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

All Implemented Interfaces:

ViewImageUpdateInterface, java.awt.event.ActionListener, java.awt.event.ComponentListener, 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

Direct Known Subclasses:

DialogDTIColorDisplay, DTIColorDisplay, ViewJFrameAnimate, ViewJFrameAnimateClip, ViewJFrameColocalizationEM, ViewJFrameColocalizationRegression, ViewJFrameHistoLUT, ViewJFrameHistoRGB, ViewJFrameImage, ViewJFrameLightBox, ViewJFramePaintVasculature, ViewJFramePlotterView, ViewJFrameRegistration, ViewJFrameRegistrationTool, ViewJFrameRenderCamera, ViewJFrameTriImage, ViewJFrameVolumeView
```
public abstract class ViewJFrameBase
extends javax.swing.JFrame
implements ViewImageUpdateInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.awt.event.ComponentListener, javax.swing.event.ChangeListener
```
This is an abstract class used to display images in a 2D planar format.

Version:

0.1 Oct 1, 1998

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

ViewJComponentEditImage, Serialized Form

Nested Class Summary
- 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
`protected javax.swing.JButton`	`absoluteGoToButton`
`protected javax.swing.JPanel`	`absoluteGoToPanel`
`protected javax.swing.JLabel`	`absoluteLabel`	Labels for the current absolute position:.
`protected javax.swing.JLabel[]`	`absoluteLabelVals`	Labels for the current absolute position values:.
`protected javax.swing.JPanel`	`absolutePanel`	JPanel containing the absoulte position labels:.
`protected javax.swing.JLabel`	`absoluteXLabel`	voxel absolute goto components*
`protected javax.swing.JTextField`	`absoluteXTextField`
`protected javax.swing.JLabel`	`absoluteYLabel`	voxel absolute goto components*
`protected javax.swing.JTextField`	`absoluteYTextField`
`protected javax.swing.JLabel`	`absoluteZLabel`	voxel absolute goto components*
`protected javax.swing.JTextField`	`absoluteZTextField`
`protected float`	`alphaBlend`	Indicates the amount of blending when two images are loaded in the image frame.
`private int`	`blue`	Blue channel value of the paint color.
`protected ModelLUT`	`defaultLUTa`	Reference to LUT for image A and to the default LUT for image A.
`protected ModelLUT`	`defaultLUTb`	Reference to LUT for image B and to the default LUT for image B.
`protected int`	`displayMode`	Indicates which image is to be acted upon when two images are displayed.
`private boolean`	`enableCloseImageB`	Tells whether the ViewMenuBuilder should allow Close Image(B) after loading image B.
`private int`	`green`	Green channel value of the paint color.
`static int`	`IMAGE_A`	Display mode image A.
`static int`	`IMAGE_A_B`	Display mode image A and B.
`static int`	`IMAGE_B`	Display mode image B.
`protected ModelImage`	`imageA`	Reference to the image A of this frame.
`protected ModelImage`	`imageB`	Reference to the image B of this frame.
`protected boolean`	`isClosing`	Whether the frame's close() method is being called.
`private int`	`lastState`	Save if last state was iconified or normal.
`protected boolean`	`linkedScrolling`	Variable indicating if images of like dimensions should be scrolled simult.
`protected ViewJFrameImage`	`linkFrame`	Holds a reference (link) to another frame so that it be updated with this frame.
`protected ViewJFrameTriImage`	`linkTriFrame`	Holds a reference (link) to another frame so that it can be updated with this frame.
`protected ModelLUT`	`LUTa`	Reference to LUT for image A and to the default LUT for image A.
`protected ModelLUT`	`LUTb`	Reference to LUT for image B and to the default LUT for image B.
`private boolean`	`newFrameCreated`
`private float`	`opacity`	Opacity value of the paint color.
`private java.util.BitSet`	`paintBitmap`	Reference to the BitSet map used in painting the image.
`protected ViewJProgressBar`	`progressBar`	Reference to progress bar.
`private int`	`red`	Red channel value of the paint color.
`protected javax.swing.JLabel`	`scannerLPS_APLabel`	scanner lps goto components*
`protected javax.swing.JTextField`	`scannerLPS_APTextField`
`protected javax.swing.JButton`	`scannerLPS_GoToButton`
`protected javax.swing.JPanel`	`scannerLPS_GoToPanel`
`protected javax.swing.JLabel`	`scannerLPS_ISLabel`	scanner lps goto components*
`protected javax.swing.JTextField`	`scannerLPS_ISTextField`
`protected javax.swing.JLabel`	`scannerLPS_RLLabel`	scanner lps goto components*
`protected javax.swing.JTextField`	`scannerLPS_RLTextField`
`protected javax.swing.JLabel`	`scannerLPSLabel`	Labels for the current scanner position:.
`protected javax.swing.JLabel[]`	`scannerLPSLabelVals`	Labels for the current scanner position values:.
`protected javax.swing.JPanel`	`scannerLPSPanel`	JPanel containing the scanner position labels:.
`protected javax.swing.JLabel`	`scannerRAS_APLabel`	scanner ras goto components*
`protected javax.swing.JTextField`	`scannerRAS_APTextField`
`protected javax.swing.JButton`	`scannerRAS_GoToButton`
`protected javax.swing.JPanel`	`scannerRAS_GoToPanel`
`protected javax.swing.JLabel`	`scannerRAS_ISLabel`	scanner ras goto components*
`protected javax.swing.JTextField`	`scannerRAS_ISTextField`
`protected javax.swing.JLabel`	`scannerRAS_RLLabel`	scanner ras goto components*
`protected javax.swing.JTextField`	`scannerRAS_RLTextField`
`protected javax.swing.JLabel`	`scannerRASLabel`	Labels for the current scanner position:.
`protected javax.swing.JLabel[]`	`scannerRASLabelVals`	Labels for the current scanner position values:.
`protected javax.swing.JPanel`	`scannerRASPanel`	JPanel containing the scanner position labels:.
`protected javax.swing.JTabbedPane`	`scannerTabbedPane`	The tabbed pane to hold teh LPS, RAS and absolution coordinate panels.
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`protected javax.swing.JTabbedPane`	`tabbedPane`	The main tabbed pane in the volume view frame.
`protected javax.swing.JButton`	`talGoToButton`
`protected javax.swing.JPanel`	`talGoToPanel`
`protected javax.swing.JLabel`	`talXLabel`	talairach goto components*
`protected javax.swing.JTextField`	`talXTextField`
`protected javax.swing.JLabel`	`talYLabel`	talairach goto components*
`protected javax.swing.JTextField`	`talYTextField`
`protected javax.swing.JLabel`	`talZLabel`	talairach goto components*
`protected javax.swing.JTextField`	`talZTextField`
`protected ViewUserInterface`	`userInterface`	Reference to the user interface.
`private java.lang.String`	`voiSavedFileName`	DOCUMENT ME!
`protected int`	`zoomMode`	DOCUMENT ME!

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

ViewJFrameBase(ModelImage _imageA, ModelImage _imageB)
Makes an image frame.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`about(int zSlice, int tSlice)`	Makes an aboutDialog box that displays information about the image slice.
`abstract void`	`actionPerformed(java.awt.event.ActionEvent event)`	Method to handle action events generated by the main UI when the current frame is selected.
`void`	`buildLabelPanel()`	The label panel of the x, y, z slider position.
`boolean`	`canCloseImageBAfterLoad()`	Returns whether or not the close image B option should appear after loading.
`void`	`close()`	Closes both image A and image B (if it exists).
`void`	`close(boolean closeAll)`	Closes both image A and image B (if it exists).
`void`	`closeImageB()`	Removes image B from the frame and resets image A to be the active frame for all image controls.
`void`	`componentHidden(java.awt.event.ComponentEvent event)`	Does nothing.
`void`	`componentMoved(java.awt.event.ComponentEvent event)`	Does nothing.
`void`	`componentResized(java.awt.event.ComponentEvent event)`	Does nothing.
`void`	`componentShown(java.awt.event.ComponentEvent event)`	Does nothing.
`protected void`	`finalize()`	Cleans memory.
`private javax.swing.filechooser.FileFilter`	`findFilter(javax.swing.JFileChooser chooser, int filterType)`	Finds the FileFilter that matches the file type.
`float`	`getAlphaBlend()`	Returns a default alphaBlend value for blending of two images.
`abstract ViewControlsImage`	`getControls()`	Gets the control widgets for the frame.
`ModelLUT`	`getDefaultLUTa()`	Accessor that returns the default LUTa for the frame.
`ModelLUT`	`getDefaultLUTb()`	Accessor that returns the default LUTb for the frame.
`int`	`getDisplayMode()`	Accessor that returns displayMode.
`abstract ModelImage`	`getImageA()`	Accessor that returns the imageA.
`abstract ModelImage`	`getImageB()`	Accessor that returns the imageB.
`java.lang.String`	`getImageNameA()`	Accessor that returns the title of image A.
`java.lang.String`	`getImageNameB()`	Accessor that returns the title of image B.
`int`	`getLastState()`	getLastState.
`ModelLUT`	`getLUTa()`	Accessor that returns LUTa.
`ModelLUT`	`getLUTb()`	Accessor that returns LUTb.
`ModelRGB`	`getRGBTA()`	Get the RGB table for image A.
`ModelRGB`	`getRGBTB()`	Get the RGB table for image B.
`ViewJFrameTriImage`	`getTriImg()`	Get the ViewJFrameTriImage reference.
`ViewUserInterface`	`getUserInterface()`	Accessor that returns the user interface.
`static void`	`handleMaskPopupMenu(java.awt.Component component, java.awt.event.MouseEvent event)`	Handles the popup menu for the Quick Mask buttons
`protected void`	`handlePaintToMaskPopupMenu(java.awt.Component component, java.awt.event.MouseEvent event)`	Handles the pop-up menu for Paint to Mask buttons (inside/outside)
`protected void`	`handleZoomPopupMenu(java.awt.Component component, java.awt.event.MouseEvent event)`	DOCUMENT ME!
`protected static int[]`	`initExtents(ModelImage img)`	Get the extents of an image.
`protected static float[]`	`initImageBuffer(int[] extents, boolean isColor, int imageType)`	Create the intensity buffer for an image.
`static ModelLUT`	`initLUT(ModelImage img)`	Creates and initializes the LUT for an image.
`protected static int[]`	`initNumSlices(ModelImage img)`	Get the total number of time slices and volume slices.
`protected static int[]`	`initPixelBuffer(int[] extents)`	Create the pixel buffer for an image.
`protected static float[]`	`initResFactor(float[] imgResols, int[] imgUnits)`	Get the resolution correction needed for non-isotropic images.
`protected static float[]`	`initResolutions(ModelImage img)`	DOCUMENT ME!
`static ModelRGB`	`initRGB(ModelImage img)`	Creates and initializes the ModelRGB for an image.
`protected static int[]`	`initSlicePositions(ModelImage img)`	Get the initial time and volume slice positions.
`protected static int[]`	`initUnits(ModelImage img)`	DOCUMENT ME!
`protected static float`	`initZoom(ModelImage img, float xResFactor, float yResFactor, int screenX, int screenY)`	Initializes the zoom variables for an image.
`private boolean`	`isImageResampleable(ModelImage image)`	Returns whether an image can be resampled to match imageA for loading into the imageB slot of the frame.
`private boolean`	`isResampleNeeded(ModelImage image)`	Returns whether a image should be resampled to match the extents and resolutions of imageA.
`void`	`loadAllVOIs(boolean quietMode)`	This method loads all VOIs to the active image from the default VOI directory for that image.
`void`	`loadAllVOIsFrom(java.lang.String voiDir, boolean quietMode)`	This method loads all VOIs to the active image from a given directory.
`boolean`	`loadImage(java.lang.Object obj, ViewJComponentEditImage compImage, boolean stackFlag, boolean doOrigins, boolean doOrients, double defaultValue, double defaultRed, double defaultGreen, double defaultBlue, boolean isQuiet)`	Loads an image into imageB slot of frame.
`void`	`loadLUT(boolean loadAll, boolean quietMode)`	This method loads the LUT for the active image.
`void`	`loadLUTandTransferFunctionFrom(boolean loadAll, java.lang.String filename, java.lang.String dirName, boolean quietMode)`	This method loads the LUT for the active image.
`static void`	`loadLUTandTransferFunctionFrom(ModelImage image, ModelStorageBase lut, boolean loadAll, java.lang.String filename, java.lang.String dirName, boolean quietMode)`	Reads the input LUT (ModelLUT or ModelRGB) from file.
`private void`	`loadResampledImage(ModelImage image)`	Resamples an image and loads it into the imageB slot.
`protected java.lang.String`	`makeString(float number, int decPts)`	Makes a string of a float with a specific number of decimal points.
`private void`	`matchImages(ModelImage imageA, ModelImage imageB, boolean doOrigins, boolean doOrients, double defaultValue, double defaultRed, double defaultGreen, double defaultBlue)`
`boolean`	`newFrameBeenCreated()`
`boolean`	`openVOI(boolean quietMode, boolean doLabels)`	This method opens an existing VOI.
`VOI[]`	`openVOI(ModelImage image, boolean quietMode)`	This method opens an existing VOI.
`java.io.File`	`pickImageFile()`	Brings up a FileChooser to pick a file.
`abstract 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.
`private boolean`	`reorderAfni(ModelImage image, int[] axisA, int[] axisB)`	Reorders the AFNI image based on the axis orientations.
`void`	`save(FileWriteOptions options, int filterType)`	Creates save dialog so that the image can be saved // This should be moved to imageModel.save();
`void`	`save(ModelImage img, FileWriteOptions options, int filterType)`	Creates save dialog so that the image can be saved // This should be moved to imageModel.save();
`void`	`save(ModelImage img, FileWriteOptions options, int filterType, boolean operateQuiet)`	Creates save dialog so that the image can be saved // This should be moved to imageModel.save();
`void`	`saveAllVOIs()`	This method saves all VOIs for the active image to the default VOI directory for that image.
`void`	`saveAllVOIsTo(java.lang.String voiDir)`	This method saves all VOIs for the active image to a given directory.
`void`	`saveLabels(boolean saveAll)`	DOCUMENT ME!
`void`	`saveLUT(boolean saveAll)`	This method saves the LUT for the active image.
`static void`	`saveLUTandTransferFunction(ModelImage image, ModelLUT lut, java.lang.String filename, java.lang.String dirName)`	Saves the ModelLUT and transfer function.
`void`	`saveLUTandTransferFunction(java.lang.String filename, java.lang.String dirName)`	This method saves the LUT for the active image.
`void`	`saveLUTAs(boolean saveAll, java.lang.String filename, java.lang.String dirName)`	This method saves the LUT for the active image.
`static void`	`saveLUTAs(ModelImage image, ModelStorageBase lut, boolean saveAll)`	Saves the LUT associated with the input image (either a ModelLUT or ModelRGB).
`void`	`saveVOI(boolean saveAllContours)`	This method saves a selected VOI - should this be in VOI structure ??!!!
`java.lang.String`	`saveVOIAs()`	DOCUMENT ME!
`void`	`saveVOIAs(boolean saveAllContours)`	This method allows the user to choose how to save the VOI.
`void`	`saveVOIIntensities()`	Save intensities in VOI to a text file of format x,y,z,intensity on each line if not color or complex.
`void`	`saveVOIIntensitiesTo(java.lang.String voiIntensitiesDir)`	Save intensities in VOI to a text file of format x,y,z,intensity on each line if not color or complex.
`protected void`	`setAbsPositionLabels(WildMagic.LibFoundation.Mathematics.Vector3f position)`	Sets the Absolute position label.
`abstract void`	`setActiveImage(int active)`	Sets the active image (image that should be processed for drawing VOIs and applying algorithms.
`abstract void`	`setAlphaBlend(int value)`	Sets the alpha blending parameter for two image display.
`abstract void`	`setControls()`	Sets the menu and controls (i.e. toolbars) of the main frame!
`void`	`setEnableCloseImageBAfterLoad(boolean enable)`	Sets whether the close image B option should appear after loading.
`abstract void`	`setEnabled(boolean flag)`	Controls whether or not the images/VOIs of the frame can be modified.
`void`	`setImageA(ModelImage image)`	Accessor that sets the imageA.
`abstract void`	`setImageB(ModelImage imageB)`	Accessor that sets the imageB.
`private int`	`setImageBAfni(ModelImage imageA, ModelImage image)`	Sets image B to an AFNI image, performing the appropriate transformations.
`void`	`setLastState(int state)`	setLastState.
`void`	`setLinkedFrame(ViewJFrameImage linkFrame)`	Accessor that sets the link Frame.
`void`	`setLinkedTriFrame(ViewJFrameTriImage linkTriFrame)`	Accessor that sets the link Frame.
`void`	`setLUTa(ModelLUT lut)`	Accessor that sets LUTa.
`void`	`setLUTb(ModelLUT lut)`	Accessor that sets LUTb.
`void`	`setLUTs(ModelLUT _LUTa, ModelLUT _LUTb)`	Sets LUTa and LUTb.
`void`	`setMessageText(java.lang.String str)`	Accessor to set the text of the main frame's text field.
`void`	`setOpacityInfo(float _OPACITY, float _alphaBlend)`	Sets RGB Information.
`void`	`setpaintBitmap(java.util.BitSet _paintBitmap)`	Sets the paint Bitmap.
`abstract void`	`setPaintBitmapSwitch(boolean flag)`	If true do not getMask on a setActiveImage command so as to keep the mask from the old active image.
`abstract void`	`setRGBTA(ModelRGB RGBT)`	Set the RGB table for image A.
`abstract void`	`setRGBTB(ModelRGB RGBT)`	Set the RGB table for image B.
`protected void`	`setScannerPosition(WildMagic.LibFoundation.Mathematics.Vector3f position)`	Sets the Scanner position label.
`abstract void`	`setTitle()`	Sets the Title bar of the frame.
`void`	`stateChanged(javax.swing.event.ChangeEvent event)`	Does nothing.
`private void`	`transformACPC(ModelImage image, float[] imgBuffer, TransMatrix xfrm, float iXres, float iYres, float iZres, int iXdim, int iYdim, int iZdim, int iTdim, int planeGap, int[] gapArray, boolean doNN, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim)`	This routine is designed to transform AFNI functional images which have already been transformed to match AFNI original images to match AFNI +acpc images.
`private void`	`transformAFNI(ModelImage image, float[] imgBuffer, float iXres, float iYres, float iZres, int iXdim, int iYdim, int iZdim, int iTdim, float ilowXmm, float ilowYmm, float ilowZmm, float ihighXmm, float ihighYmm, float ihighZmm, int planeGap, int[] gapArray, boolean doNN, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, float olowXmm, float olowYmm, float olowZmm, float ohighXmm, float ohighYmm, float ohighZmm)`	This routine is designed to transform AFNI functional images and AFNI 3D + time anatomical images to match AFNI original 3D anatomical images.
`private void`	`transformTalairach(ModelImage image, float[] imgBuffer, TransMatrix xfrm, float iXres, float iYres, float iZres, int iXdim, int iYdim, int iZdim, int iTdim, int planeGap, int[] gapArray, boolean doNN, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, int botX, int botY, int botZ, int topX, int topY, int topZ)`	This routine is designed to transform AFNI functional images which have already been transformed to match AFNI original images to match AFNI +tlrc images.
`abstract boolean`	`updateImageExtents()`	The extents on this image have changed, so the extents need to be read in again and menus, panes and slide bars adjusted accordingly.
`void`	`windowActivated(java.awt.event.WindowEvent event)`	Tells the UI that this frame is the currently active one.
`void`	`windowClosed(java.awt.event.WindowEvent event)`	Does nothing.
`void`	`windowClosing(java.awt.event.WindowEvent event)`	Cleans up the frame before closing.
`void`	`windowDeactivated(java.awt.event.WindowEvent event)`	Does nothing.
`void`	`windowDeiconified(java.awt.event.WindowEvent event)`	Does nothing.
`void`	`windowIconified(java.awt.event.WindowEvent event)`	Does nothing.
`void`	`windowOpened(java.awt.event.WindowEvent event)`	Does nothing.

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, setCursor, 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

Methods inherited from interface gov.nih.mipav.view.ViewImageUpdateInterface
setSlice, setTimeSlice, updateImages, updateImages, updateImages

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - IMAGE_A
```
public static final int IMAGE_A
```
    Display mode image A.
    
    See Also:
    
    Constant Field Values
  - IMAGE_B
```
public static final int IMAGE_B
```
    Display mode image B.
    
    See Also:
    
    Constant Field Values
  - IMAGE_A_B
```
public static final int IMAGE_A_B
```
    Display mode image A and B.
    
    See Also:
    
    Constant Field Values
  - zoomMode
```
protected int zoomMode
```
    DOCUMENT ME!
  - absoluteLabel
```
protected javax.swing.JLabel absoluteLabel
```
    Labels for the current absolute position:.
  - absoluteLabelVals
```
protected javax.swing.JLabel[] absoluteLabelVals
```
    Labels for the current absolute position values:.
  - absolutePanel
```
protected javax.swing.JPanel absolutePanel
```
    JPanel containing the absoulte position labels:.
  - alphaBlend
```
protected float alphaBlend
```
    Indicates the amount of blending when two images are loaded in the image frame.
  - displayMode
```
protected int displayMode
```
    Indicates which image is to be acted upon when two images are displayed.
  - imageA
```
protected ModelImage imageA
```
    Reference to the image A of this frame.
  - imageB
```
protected ModelImage imageB
```
    Reference to the image B of this frame.
  - linkFrame
```
protected ViewJFrameImage linkFrame
```
    Holds a reference (link) to another frame so that it be updated with this frame.
  - linkTriFrame
```
protected ViewJFrameTriImage linkTriFrame
```
    Holds a reference (link) to another frame so that it can be updated with this frame.
  - defaultLUTa
```
protected ModelLUT defaultLUTa
```
    Reference to LUT for image A and to the default LUT for image A.
  - LUTa
```
protected ModelLUT LUTa
```
    Reference to LUT for image A and to the default LUT for image A.
  - defaultLUTb
```
protected ModelLUT defaultLUTb
```
    Reference to LUT for image B and to the default LUT for image B.
  - LUTb
```
protected ModelLUT LUTb
```
    Reference to LUT for image B and to the default LUT for image B.
  - progressBar
```
protected ViewJProgressBar progressBar
```
    Reference to progress bar.
  - scannerLPSLabel
```
protected javax.swing.JLabel scannerLPSLabel
```
    Labels for the current scanner position:.
  - scannerRASLabel
```
protected javax.swing.JLabel scannerRASLabel
```
    Labels for the current scanner position:.
  - scannerLPSLabelVals
```
protected javax.swing.JLabel[] scannerLPSLabelVals
```
    Labels for the current scanner position values:.
  - scannerRASLabelVals
```
protected javax.swing.JLabel[] scannerRASLabelVals
```
    Labels for the current scanner position values:.
  - scannerLPSPanel
```
protected javax.swing.JPanel scannerLPSPanel
```
    JPanel containing the scanner position labels:.
  - scannerRASPanel
```
protected javax.swing.JPanel scannerRASPanel
```
    JPanel containing the scanner position labels:.
  - tabbedPane
```
protected javax.swing.JTabbedPane tabbedPane
```
    The main tabbed pane in the volume view frame.
  - scannerTabbedPane
```
protected javax.swing.JTabbedPane scannerTabbedPane
```
    The tabbed pane to hold teh LPS, RAS and absolution coordinate panels.
  - userInterface
```
protected ViewUserInterface userInterface
```
    Reference to the user interface.
  - isClosing
```
protected boolean isClosing
```
    Whether the frame's close() method is being called.
  - blue
```
private int blue
```
    Blue channel value of the paint color.
  - enableCloseImageB
```
private boolean enableCloseImageB
```
    Tells whether the ViewMenuBuilder should allow Close Image(B) after loading image B.
  - newFrameCreated
```
private boolean newFrameCreated
```
  - green
```
private int green
```
    Green channel value of the paint color.
  - lastState
```
private int lastState
```
    Save if last state was iconified or normal.
  - opacity
```
private float opacity
```
    Opacity value of the paint color.
  - paintBitmap
```
private java.util.BitSet paintBitmap
```
    Reference to the BitSet map used in painting the image.
  - red
```
private int red
```
    Red channel value of the paint color.
  - voiSavedFileName
```
private java.lang.String voiSavedFileName
```
    DOCUMENT ME!
  - linkedScrolling
```
protected boolean linkedScrolling
```
    Variable indicating if images of like dimensions should be scrolled simult.
  - absoluteXLabel
```
protected javax.swing.JLabel absoluteXLabel
```
    voxel absolute goto components*
  - absoluteYLabel
```
protected javax.swing.JLabel absoluteYLabel
```
    voxel absolute goto components*
  - absoluteZLabel
```
protected javax.swing.JLabel absoluteZLabel
```
    voxel absolute goto components*
  - absoluteXTextField
```
protected javax.swing.JTextField absoluteXTextField
```
  - absoluteYTextField
```
protected javax.swing.JTextField absoluteYTextField
```
  - absoluteZTextField
```
protected javax.swing.JTextField absoluteZTextField
```
  - absoluteGoToButton
```
protected javax.swing.JButton absoluteGoToButton
```
  - absoluteGoToPanel
```
protected javax.swing.JPanel absoluteGoToPanel
```
  - scannerLPS_RLLabel
```
protected javax.swing.JLabel scannerLPS_RLLabel
```
    scanner lps goto components*
  - scannerLPS_APLabel
```
protected javax.swing.JLabel scannerLPS_APLabel
```
    scanner lps goto components*
  - scannerLPS_ISLabel
```
protected javax.swing.JLabel scannerLPS_ISLabel
```
    scanner lps goto components*
  - scannerLPS_RLTextField
```
protected javax.swing.JTextField scannerLPS_RLTextField
```
  - scannerLPS_APTextField
```
protected javax.swing.JTextField scannerLPS_APTextField
```
  - scannerLPS_ISTextField
```
protected javax.swing.JTextField scannerLPS_ISTextField
```
  - scannerLPS_GoToButton
```
protected javax.swing.JButton scannerLPS_GoToButton
```
  - scannerLPS_GoToPanel
```
protected javax.swing.JPanel scannerLPS_GoToPanel
```
  - scannerRAS_RLLabel
```
protected javax.swing.JLabel scannerRAS_RLLabel
```
    scanner ras goto components*
  - scannerRAS_APLabel
```
protected javax.swing.JLabel scannerRAS_APLabel
```
    scanner ras goto components*
  - scannerRAS_ISLabel
```
protected javax.swing.JLabel scannerRAS_ISLabel
```
    scanner ras goto components*
  - scannerRAS_RLTextField
```
protected javax.swing.JTextField scannerRAS_RLTextField
```
  - scannerRAS_APTextField
```
protected javax.swing.JTextField scannerRAS_APTextField
```
  - scannerRAS_ISTextField
```
protected javax.swing.JTextField scannerRAS_ISTextField
```
  - scannerRAS_GoToButton
```
protected javax.swing.JButton scannerRAS_GoToButton
```
  - scannerRAS_GoToPanel
```
protected javax.swing.JPanel scannerRAS_GoToPanel
```
  - talXLabel
```
protected javax.swing.JLabel talXLabel
```
    talairach goto components*
  - talYLabel
```
protected javax.swing.JLabel talYLabel
```
    talairach goto components*
  - talZLabel
```
protected javax.swing.JLabel talZLabel
```
    talairach goto components*
  - talXTextField
```
protected javax.swing.JTextField talXTextField
```
  - talYTextField
```
protected javax.swing.JTextField talYTextField
```
  - talZTextField
```
protected javax.swing.JTextField talZTextField
```
  - talGoToButton
```
protected javax.swing.JButton talGoToButton
```
  - talGoToPanel
```
protected javax.swing.JPanel talGoToPanel
```
- Constructor Detail
  - ViewJFrameBase
```
public ViewJFrameBase(ModelImage _imageA,
                      ModelImage _imageB)
```
    Makes an image frame.
    
    Parameters:
    
    _imageA - model image A
    
    _imageB - model image B
- Method Detail
  - actionPerformed
```
public abstract void actionPerformed(java.awt.event.ActionEvent event)
```
    Method to handle action events generated by the main UI when the current frame is selected. Implemented by specific frame classes.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Parameters:
    
    event - the event from the UI
  - getControls
```
public abstract ViewControlsImage getControls()
```
    Gets the control widgets for the frame.
    
    Returns:
    
    the frame's image controls
  - getImageA
```
public abstract ModelImage getImageA()
```
    Accessor that returns the imageA.
    
    Returns:
    
    imageA
  - getImageB
```
public abstract ModelImage getImageB()
```
    Accessor that returns the imageB.
    
    Returns:
    
    imageB
  - removeControls
```
public abstract 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. Abstract and must be extended.
  - setActiveImage
```
public abstract void setActiveImage(int active)
```
    Sets the active image (image that should be processed for drawing VOIs and applying algorithms.
    
    Parameters:
    
    active - IMAGE_A or IMAGE_B
  - setAlphaBlend
```
public abstract void setAlphaBlend(int value)
```
    Sets the alpha blending parameter for two image display.
    
    Parameters:
    
    value - amount [0,100] that is the percentage of Image A to be displayed and (1-percentage) of Image B to be displayed
  - setControls
```
public abstract void setControls()
```
    Sets the menu and controls (i.e. toolbars) of the main frame! This puts only the menus and controls needed to controls the operations of this frame. Different image frames have different menu and controls.
  - setEnabled
```
public abstract void setEnabled(boolean flag)
```
    Controls whether or not the images/VOIs of the frame can be modified.
    
    Overrides:
    
    setEnabled in class java.awt.Component
    
    Parameters:
    
    flag - if true the image/VOIs can be modified; if false image/VOIs can NOT be modified
  - setImageB
```
public abstract void setImageB(ModelImage imageB)
```
    Accessor that sets the imageB.
    
    Parameters:
    
    imageB - The image to make image-B in this frame.
  - setPaintBitmapSwitch
```
public abstract void setPaintBitmapSwitch(boolean flag)
```
    If true do not getMask on a setActiveImage command so as to keep the mask from the old active image.
    
    Parameters:
    
    flag - if true do not getMask on a setActiveImage command
  - setRGBTA
```
public abstract void setRGBTA(ModelRGB RGBT)
```
    Set the RGB table for image A.
    
    Parameters:
    
    RGBT - the RGB table to use for image A
  - setRGBTB
```
public abstract void setRGBTB(ModelRGB RGBT)
```
    Set the RGB table for image B.
    
    Parameters:
    
    RGBT - the RGB table to use for image B
  - setTitle
```
public abstract void setTitle()
```
    Sets the Title bar of the frame.
  - updateImageExtents
```
public abstract boolean updateImageExtents()
```
    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
    
    Returns:
    
    true if the update was successful, false otherwise
    
    See Also:
    
    ViewImageUpdateInterface
  - about
```
public void about(int zSlice,
                  int tSlice)
```
    Makes an aboutDialog box that displays information about the image slice.
    
    Parameters:
    
    zSlice - index to slice in z-Plane about the specific image slice
    
    tSlice - index to slice in time about the specific image slice
  - buildLabelPanel
```
public void buildLabelPanel()
```
    The label panel of the x, y, z slider position.
  - canCloseImageBAfterLoad
```
public boolean canCloseImageBAfterLoad()
```
    Returns whether or not the close image B option should appear after loading.
    
    Returns:
    
    whether the "Close image B" option should appear after image B is loaded
  - newFrameBeenCreated
```
public boolean newFrameBeenCreated()
```
  - close
```
public void close()
```
    Closes both image A and image B (if it exists). It ensures the images are un-registered from the main-frame then removes any display listeners.
  - close
```
public void close(boolean closeAll)
```
    Closes both image A and image B (if it exists). It ensures the images are un-registered from the main-frame then removes any display listeners.
  - closeImageB
```
public void closeImageB()
```
    Removes image B from the frame and resets image A to be the active frame for all image controls. Ensures the image is removed, disconnected from the frame and un-registered. Also informs the garbage-collector to release any held memory.
  - componentHidden
```
public void componentHidden(java.awt.event.ComponentEvent event)
```
    Does nothing.
    
    Specified by:
    
    componentHidden in interface java.awt.event.ComponentListener
    
    Parameters:
    
    event - the component event
  - componentMoved
```
public void componentMoved(java.awt.event.ComponentEvent event)
```
    Does nothing.
    
    Specified by:
    
    componentMoved in interface java.awt.event.ComponentListener
    
    Parameters:
    
    event - the component event
  - componentResized
```
public void componentResized(java.awt.event.ComponentEvent event)
```
    Does nothing.
    
    Specified by:
    
    componentResized in interface java.awt.event.ComponentListener
    
    Parameters:
    
    event - the component event
  - componentShown
```
public void componentShown(java.awt.event.ComponentEvent event)
```
    Does nothing.
    
    Specified by:
    
    componentShown in interface java.awt.event.ComponentListener
    
    Parameters:
    
    event - the component event
  - getAlphaBlend
```
public float getAlphaBlend()
```
    Returns a default alphaBlend value for blending of two images.
    
    Returns:
    
    a default alphaBlend value
  - getDisplayMode
```
public int getDisplayMode()
```
    Accessor that returns displayMode.
    
    Returns:
    
    displayMode
  - getImageNameA
```
public java.lang.String getImageNameA()
```
    Accessor that returns the title of image A.
    
    Returns:
    
    frame title for Image A
  - getImageNameB
```
public java.lang.String getImageNameB()
```
    Accessor that returns the title of image B.
    
    Returns:
    
    frame title for Image B
  - getLastState
```
public int getLastState()
```
    getLastState.
    
    Returns:
    
    lastState Should be either Frame.NORMAL or Frame.ICONIFIED
  - getLUTa
```
public ModelLUT getLUTa()
```
    Accessor that returns LUTa.
    
    Returns:
    
    LUTa
  - getLUTb
```
public ModelLUT getLUTb()
```
    Accessor that returns LUTb.
    
    Returns:
    
    LUTb
  - getDefaultLUTa
```
public ModelLUT getDefaultLUTa()
```
    Accessor that returns the default LUTa for the frame.
    
    Returns:
    
    defaultLUTa
  - getDefaultLUTb
```
public ModelLUT getDefaultLUTb()
```
    Accessor that returns the default LUTb for the frame.
    
    Returns:
    
    defaultLUTb
  - getRGBTA
```
public ModelRGB getRGBTA()
```
    Get the RGB table for image A.
    
    Returns:
    
    null (may be overridden by inheriting classes)
  - getRGBTB
```
public ModelRGB getRGBTB()
```
    Get the RGB table for image B.
    
    Returns:
    
    null (may be overridden by inheriting classes)
  - getTriImg
```
public ViewJFrameTriImage getTriImg()
```
    Get the ViewJFrameTriImage reference.
    
    Returns:
    
    linkTriFrame ViewJFrameTriImage.
  - getUserInterface
```
public ViewUserInterface getUserInterface()
```
    Accessor that returns the user interface.
    
    Returns:
    
    the user interface
  - loadAllVOIs
```
public void loadAllVOIs(boolean quietMode)
```
    This method loads all VOIs to the active image from the default VOI directory for that image.
    
    Parameters:
    
    quietMode - if true indicates that warnings should not be displayed.
  - loadAllVOIsFrom
```
public void loadAllVOIsFrom(java.lang.String voiDir,
                            boolean quietMode)
```
    This method loads all VOIs to the active image from a given directory.
    
    Parameters:
    
    voiDir - the directory to load voi's from
    
    quietMode - if true indicates that warnings should not be displayed.
  - loadImage
```
public boolean loadImage(java.lang.Object obj,
                         ViewJComponentEditImage compImage,
                         boolean stackFlag,
                         boolean doOrigins,
                         boolean doOrients,
                         double defaultValue,
                         double defaultRed,
                         double defaultGreen,
                         double defaultBlue,
                         boolean isQuiet)
```
    Loads an image into imageB slot of frame. Matches the imageB resolutions and dimensions to imageA, and can optionally match the images' origins and orientations.
    
    Parameters:
    
    obj - an object which is either a ModelImage to be loaded into the modelimage (as say, imageB, imported from another frame) or a File to be read in via FileIO.readImage(...)
    
    compImage - image component where image is set so that it can be displayed.
    
    stackFlag - flag indicating multi file
    
    doOrigins - when calling MatchImages to match resolutions and dimensions, should origins be matched too?
    
    doOrients - when calling MatchImages to match resolutions and dimensions, should orientations be matched too?
    
    Returns:
    
    true if the load was successful, false otherwise
    
    See Also:
    
    JDialogLoadImage
  - matchImages
```
private void matchImages(ModelImage imageA,
                         ModelImage imageB,
                         boolean doOrigins,
                         boolean doOrients,
                         double defaultValue,
                         double defaultRed,
                         double defaultGreen,
                         double defaultBlue)
```
  - loadLUT
```
public void loadLUT(boolean loadAll,
                    boolean quietMode)
```
    This method loads the LUT for the active image. If the image is not a color image then both the functions and the LUT data are loaded. If this is a color image, then only the functions are loaded.
    
    Parameters:
    
    loadAll - boolean indicating that both lut and transfer functions should be loaded. If false, then only transfer functions are loaded.
    
    quietMode - if true indicates that warnings should not be displayed.
  - loadLUTandTransferFunctionFrom
```
public void loadLUTandTransferFunctionFrom(boolean loadAll,
                                           java.lang.String filename,
                                           java.lang.String dirName,
                                           boolean quietMode)
```
    This method loads the LUT for the active image. If the image is not a color image then both the functions and the LUT data are loaded. If this is a color image, then only the functions are loaded.
    
    Parameters:
    
    loadAll - boolean indicating that both lut and transfer functions should be loaded. If false, then only transfer functions are loaded.
    
    filename - filename to save LUT as
    
    dirName - directory to save LUT to
    
    quietMode - if true indicates that warnings should not be displayed.
  - loadLUTandTransferFunctionFrom
```
public static void loadLUTandTransferFunctionFrom(ModelImage image,
                                                  ModelStorageBase lut,
                                                  boolean loadAll,
                                                  java.lang.String filename,
                                                  java.lang.String dirName,
                                                  boolean quietMode)
```
    Reads the input LUT (ModelLUT or ModelRGB) from file.
    
    Parameters:
    
    image -
    
    lut -
    
    loadAll -
    
    filename -
    
    dirName -
    
    quietMode -
  - openVOI
```
public boolean openVOI(boolean quietMode,
                       boolean doLabels)
```
    This method opens an existing VOI.
    
    Parameters:
    
    quietMode - if true indicates that warnings should not be displayed.
    
    doLabels - DOCUMENT ME!
    
    Returns:
    
    whether a VOI was successfully opened (ie - the dialog wasn't cancelled)
  - openVOI
```
public VOI[] openVOI(ModelImage image,
                     boolean quietMode)
```
    This method opens an existing VOI.
    
    Parameters:
    
    image - image where VOI(s) are to registered
    
    quietMode - if true indicates that warnings should not be displayed.
    
    Returns:
    
    the VOI(s)
  - pickImageFile
```
public java.io.File pickImageFile()
```
    Brings up a FileChooser to pick a file.
    
    Returns:
    
    File the File the chooser picks.
  - save
```
public void save(FileWriteOptions options,
                 int filterType)
```
    Creates save dialog so that the image can be saved // This should be moved to imageModel.save();
    
    Parameters:
    
    options - File-write options.
    
    filterType - only used if >= 0
  - save
```
public void save(ModelImage img,
                 FileWriteOptions options,
                 int filterType)
```
    Creates save dialog so that the image can be saved // This should be moved to imageModel.save();
    
    Parameters:
    
    img - DOCUMENT ME!
    
    options - DOCUMENT ME!
    
    filterType - only used if value >= 0
  - save
```
public void save(ModelImage img,
                 FileWriteOptions options,
                 int filterType,
                 boolean operateQuiet)
```
    Creates save dialog so that the image can be saved // This should be moved to imageModel.save();
    
    Parameters:
    
    img - DOCUMENT ME!
    
    options - DOCUMENT ME!
    
    filterType - only used if value >= 0
    
    operateQuiet - informs the FileIO to not notify user of errors or interrogate for more information.
  - saveAllVOIs
```
public void saveAllVOIs()
```
    This method saves all VOIs for the active image to the default VOI directory for that image.
  - saveAllVOIsTo
```
public void saveAllVOIsTo(java.lang.String voiDir)
```
    This method saves all VOIs for the active image to a given directory.
    
    Parameters:
    
    voiDir - directory that contains VOIs for this image.
  - saveLabels
```
public void saveLabels(boolean saveAll)
```
    DOCUMENT ME!
    
    Parameters:
    
    saveAll - DOCUMENT ME!
  - saveLUT
```
public void saveLUT(boolean saveAll)
```
    This method saves the LUT for the active image. If the image is not a color image then both the functions and the LUT data are saved. If this is a color image, then only the functions are saved.
    
    Parameters:
    
    saveAll - - boolean indicating that both lut and transfer functions should be saved. If false, then only transfer functions are saved.
  - saveLUTAs
```
public void saveLUTAs(boolean saveAll,
                      java.lang.String filename,
                      java.lang.String dirName)
```
    This method saves the LUT for the active image. If the image is not a color image then both the functions and the LUT data are saved. If this is a color image, then only the functions are saved.
    
    Parameters:
    
    saveAll - boolean indicating that both lut and transfer functions should be saved. If false, then only transfer functions are saved.
    If either filename or directory is null, then the user will be prompted for a filename.
    
    filename - filename to save LUT as
    
    dirName - directory to save LUT to
  - saveLUTAs
```
public static void saveLUTAs(ModelImage image,
                             ModelStorageBase lut,
                             boolean saveAll)
```
    Saves the LUT associated with the input image (either a ModelLUT or ModelRGB).
    
    Parameters:
    
    image -
    
    lut -
    
    saveAll -
  - saveLUTandTransferFunction
```
public void saveLUTandTransferFunction(java.lang.String filename,
                                       java.lang.String dirName)
```
    This method saves the LUT for the active image. If the image is not a color image then both the functions and the LUT data are saved. If this is a color image, then only the functions are saved.
    
    Parameters:
    
    filename - filename to save LUT as
    
    dirName - directory to save LUT to
  - saveLUTandTransferFunction
```
public static void saveLUTandTransferFunction(ModelImage image,
                                              ModelLUT lut,
                                              java.lang.String filename,
                                              java.lang.String dirName)
```
    Saves the ModelLUT and transfer function.
    
    Parameters:
    
    image -
    
    lut -
    
    filename -
    
    dirName -
  - saveVOI
```
public void saveVOI(boolean saveAllContours)
```
    This method saves a selected VOI - should this be in VOI structure ??!!!
    
    Parameters:
    
    saveAllContours - if true all contours are saved
  - saveVOIAs
```
public java.lang.String saveVOIAs()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - saveVOIAs
```
public void saveVOIAs(boolean saveAllContours)
```
    This method allows the user to choose how to save the VOI.
    
    Parameters:
    
    saveAllContours - if true all contours are saved
  - saveVOIIntensities
```
public void saveVOIIntensities()
```
    Save intensities in VOI to a text file of format x,y,z,intensity on each line if not color or complex. If color use format x,y,z,a,r,g,b on each line and if complex use format x,y,z,real,imaginary on each line.
  - saveVOIIntensitiesTo
```
public void saveVOIIntensitiesTo(java.lang.String voiIntensitiesDir)
```
    Save intensities in VOI to a text file of format x,y,z,intensity on each line if not color or complex. If color use format x,y,z,a,r,g,b on each line and if complex use format x,y,z,real,imaginary on each line.
  - setEnableCloseImageBAfterLoad
```
public void setEnableCloseImageBAfterLoad(boolean enable)
```
    Sets whether the close image B option should appear after loading.
    
    Parameters:
    
    enable - whether the "Close image B" option should appear after image B is loaded
  - setImageA
```
public void setImageA(ModelImage image)
```
    Accessor that sets the imageA.
    
    Parameters:
    
    image - The image to make image-A in this frame.
  - setLastState
```
public void setLastState(int state)
```
    setLastState.
    
    Parameters:
    
    state - Should be either Frame.NORMAL or Frame.ICONIFIED
  - setLinkedFrame
```
public void setLinkedFrame(ViewJFrameImage linkFrame)
```
    Accessor that sets the link Frame.
    
    Parameters:
    
    linkFrame - set frame to link to.
  - setLinkedTriFrame
```
public void setLinkedTriFrame(ViewJFrameTriImage linkTriFrame)
```
    Accessor that sets the link Frame.
    
    Parameters:
    
    linkTriFrame - set frame to link to.
  - setLUTa
```
public void setLUTa(ModelLUT lut)
```
    Accessor that sets LUTa.
    
    Parameters:
    
    lut - DOCUMENT ME!
  - setLUTb
```
public void setLUTb(ModelLUT lut)
```
    Accessor that sets LUTb.
    
    Parameters:
    
    lut - DOCUMENT ME!
  - setLUTs
```
public void setLUTs(ModelLUT _LUTa,
                    ModelLUT _LUTb)
```
    Sets LUTa and LUTb.
    
    Parameters:
    
    _LUTa - DOCUMENT ME!
    
    _LUTb - DOCUMENT ME!
  - setMessageText
```
public final void setMessageText(java.lang.String str)
```
    Accessor to set the text of the main frame's text field.
    
    Parameters:
    
    str - string to be display in the main frame's text field
  - setOpacityInfo
```
public void setOpacityInfo(float _OPACITY,
                           float _alphaBlend)
```
    Sets RGB Information.
    
    Parameters:
    
    _OPACITY - DOCUMENT ME!
    
    _alphaBlend - DOCUMENT ME!
  - setpaintBitmap
```
public void setpaintBitmap(java.util.BitSet _paintBitmap)
```
    Sets the paint Bitmap.
    
    Parameters:
    
    _paintBitmap - DOCUMENT ME!
  - stateChanged
```
public void stateChanged(javax.swing.event.ChangeEvent event)
```
    Does nothing.
    
    Specified by:
    
    stateChanged in interface javax.swing.event.ChangeListener
    
    Parameters:
    
    event - the change event
  - windowActivated
```
public void windowActivated(java.awt.event.WindowEvent event)
```
    Tells the UI that this frame is the currently active one.
    
    Specified by:
    
    windowActivated in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event
  - windowClosed
```
public void windowClosed(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowClosed in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event
  - windowClosing
```
public void windowClosing(java.awt.event.WindowEvent event)
```
    Cleans up the frame before closing.
    
    Specified by:
    
    windowClosing in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event that triggered this method
  - windowDeactivated
```
public void windowDeactivated(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowDeactivated in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event
  - windowDeiconified
```
public void windowDeiconified(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowDeiconified in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event
  - windowIconified
```
public void windowIconified(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowIconified in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event
  - windowOpened
```
public void windowOpened(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowOpened in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event
  - finalize
```
protected void finalize()
                 throws java.lang.Throwable
```
    Cleans memory.
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable - the Exception raised by this method
  - makeString
```
protected java.lang.String makeString(float number,
                                      int decPts)
```
    Makes a string of a float with a specific number of decimal points.
    
    Parameters:
    
    number - number to be converted to a string
    
    decPts - the number of decimal points
    
    Returns:
    
    string representation of the number
  - setAbsPositionLabels
```
protected void setAbsPositionLabels(WildMagic.LibFoundation.Mathematics.Vector3f position)
```
    Sets the Absolute position label.
    
    Parameters:
    
    position - DOCUMENT ME!
  - setScannerPosition
```
protected void setScannerPosition(WildMagic.LibFoundation.Mathematics.Vector3f position)
```
    Sets the Scanner position label.
    
    Parameters:
    
    position - DOCUMENT ME!
  - handleZoomPopupMenu
```
protected void handleZoomPopupMenu(java.awt.Component component,
                                   java.awt.event.MouseEvent event)
```
    DOCUMENT ME!
    
    Parameters:
    
    component - DOCUMENT ME!
    
    event - DOCUMENT ME!
  - handleMaskPopupMenu
```
public static void handleMaskPopupMenu(java.awt.Component component,
                                       java.awt.event.MouseEvent event)
```
    Handles the popup menu for the Quick Mask buttons
    
    Parameters:
    
    component - DOCUMENT ME!
    
    event - DOCUMENT ME!
  - handlePaintToMaskPopupMenu
```
protected void handlePaintToMaskPopupMenu(java.awt.Component component,
                                          java.awt.event.MouseEvent event)
```
    Handles the pop-up menu for Paint to Mask buttons (inside/outside)
    
    Parameters:
    
    component - DOCUMENT ME!
    
    event - DOCUMENT ME!
  - initExtents
```
protected static int[] initExtents(ModelImage img)
```
    Get the extents of an image. (don't know why this is really needed...)
    
    Parameters:
    
    img - the image
    
    Returns:
    
    the image's extents
  - initImageBuffer
```
protected static float[] initImageBuffer(int[] extents,
                                         boolean isColor,
                                         int imageType)
```
    Create the intensity buffer for an image.
    
    Parameters:
    
    extents - the extents of the image
    
    isColor - whether the image is in color
    
    Returns:
    
    a buffer which is big enough to contain the image intensity data
  - initNumSlices
```
protected static int[] initNumSlices(ModelImage img)
```
    Get the total number of time slices and volume slices.
    
    Parameters:
    
    img - the image to get the slices of
    
    Returns:
    
    an array containing the number of volume slices (in the first element) and the number of time slices in the image (in the second element)
  - initPixelBuffer
```
protected static int[] initPixelBuffer(int[] extents)
```
    Create the pixel buffer for an image.
    
    Parameters:
    
    extents - the extents of the image
    
    Returns:
    
    a buffer which is big enough to contain the image pixel data
  - initResFactor
```
protected static float[] initResFactor(float[] imgResols,
                                       int[] imgUnits)
```
    Get the resolution correction needed for non-isotropic images.
    
    Parameters:
    
    imgResols - the image resolution
    
    imgUnits - the image units of measure
    
    Returns:
    
    the resolution correction factor in the x (the first element) and y (the second element) dimensions
  - initResolutions
```
protected static float[] initResolutions(ModelImage img)
```
    DOCUMENT ME!
    
    Parameters:
    
    img - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - initSlicePositions
```
protected static int[] initSlicePositions(ModelImage img)
```
    Get the initial time and volume slice positions.
    
    Parameters:
    
    img - the image to get the slice positions of
    
    Returns:
    
    an array containing the slice in the volume (in the first element) and the time slice (in the second element)
  - initUnits
```
protected static int[] initUnits(ModelImage img)
```
    DOCUMENT ME!
    
    Parameters:
    
    img - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - initLUT
```
public static ModelLUT initLUT(ModelImage img)
                        throws java.lang.OutOfMemoryError
```
    Creates and initializes the LUT for an image.
    
    Parameters:
    
    img - the image to create a LUT for
    
    Returns:
    
    a LUT for the image img (null if a color image)
    
    Throws:
    
    java.lang.OutOfMemoryError - if enough memory cannot be allocated for this method
  - initRGB
```
public static ModelRGB initRGB(ModelImage img)
                        throws java.lang.OutOfMemoryError
```
    Creates and initializes the ModelRGB for an image.
    
    Parameters:
    
    img - the image to create a ModelRGB for
    
    Returns:
    
    a ModelRGB for the image img (null if NOT a color image)
    
    Throws:
    
    java.lang.OutOfMemoryError - if enough memory cannot be allocated for this method
  - initZoom
```
protected static float initZoom(ModelImage img,
                                float xResFactor,
                                float yResFactor,
                                int screenX,
                                int screenY)
```
    Initializes the zoom variables for an image.
    
    Parameters:
    
    img - the image to use to initialize the zoom
    
    xResFactor - correction factor in the x direction for images that are do not have isotropic voxels
    
    yResFactor - correction factor in the x direction for images that are do not have isotropic voxels
    
    Returns:
    
    the initial zoom to use for this image
  - findFilter
```
private javax.swing.filechooser.FileFilter findFilter(javax.swing.JFileChooser chooser,
                                                      int filterType)
```
    Finds the FileFilter that matches the file type.
    
    Parameters:
    
    chooser - JFileChooser
    
    filterType - int the file filter type
    
    Returns:
    
    FileFilter the filter that matches the filter type.
  - isImageResampleable
```
private boolean isImageResampleable(ModelImage image)
```
    Returns whether an image can be resampled to match imageA for loading into the imageB slot of the frame.
    
    Parameters:
    
    image - the image to check
    
    Returns:
    
    true if the image is either 3D or 4D (but not if the 4th dim differs)
  - isResampleNeeded
```
private boolean isResampleNeeded(ModelImage image)
```
    Returns whether a image should be resampled to match the extents and resolutions of imageA.
    
    Parameters:
    
    image - the image to check against imageA
    
    Returns:
    
    true if a resampling of the image is required
  - loadResampledImage
```
private void loadResampledImage(ModelImage image)
```
    Resamples an image and loads it into the imageB slot. This image should already be matched against imageA.
    
    Parameters:
    
    image - the image to resample and load as imageB
  - reorderAfni
```
private boolean reorderAfni(ModelImage image,
                            int[] axisA,
                            int[] axisB)
```
    Reorders the AFNI image based on the axis orientations. B0 to A1 indicates changing x to y; B0 to A2 indicates a change from x to z.
    
    Parameters:
    
    image - Image to reorder.
    
    axisA - axis indices orientation of reordered image
    
    axisB - axis indices orientation of original image
    
    Returns:
    
    true if the reordering of the Afni file is successful, false otherwise
  - setImageBAfni
```
private int setImageBAfni(ModelImage imageA,
                          ModelImage image)
```
    Sets image B to an AFNI image, performing the appropriate transformations.
    
    Parameters:
    
    imageA - Image A.
    
    image - AFNI image to set to image A.
    
    Returns:
    
    -1 if failure; 0 if no tranformation needed; and 1 if transformation and set successful.
  - transformACPC
```
private void transformACPC(ModelImage image,
                           float[] imgBuffer,
                           TransMatrix xfrm,
                           float iXres,
                           float iYres,
                           float iZres,
                           int iXdim,
                           int iYdim,
                           int iZdim,
                           int iTdim,
                           int planeGap,
                           int[] gapArray,
                           boolean doNN,
                           float oXres,
                           float oYres,
                           float oZres,
                           int oXdim,
                           int oYdim,
                           int oZdim)
```
    This routine is designed to transform AFNI functional images which have already been transformed to match AFNI original images to match AFNI +acpc images.
    AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states:
    
    "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."
    
    A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure." At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."
    
    Thus, the intensity data is interpolated with trilinear interpolation and the threshold data is interpolated with nearest neighbor interpolation.
    
    Parameters:
    
    image - image being created
    
    imgBuffer - source image array
    
    xfrm - transformation matrix to be applied
    
    iXres - input x resolution
    
    iYres - input y resolution
    
    iZres - input z resolution
    
    iXdim - input x dimesnion
    
    iYdim - input y dimension
    
    iZdim - input z dimension
    
    iTdim - input t dimension
    
    planeGap - -1 if no zero filled gaps, 0 for x axis gaps, 1 for y axis, 2 for z axis
    
    gapArray - array of coordinates at which the zero filled planes occur
    
    doNN - true if functional, false if anatomical
    
    oXres - output x resolution
    
    oYres - output y resolution
    
    oZres - output z resolution
    
    oXdim - output x dimension
    
    oYdim - output y dimension
    
    oZdim - output z dimension
  - transformAFNI
```
private void transformAFNI(ModelImage image,
                           float[] imgBuffer,
                           float iXres,
                           float iYres,
                           float iZres,
                           int iXdim,
                           int iYdim,
                           int iZdim,
                           int iTdim,
                           float ilowXmm,
                           float ilowYmm,
                           float ilowZmm,
                           float ihighXmm,
                           float ihighYmm,
                           float ihighZmm,
                           int planeGap,
                           int[] gapArray,
                           boolean doNN,
                           float oXres,
                           float oYres,
                           float oZres,
                           int oXdim,
                           int oYdim,
                           int oZdim,
                           float olowXmm,
                           float olowYmm,
                           float olowZmm,
                           float ohighXmm,
                           float ohighYmm,
                           float ohighZmm)
```
    This routine is designed to transform AFNI functional images and AFNI 3D + time anatomical images to match AFNI original 3D anatomical images. Here the 3 axes of the 2 images are parallel and the spatial orientation of the 2 sets of axes are identical.
    AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states:
    
    "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."
    
    A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure."
    
    At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."
    
    Thus, the intensity data is interpolated with trilinear interpolation and the threshold data is interpolated with nearest neighbor interpolation.
    
    Parameters:
    
    image - image being created
    
    imgBuffer - source image array
    
    iXres - input x resolution
    
    iYres - input y resolution
    
    iZres - input z resolution
    
    iXdim - input x dimesnion
    
    iYdim - input y dimension
    
    iZdim - input z dimension
    
    iTdim - input t dimension
    
    ilowXmm - lowest valid input x location in space in millimeters
    
    ilowYmm - lowest valid input y location in space in millimeters
    
    ilowZmm - lowest valid input z location in space in millimeters
    
    ihighXmm - highest valid input x location in space in millimeters
    
    ihighYmm - highest valid input y location in space in millimeters
    
    ihighZmm - highest valid input z location in space in millimeters
    
    planeGap - -1 if no zero filled gaps, 0 for x axis gaps, 1 for y axis, 2 for z axis
    
    gapArray - array of coordinates at which the zero filled planes occur
    
    doNN - true if functional, false if anatomical
    
    oXres - output x resolution
    
    oYres - output y resolution
    
    oZres - output z resolution
    
    oXdim - output x dimension
    
    oYdim - output y dimension
    
    oZdim - output z dimension
    
    olowXmm - lowest valid output x location in space in millimeters
    
    olowYmm - lowest valid output y location in space in millimeters
    
    olowZmm - lowest valid output z location in space in millimeters
    
    ohighXmm - highest valid output x location in space in millimeters
    
    ohighYmm - highest valid output y location in space in millimeters
    
    ohighZmm - highest valid output z location in space in millimeters
  - transformTalairach
```
private void transformTalairach(ModelImage image,
                                float[] imgBuffer,
                                TransMatrix xfrm,
                                float iXres,
                                float iYres,
                                float iZres,
                                int iXdim,
                                int iYdim,
                                int iZdim,
                                int iTdim,
                                int planeGap,
                                int[] gapArray,
                                boolean doNN,
                                float oXres,
                                float oYres,
                                float oZres,
                                int oXdim,
                                int oYdim,
                                int oZdim,
                                int botX,
                                int botY,
                                int botZ,
                                int topX,
                                int topY,
                                int topZ)
```
    This routine is designed to transform AFNI functional images which have already been transformed to match AFNI original images to match AFNI +tlrc images.
    AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states:
    
    "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."
    
    A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure." At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."
    
    Thus, the intensity data is interpolated with trilinear interpolation and the threshold data is interpolated with nearest neighbor interpolation.
    
    Parameters:
    
    image - image being created
    
    imgBuffer - source image array
    
    xfrm - transformation matrix to be applied
    
    iXres - input x resolution
    
    iYres - input y resolution
    
    iZres - input z resolution
    
    iXdim - input x dimesnion
    
    iYdim - input y dimension
    
    iZdim - input z dimension
    
    iTdim - input t dimension
    
    planeGap - -1 if no zero filled gaps, 0 for x axis gaps, 1 for y axis, 2 for z axis
    
    gapArray - array of coordinates at which the zero filled planes occur
    
    doNN - true if functional, false if anatomical
    
    oXres - output x resolution
    
    oYres - output y resolution
    
    oZres - output z resolution
    
    oXdim - output x dimension
    
    oYdim - output y dimension
    
    oZdim - output z dimension
    
    botX - lowest x output value in this 1 of the 12 Talairach regions
    
    botY - lowest y output value in this 1 of the 12 Talairach regions
    
    botZ - lowest z output value in this 1 of the 12 Talairach regions
    
    topX - highest x output value in this 1 of the 12 Talairach regions
    
    topY - highest y output value in this 1 of the 12 Talairach regions
    
    topZ - highest z output value in this 1 of the 12 Talairach regions

Class ViewJFrameBase

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 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 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

Methods inherited from interface gov.nih.mipav.view.ViewImageUpdateInterface

Field Detail

serialVersionUID

IMAGE_A

IMAGE_B

IMAGE_A_B

zoomMode

absoluteLabel

absoluteLabelVals

absolutePanel

alphaBlend

displayMode

imageA

imageB

linkFrame

linkTriFrame

defaultLUTa

LUTa

defaultLUTb

LUTb

progressBar

scannerLPSLabel

scannerRASLabel

scannerLPSLabelVals

scannerRASLabelVals

scannerLPSPanel

scannerRASPanel

tabbedPane

scannerTabbedPane

userInterface

isClosing

blue

enableCloseImageB

newFrameCreated

green

lastState

opacity

paintBitmap

red

voiSavedFileName

linkedScrolling

absoluteXLabel

absoluteYLabel

absoluteZLabel

absoluteXTextField

absoluteYTextField

absoluteZTextField

absoluteGoToButton

absoluteGoToPanel

scannerLPS_RLLabel

scannerLPS_APLabel

scannerLPS_ISLabel

scannerLPS_RLTextField

scannerLPS_APTextField

scannerLPS_ISTextField

scannerLPS_GoToButton

scannerLPS_GoToPanel

scannerRAS_RLLabel