMENT ME!
  - pixBuffer
```
private int[] pixBuffer
```
    DOCUMENT ME!
  - pixBufferB
```
private int[] pixBufferB
```
    DOCUMENT ME!
  - pixBufferCompA
```
private int[] pixBufferCompA
```
    DOCUMENT ME!
  - pixBufferCompB
```
private int[] pixBufferCompB
```
    DOCUMENT ME!
  - pixelIncrement
```
private float pixelIncrement
```
    DOCUMENT ME!
  - pixelIncrementButton
```
private javax.swing.JButton pixelIncrementButton
```
    DOCUMENT ME!
  - pointSetA
```
private double[][] pointSetA
```
    DOCUMENT ME!
  - pointSetB
```
private double[][] pointSetB
```
    DOCUMENT ME!
  - pointSetBT
```
private double[][] pointSetBT
```
    DOCUMENT ME!
  - refMark
```
private int refMark
```
    DOCUMENT ME!
  - refMarkButton
```
private javax.swing.JToggleButton refMarkButton
```
    DOCUMENT ME!
  - refMarkMinusButton
```
private javax.swing.JButton refMarkMinusButton
```
    DOCUMENT ME!
  - regButton
```
private javax.swing.JToggleButton regButton
```
    DOCUMENT ME!
  - RGBa
```
private ModelRGB RGBa
```
    DOCUMENT ME!
  - RGBb
```
private ModelRGB RGBb
```
    DOCUMENT ME!
  - rightButton
```
private javax.swing.JButton rightButton
```
    DOCUMENT ME!
  - rotateButton
```
private javax.swing.JToggleButton rotateButton
```
    DOCUMENT ME!
  - scrollPane
```
private javax.swing.JScrollPane scrollPane
```
    DOCUMENT ME!
  - scrollPaneSeparateA
```
private javax.swing.JScrollPane scrollPaneSeparateA
```
    DOCUMENT ME!
  - scrollPaneSeparateB
```
private javax.swing.JScrollPane scrollPaneSeparateB
```
    DOCUMENT ME!
  - scrollPaneSize
```
private int scrollPaneSize
```
    DOCUMENT ME!
  - secondImage
```
private ModelImage secondImage
```
    DOCUMENT ME!
  - separatePanel
```
private javax.swing.JPanel separatePanel
```
    DOCUMENT ME!
  - showVOIs
```
private javax.swing.JCheckBoxMenuItem showVOIs
```
    DOCUMENT ME!
  - tabbedPane
```
private javax.swing.JTabbedPane tabbedPane
```
    DOCUMENT ME!
  - toolBar
```
private javax.swing.JToolBar toolBar
```
    DOCUMENT ME!
  - toolBar2
```
private javax.swing.JToolBar toolBar2
```
    DOCUMENT ME!
  - toolBarSep
```
private javax.swing.JToolBar toolBarSep
```
    DOCUMENT ME!
  - topPanel
```
private javax.swing.JPanel topPanel
```
    DOCUMENT ME!
  - translateButton
```
private javax.swing.JToggleButton translateButton
```
    DOCUMENT ME!
  - upButton
```
private javax.swing.JButton upButton
```
    DOCUMENT ME!
  - userInterface
```
private ViewUserInterface userInterface
```
    DOCUMENT ME!
  - xCoords
```
private int[] xCoords
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - xfrm
```
private TransMatrix xfrm
```
    DOCUMENT ME!
  - xfrmBA
```
private TransMatrix xfrmBA
```
    DOCUMENT ME!
  - xfrmD
```
private TransMatrix xfrmD
```
    DOCUMENT ME!
  - xfrmH
```
private TransMatrix xfrmH
```
    DOCUMENT ME!
  - xOrg
```
private int[] xOrg
```
    DOCUMENT ME!
  - xRes
```
private float xRes
```
    DOCUMENT ME!
  - xRotation
```
private float xRotation
```
    DOCUMENT ME!
  - xScreen
```
private int xScreen
```
    DOCUMENT ME!
  - yScreen
```
private int yScreen
```
    DOCUMENT ME!
  - yCoords
```
private int[] yCoords
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - yOrg
```
private int[] yOrg
```
    DOCUMENT ME!
  - yRes
```
private float yRes
```
    DOCUMENT ME!
  - yRotation
```
private float yRotation
```
    DOCUMENT ME!
  - zoom
```
private float zoom
```
    DOCUMENT ME!
  - costFunctionTextArea
```
private javax.swing.JTextArea costFunctionTextArea
```
  - costFunctionScrollPane
```
private javax.swing.JScrollPane costFunctionScrollPane
```
    Scroll Pane for the Text Area
  - simpleImg1
```
private ModelSimpleImage simpleImg1
```
    Holds extents, other info about firstImage and SecondImage
  - simpleImg2
```
private ModelSimpleImage simpleImg2
```
    Holds extents, other info about firstImage and SecondImage
  - tMatrix
```
private TransMatrix tMatrix
```
    Identity matrix for testing cost
  - algoCost
```
private AlgorithmCostFunctions2D algoCost
```
  - calculateCostButton
```
private javax.swing.JButton calculateCostButton
```
  - voiManager
```
private VOIManagerInterface voiManager
```
- Constructor Detail
  - ViewJFrameRegistrationTool
```
public ViewJFrameRegistrationTool(ModelImage _image,
                                  ModelImage _image2,
                                  ModelStorageBase _LUT,
                                  ModelStorageBase _LUT2)
```
    Makes a frame of the manually registered image.
    
    Parameters:
    
    _image - the first image
    
    _image2 - the second image
    
    _LUT - lut for the first image
    
    _LUT2 - lut for the second image
- Method Detail
  - SQR
```
public static final double SQR(double x)
```
    SQR = x^2.
    
    Parameters:
    
    x - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Calls various methods depending on the action.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Specified by:
    
    actionPerformed in class ViewJFrameBase
    
    Parameters:
    
    event - event that triggered function
  - buildXfrm
```
public TransMatrix buildXfrm(double[] p1,
                             double[] p2,
                             Jama.Matrix R)
```
    Builds 4x4 transformation matrix from R and T T=p2-R*p1.
    
    Parameters:
    
    p1 - from Match
    
    p2 - from Match
    
    R - matrix from Match
    
    Returns:
    
    transformation matrix
  - calculateResiduals
```
public void calculateResiduals()
```
    Calculates the residuals of the least squares fit.
  - close
```
public void close()
```
    Disposes of components and frame.
    
    Overrides:
    
    close in class ViewJFrameBase
  - componentResized
```
public void componentResized(java.awt.event.ComponentEvent event)
```
    Resizes frame and all components.
    
    Specified by:
    
    componentResized in interface java.awt.event.ComponentListener
    
    Overrides:
    
    componentResized in class ViewJFrameBase
    
    Parameters:
    
    event - event that triggered function
  - euclideanDistance
```
public double euclideanDistance(double[] ptA,
                                double[] ptB)
```
    Calculates the Euclidean distance.
    
    Parameters:
    
    ptA - point A
    
    ptB - point B
    
    Returns:
    
    the euclidean distatnce between points
  - finalize
```
public void finalize()
```
    Finalizes and closes the window.
    
    Overrides:
    
    finalize in class ViewJFrameBase
  - focusGained
```
public void focusGained(java.awt.event.FocusEvent event)
```
    Currently unused.
    
    Specified by:
    
    focusGained in interface java.awt.event.FocusListener
    
    Parameters:
    
    event - DOCUMENT ME!
  - focusLost
```
public void focusLost(java.awt.event.FocusEvent event)
```
    Currently unused.
    
    Specified by:
    
    focusLost in interface java.awt.event.FocusListener
    
    Parameters:
    
    event - DOCUMENT ME!
  - getControls
```
public ViewControlsImage getControls()
```
    Gets control widgets for frame.
    
    Specified by:
    
    getControls in class ViewJFrameBase
    
    Returns:
    
    controls
  - getImageA
```
public ModelImage getImageA()
```
    Returns the reference to imageA.
    
    Specified by:
    
    getImageA in class ViewJFrameBase
    
    Returns:
    
    image
  - getImageB
```
public ModelImage getImageB()
```
    Returns the reference to imageB.
    
    Specified by:
    
    getImageB in class ViewJFrameBase
    
    Returns:
    
    imageB
  - itemStateChanged
```
public void itemStateChanged(java.awt.event.ItemEvent event)
```
    sets the flags for the checkboxes.
    
    Specified by:
    
    itemStateChanged in interface java.awt.event.ItemListener
    
    Parameters:
    
    event - event that triggered this function
  - removeControls
```
public void removeControls()
```
    Removes the menu and controls of the main frame so that a new frame can load the main frame with the proper controls. Currently unused.
    
    Specified by:
    
    removeControls in class ViewJFrameBase
  - setActiveImage
```
public void setActiveImage(int active)
```
    Sets the active image for drawing VOIs. VOIs are only drawn in the active image. In addition, algorithms are executed on the active window.
    
    Specified by:
    
    setActiveImage in interface VOIManagerInterfaceListener
    
    Specified by:
    
    setActiveImage in class ViewJFrameBase
    
    Parameters:
    
    active - IMAGE_A or IMAGE_B
  - setAlphaBlend
```
public void setAlphaBlend(int value)
```
    Sets the alpha blending of parameter for two image displaying. Currently unused.
    
    Specified by:
    
    setAlphaBlend in class ViewJFrameBase
    
    Parameters:
    
    value - amount [0,100] that is the percentage of Image A to be displayed
  - setControls
```
public void setControls()
```
    Sets the menu and controls (i.e. toolbars) of the main frame! This puts the menus and controls needed to controls the operations of this frame. Different image frames have different menu and controls. Currently unused.
    
    Specified by:
    
    setControls in class ViewJFrameBase
  - setDefaultMode
```
public void setDefaultMode()
```
    setDefaultMode.
  - setEnabled
```
public void setEnabled(boolean flag)
```
    Controls whether or not the images/VOIs of the frame can be modified. Currently unused.
    
    Specified by:
    
    setEnabled in class ViewJFrameBase
    
    Parameters:
    
    flag - if true the image/VOIs can be modified; if false image/VOIs can NOT be modified
  - setImageB
```
public void setImageB(ModelImage _imageB)
```
    Sets the reference to imageB. Currently unused.
    
    Specified by:
    
    setImageB in class ViewJFrameBase
    
    Parameters:
    
    _imageB - Image to set the frame to
  - setLUTa
```
public void setLUTa(ModelLUT LUT)
```
    Sets the model LUT for the imageA.
    
    Overrides:
    
    setLUTa in class ViewJFrameBase
    
    Parameters:
    
    LUT - the model LUT
  - setLUTb
```
public void setLUTb(ModelLUT LUT)
```
    setLUTb - accessor that sets the model LUTb for the imageB.
    
    Overrides:
    
    setLUTb in class ViewJFrameBase
    
    Parameters:
    
    LUT - the model LUT
  - setMode
```
public void setMode(int mode)
```
    sets mode.
    
    Parameters:
    
    mode - DOCUMENT ME!
  - setMove
```
public void setMove(float xStart,
                    float yStart,
                    float xFinish,
                    float yFinish)
```
    If doDrag == false, this routine processes movements generated by mouse presses and releases. The mouse press location sets (xStart,yStart) and the mouse release location sets (xFinish,yFinish). If doDrag == true, this routine processes movements generated by mouse press and drag events.
    
    Parameters:
    
    xStart - DOCUMENT ME!
    
    yStart - DOCUMENT ME!
    
    xFinish - DOCUMENT ME!
    
    yFinish - DOCUMENT ME!
  - setPaintBitmapSwitch
```
public void setPaintBitmapSwitch(boolean paintBitmapSwitch)
```
    When switching the active image, take the paintBitmap of the previous active image as the paintBitmap of the new active image.
    
    Specified by:
    
    setPaintBitmapSwitch in class ViewJFrameBase
    
    Parameters:
    
    paintBitmapSwitch - if true don't copy the new acitve image mask
  - setRGBTA
```
public void setRGBTA(ModelRGB RGBT)
```
    Sets the RGB LUT table for ARGB image A.
    
    Specified by:
    
    setRGBTA in class ViewJFrameBase
    
    Parameters:
    
    RGBT - the new RGB LUT to be applied to the image
  - setRGBTB
```
public void setRGBTB(ModelRGB RGBT)
```
    Sets the RGB LUT table for ARGB image B.
    
    Specified by:
    
    setRGBTB in class ViewJFrameBase
    
    Parameters:
    
    RGBT - the new RGB LUT to be applied to the image
  - setRotationCenter
```
public void setRotationCenter(float xRot,
                              float yRot)
```
    Sets the coordinates of the point the will be the new image rotation center.
    
    Parameters:
    
    xRot - DOCUMENT ME!
    
    yRot - DOCUMENT ME!
  - setSlice
```
public void setSlice(int slice)
```
    Not used.
    
    Specified by:
    
    setSlice in interface ViewImageUpdateInterface
    
    Parameters:
    
    slice - DOCUMENT ME!
  - setTimeSlice
```
public void setTimeSlice(int slice)
```
    Not used.
    
    Specified by:
    
    setTimeSlice in interface ViewImageUpdateInterface
    
    Parameters:
    
    slice - DOCUMENT ME!
  - setTitle
```
public void setTitle()
```
    sets the title of the frame with the image name and magnification.
    
    Specified by:
    
    setTitle in class ViewJFrameBase
  - stateChanged
```
public void stateChanged(javax.swing.event.ChangeEvent e)
```
    sets values based on knob along slider and catches the tabbed pane switching events.
    
    Specified by:
    
    stateChanged in interface javax.swing.event.ChangeListener
    
    Overrides:
    
    stateChanged in class ViewJFrameBase
    
    Parameters:
    
    e - event that triggered this function
  - updateFrame
```
public void updateFrame(float sX,
                        float sY)
```
    DOCUMENT ME!
    
    Parameters:
    
    sX - zoom in the x dimension
    
    sY - zoom in the y dimension
  - updateImageExtents
```
public boolean updateImageExtents()
```
    This methods calls the componentImage's REPAINT method to redraw the screen. The extents on this image have changed, so the extents need to be read in again and menus, panes and slide bars adjusted accordingly.
    
    Specified by:
    
    updateImageExtents in interface ViewImageUpdateInterface
    
    Specified by:
    
    updateImageExtents in class ViewJFrameBase
    
    Returns:
    
    DOCUMENT ME!
    
    See Also:
    
    ViewImageUpdateInterface
  - updateImages
```
public final boolean updateImages()
```
    This methods calls the componentImage's update method to redraw the screen.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Returns:
    
    boolean confirming successful update
  - updateImages
```
public final boolean updateImages(boolean forceShow)
```
    Calls the componentImage's update method to redraw the screen. Without LUT changes.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Parameters:
    
    forceShow - forces show to re import image and calc. java image
    
    Returns:
    
    boolean confirming successful update
  - updateImages
```
public final boolean updateImages(ModelLUT LUTa,
                                  ModelLUT LUTb,
                                  boolean forceShow,
                                  int interpMode)
```
    This methods calls the componentImage's update method to redraw the screen.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Parameters:
    
    LUTa - LUT used to update imageA
    
    LUTb - LUT used to update imageB
    
    forceShow - forces show to re import image and calc. java image
    
    interpMode - image interpolation method (Nearest or Smooth)
    
    Returns:
    
    boolean confirming successful update
  - windowActivated
```
public void windowActivated(java.awt.event.WindowEvent event)
```
    unchanged.
    
    Specified by:
    
    windowActivated in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowActivated in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowClosed
```
public void windowClosed(java.awt.event.WindowEvent event)
```
    unchanged.
    
    Specified by:
    
    windowClosed in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowClosed in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowClosing
```
public void windowClosing(java.awt.event.WindowEvent event)
```
    Calls dispose.
    
    Specified by:
    
    windowClosing in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowClosing in class ViewJFrameBase
    
    Parameters:
    
    event - event that triggered function
  - windowDeactivated
```
public void windowDeactivated(java.awt.event.WindowEvent event)
```
    unchanged.
    
    Specified by:
    
    windowDeactivated in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowDeactivated in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowDeiconified
```
public void windowDeiconified(java.awt.event.WindowEvent event)
```
    unchanged.
    
    Specified by:
    
    windowDeiconified in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowDeiconified in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowIconified
```
public void windowIconified(java.awt.event.WindowEvent event)
```
    unchanged.
    
    Specified by:
    
    windowIconified in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowIconified in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowOpened
```
public void windowOpened(java.awt.event.WindowEvent event)
```
    Unchanged.
    
    Specified by:
    
    windowOpened in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowOpened in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - addControlPanel
```
private void addControlPanel(java.awt.Component c,
                             java.awt.GridBagConstraints gbc,
                             int x,
                             int y,
                             int w,
                             int h)
```
    Adds a component to the control panel.
    
    Parameters:
    
    c - component
    
    gbc - GridBagConstraints
    
    x - DOCUMENT ME!
    
    y - DOCUMENT ME!
    
    w - DOCUMENT ME!
    
    h - DOCUMENT ME!
  - addTopPanel
```
private void addTopPanel(java.awt.Component c,
                         java.awt.GridBagConstraints gbc,
                         int x,
                         int y,
                         int w,
                         int h)
```
    Adds a component to the top panel.
    
    Parameters:
    
    c - component
    
    gbc - GridbagConstraints
    
    x - DOCUMENT ME!
    
    y - DOCUMENT ME!
    
    w - DOCUMENT ME!
    
    h - DOCUMENT ME!
  - buildControlPanel
```
private void buildControlPanel()
```
    panel that sets the at rest frame number and the desired frames per second.
  - buildMenu
```
private void buildMenu()
```
    this method builds a menu which contains the options Save image as and Close Registration.
  - buildRegistrationToolBar
```
private javax.swing.JToolBar buildRegistrationToolBar(java.awt.event.ActionListener al,
                                                      boolean both)
```
    builds the first registration toolbar.
    
    Parameters:
    
    al - ActionListener
    
    both - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - buildScrollPanes
```
private void buildScrollPanes()
```
    Make a scroll frame and puts an image component into it.
  - buildToolBar2
```
private javax.swing.JToolBar buildToolBar2(java.awt.event.ActionListener al)
```
    builds the second registration toolbar.
    
    Parameters:
    
    al - ActionListener
    
    Returns:
    
    DOCUMENT ME!
  - init
```
private void init()
```
    Creates the GUI.
  - leastSquares
```
private boolean leastSquares()
```
    This code comes from matchBtoA() and buildXfrm(double p1[],double p2[], Matrix R) in AlgorithmRegLeastSquares.
    
    Returns:
    
    DOCUMENT ME!
  - makeSeparator
```
private javax.swing.JButton makeSeparator()
```
    makes a separator for the use in the toolbars.
    
    Returns:
    
    DOCUMENT ME!
  - tpSpline
```
private void tpSpline()
```
    Thin-plate registration method.
  - transform
```
private void transform()
```
    Transforms the image.
  - transformC
```
private void transformC()
```
    Transforms color image.
  - calculateCostFunctionValues
```
private void calculateCostFunctionValues()
```
  - PointerActive
```
public void PointerActive(boolean bActive)
```
    Specified by:
    
    PointerActive in interface VOIManagerInterfaceListener
  - PropDown
```
public WildMagic.LibFoundation.Mathematics.Vector3f PropDown(int iActive)
```
    Specified by:
    
    PropDown in interface VOIManagerInterfaceListener
  - PropUp
```
public WildMagic.LibFoundation.Mathematics.Vector3f PropUp(int iActive)
```
    Specified by:
    
    PropUp in interface VOIManagerInterfaceListener
  - create3DVOI
```
public void create3DVOI(boolean bIntersection)
```
    Specified by:
    
    create3DVOI in interface VOIManagerInterfaceListener
  - getActiveImage
```
public ModelImage getActiveImage()
```
    Specified by:
    
    getActiveImage in interface VOIManagerInterfaceListener
  - getActiveLUT
```
public ModelLUT getActiveLUT()
```
    Specified by:
    
    getActiveLUT in interface VOIManagerInterfaceListener
  - getActiveRGB
```
public ModelRGB getActiveRGB()
```
    Specified by:
    
    getActiveRGB in interface VOIManagerInterfaceListener
  - getCenterPt
```
public WildMagic.LibFoundation.Mathematics.Vector3f getCenterPt()
```
    Specified by:
    
    getCenterPt in interface VOIManagerInterfaceListener
  - getFrame
```
public javax.swing.JFrame getFrame()
```
    Specified by:
    
    getFrame in interface VOIManagerInterfaceListener
  - setActiveImage
```
public void setActiveImage(ModelImage kImage)
```
    Specified by:
    
    setActiveImage in interface VOIManagerInterfaceListener
  - getVOIManager
```
public VOIManagerInterface getVOIManager()
```
    Specified by:
    
    getVOIManager in interface VOIManagerInterfaceListener
  - setCenter
```
public void setCenter(WildMagic.LibFoundation.Mathematics.Vector3f kCenter)
```
    Specified by:
    
    setCenter in interface VOIManagerInterfaceListener
  - setCursor
```
public void setCursor(java.awt.Cursor kCursor)
```
    Specified by:
    
    setCursor in interface VOIManagerInterfaceListener
    
    Overrides:
    
    setCursor in class java.awt.Window
  - setModified
```
public void setModified()
```
    Specified by:
    
    setModified in interface VOIManagerInterfaceListener
  - updateData
```
public void updateData()
```
    Specified by:
    
    updateData in interface VOIManagerInterfaceListener
  - setPaintMask
```
public void setPaintMask(java.util.BitSet mask)
```
    Specified by:
    
    setPaintMask in interface VOIManagerInterfaceListener
  - paintToShortMask
```
public void paintToShortMask()
```
    Specified by:
    
    paintToShortMask in interface VOIManagerInterfaceListener
  - paintToUbyteMask
```
public void paintToUbyteMask()
```
    Specified by:
    
    paintToUbyteMask in interface VOIManagerInterfaceListener
  - maskToPaint
```
public void maskToPaint()
```
    Specified by:
    
    maskToPaint in interface VOIManagerInterfaceListener
  - initVOI
```
private void initVOI()
```
  - addSphereVOIs
```
public void addSphereVOIs(VOI annotations)
```
    Specified by:
    
    addSphereVOIs in interface VOIManagerInterfaceListener

Class ViewJFrameRegistrationTool

Nested Class Summary

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

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

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.ViewJFrameBase

Fields inherited from class javax.swing.JFrame

Fields inherited from class java.awt.Frame

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.ViewJFrameBase

Methods inherited from class javax.swing.JFrame

Methods inherited from class java.awt.Frame

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 java.awt.MenuContainer

Field Detail

serialVersionUID

ROTATIONCENTER

REFMARK

ADJMARK

toggleArray

serif12

adjMark

adjMarkButton

adjMarkMinusButton

alphaSlider

bothPanel

bufferFactor

bufferSize

buttonArray

ccwButton

componentImage

componentImageA

componentImageB

controlPanel

controls

copyAdjToRefButton

copyRefToAdjButton

cpGBC

cpGBL

curAdjMark

curRefMark

cwButton

defaultModeButton

degreeIncrement

degreeIncrementButton

doDrag

doneLeastSquares

doRegionB

downButton

etchedBorder

extents

fileMenu

firstDraw

font12

gbc

helpMenu

i

j

image

imageBufferA

imageBufferB

imageBufferOriginalB

imageSize

itemClose

itemHelp

leftButton

logMagDisplay

lsPerformed

mode

movementGroup