Package gov.nih.mipav.view

Class ViewJFrameBase

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, ActionListener, ComponentListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, ChangeListener, RootPaneContainer, 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 JFrame
implements ViewImageUpdateInterface, ActionListener, WindowListener, ComponentListener, 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

JFrame.AccessibleJFrame

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

Frame.AccessibleAWTFrame

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

Window.AccessibleAWTWindow, Window.Type

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field	Description
protected JButton	absoluteGoToButton
protected JPanel	absoluteGoToPanel
protected JLabel	absoluteLabel	Labels for the current absolute position:.
protected JLabel[]	absoluteLabelVals	Labels for the current absolute position values:.
protected JPanel	absolutePanel	JPanel containing the absoulte position labels:.
protected JLabel	absoluteXLabel	voxel absolute goto components*
protected JTextField	absoluteXTextField
protected JLabel	absoluteYLabel	voxel absolute goto components*
protected JTextField	absoluteYTextField
protected JLabel	absoluteZLabel	voxel absolute goto components*
protected 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 final int	IMAGE_A	Display mode image A.
static final int	IMAGE_A_B	Display mode image A and B.
static final 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 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 JLabel	scannerLPS_APLabel	scanner lps goto components*
protected JTextField	scannerLPS_APTextField
protected JButton	scannerLPS_GoToButton
protected JPanel	scannerLPS_GoToPanel
protected JLabel	scannerLPS_ISLabel	scanner lps goto components*
protected JTextField	scannerLPS_ISTextField
protected JLabel	scannerLPS_RLLabel	scanner lps goto components*
protected JTextField	scannerLPS_RLTextField
protected JLabel	scannerLPSLabel	Labels for the current scanner position:.
protected JLabel[]	scannerLPSLabelVals	Labels for the current scanner position values:.
protected JPanel	scannerLPSPanel	JPanel containing the scanner position labels:.
protected JLabel	scannerRAS_APLabel	scanner ras goto components*
protected JTextField	scannerRAS_APTextField
protected JButton	scannerRAS_GoToButton
protected JPanel	scannerRAS_GoToPanel
protected JLabel	scannerRAS_ISLabel	scanner ras goto components*
protected JTextField	scannerRAS_ISTextField
protected JLabel	scannerRAS_RLLabel	scanner ras goto components*
protected JTextField	scannerRAS_RLTextField
protected JLabel	scannerRASLabel	Labels for the current scanner position:.
protected JLabel[]	scannerRASLabelVals	Labels for the current scanner position values:.
protected JPanel	scannerRASPanel	JPanel containing the scanner position labels:.
protected JTabbedPane	scannerTabbedPane	The tabbed pane to hold teh LPS, RAS and absolution coordinate panels.
private static final long	serialVersionUID	Use serialVersionUID for interoperability.
protected JTabbedPane	tabbedPane	The main tabbed pane in the volume view frame.
protected JButton	talGoToButton
protected JPanel	talGoToPanel
protected JLabel	talXLabel	talairach goto components*
protected JTextField	talXTextField
protected JLabel	talYLabel	talairach goto components*
protected JTextField	talYTextField
protected JLabel	talZLabel	talairach goto components*
protected JTextField	talZTextField
protected ViewUserInterface	userInterface	Reference to the user interface.
private 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

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(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(ComponentEvent event)	Does nothing.
void	componentMoved(ComponentEvent event)	Does nothing.
void	componentResized(ComponentEvent event)	Does nothing.
void	componentShown(ComponentEvent event)	Does nothing.
protected void	finalize()	Cleans memory.
private FileFilter	findFilter(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.
String	getImageNameA()	Accessor that returns the title of image A.
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(Component component, MouseEvent event)	Handles the popup menu for the Quick Mask buttons
protected void	handlePaintToMaskPopupMenu(Component component, MouseEvent event)	Handles the pop-up menu for Paint to Mask buttons (inside/outside)
protected void	handleZoomPopupMenu(Component component, 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(String voiDir, boolean quietMode)	This method loads all VOIs to the active image from a given directory.
boolean	loadImage(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, String filename, String dirName, boolean quietMode)	This method loads the LUT for the active image.
static void	loadLUTandTransferFunctionFrom(ModelImage image, ModelStorageBase lut, boolean loadAll, String filename, 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 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.
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(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, String filename, String dirName)	Saves the ModelLUT and transfer function.
void	saveLUTandTransferFunction(String filename, String dirName)	This method saves the LUT for the active image.
void	saveLUTAs(boolean saveAll, String filename, 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 ??!!!
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(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.
final void	setMessageText(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(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(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(WindowEvent event)	Tells the UI that this frame is the currently active one.
void	windowClosed(WindowEvent event)	Does nothing.
void	windowClosing(WindowEvent event)	Cleans up the frame before closing.
void	windowDeactivated(WindowEvent event)	Does nothing.
void	windowDeiconified(WindowEvent event)	Does nothing.
void	windowIconified(WindowEvent event)	Does nothing.
void	windowOpened(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 Details

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 JLabel absoluteLabel

Labels for the current absolute position:.

absoluteLabelVals

protected JLabel[] absoluteLabelVals

Labels for the current absolute position values:.

absolutePanel

protected 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 JLabel scannerLPSLabel

Labels for the current scanner position:.

scannerRASLabel

protected JLabel scannerRASLabel

Labels for the current scanner position:.

scannerLPSLabelVals

protected JLabel[] scannerLPSLabelVals

Labels for the current scanner position values:.

scannerRASLabelVals

protected JLabel[] scannerRASLabelVals

Labels for the current scanner position values:.

scannerLPSPanel

protected JPanel scannerLPSPanel

JPanel containing the scanner position labels:.

scannerRASPanel

protected JPanel scannerRASPanel

JPanel containing the scanner position labels:.

tabbedPane

protected JTabbedPane tabbedPane

The main tabbed pane in the volume view frame.

scannerTabbedPane

protected 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 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 String voiSavedFileName

DOCUMENT ME!

linkedScrolling

protected boolean linkedScrolling

Variable indicating if images of like dimensions should be scrolled simult.

absoluteXLabel

protected JLabel absoluteXLabel

voxel absolute goto components*

absoluteYLabel

protected JLabel absoluteYLabel

voxel absolute goto components*

absoluteZLabel

protected JLabel absoluteZLabel

voxel absolute goto components*

absoluteXTextField

protected JTextField absoluteXTextField

absoluteYTextField

protected JTextField absoluteYTextField

absoluteZTextField

protected JTextField absoluteZTextField

absoluteGoToButton

protected JButton absoluteGoToButton

absoluteGoToPanel

protected JPanel absoluteGoToPanel

scannerLPS_RLLabel

protected JLabel scannerLPS_RLLabel

scanner lps goto components*

scannerLPS_APLabel

protected JLabel scannerLPS_APLabel

scanner lps goto components*

scannerLPS_ISLabel

protected JLabel scannerLPS_ISLabel

scanner lps goto components*

scannerLPS_RLTextField

protected JTextField scannerLPS_RLTextField

scannerLPS_APTextField

protected JTextField scannerLPS_APTextField

scannerLPS_ISTextField

protected JTextField scannerLPS_ISTextField

scannerLPS_GoToButton

protected JButton scannerLPS_GoToButton

scannerLPS_GoToPanel

protected JPanel scannerLPS_GoToPanel

scannerRAS_RLLabel

protected JLabel scannerRAS_RLLabel

scanner ras goto components*

scannerRAS_APLabel

protected JLabel scannerRAS_APLabel

scanner ras goto components*

scannerRAS_ISLabel

protected JLabel scannerRAS_ISLabel

scanner ras goto components*

scannerRAS_RLTextField

protected JTextField scannerRAS_RLTextField

scannerRAS_APTextField

protected JTextField scannerRAS_APTextField

scannerRAS_ISTextField

protected JTextField scannerRAS_ISTextField

scannerRAS_GoToButton

protected JButton scannerRAS_GoToButton

scannerRAS_GoToPanel

protected JPanel scannerRAS_GoToPanel

talXLabel

protected JLabel talXLabel

talairach goto components*

talYLabel

protected JLabel talYLabel

talairach goto components*

talZLabel

protected JLabel talZLabel

talairach goto components*

talXTextField

protected JTextField talXTextField

talYTextField

protected JTextField talYTextField

talZTextField

protected JTextField talZTextField

talGoToButton

protected JButton talGoToButton

talGoToPanel

protected JPanel talGoToPanel

Constructor Details

ViewJFrameBase

public ViewJFrameBase(ModelImage _imageA,
 ModelImage _imageB)

Makes an image frame.

Parameters:

_imageA - model image A

_imageB - model image B

Method Details

actionPerformed

public abstract void actionPerformed(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 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 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(ComponentEvent event)

Does nothing.

Specified by:

componentHidden in interface ComponentListener

Parameters:

event - the component event

componentMoved

public void componentMoved(ComponentEvent event)

Does nothing.

Specified by:

componentMoved in interface ComponentListener

Parameters:

event - the component event

componentResized

public void componentResized(ComponentEvent event)

Does nothing.

Specified by:

componentResized in interface ComponentListener

Parameters:

event - the component event

componentShown

public void componentShown(ComponentEvent event)

Does nothing.

Specified by:

componentShown in interface 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 String getImageNameA()

Accessor that returns the title of image A.

Returns:

frame title for Image A

getImageNameB

public 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(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(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,
 String filename,
 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,
 String filename,
 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 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(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,
 String filename,
 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(String filename,
 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,
 String filename,
 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 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(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(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(BitSet _paintBitmap)

Sets the paint Bitmap.

Parameters:

_paintBitmap - DOCUMENT ME!

stateChanged

public void stateChanged(ChangeEvent event)

Does nothing.

Specified by:

stateChanged in interface ChangeListener

Parameters:

event - the change event

windowActivated

public void windowActivated(WindowEvent event)

Tells the UI that this frame is the currently active one.

Specified by:

windowActivated in interface WindowListener

Parameters:

event - the window event

windowClosed

public void windowClosed(WindowEvent event)

Does nothing.

Specified by:

windowClosed in interface WindowListener

Parameters:

event - the window event

windowClosing

public void windowClosing(WindowEvent event)

Cleans up the frame before closing.

Specified by:

windowClosing in interface WindowListener

Parameters:

event - the window event that triggered this method

windowDeactivated

public void windowDeactivated(WindowEvent event)

Does nothing.

Specified by:

windowDeactivated in interface WindowListener

Parameters:

event - the window event

windowDeiconified

public void windowDeiconified(WindowEvent event)

Does nothing.

Specified by:

windowDeiconified in interface WindowListener

Parameters:

event - the window event

windowIconified

public void windowIconified(WindowEvent event)

Does nothing.

Specified by:

windowIconified in interface WindowListener

Parameters:

event - the window event

windowOpened

public void windowOpened(WindowEvent event)

Does nothing.

Specified by:

windowOpened in interface WindowListener

Parameters:

event - the window event

finalize

protected void finalize()
                 throws Throwable

Cleans memory.

Overrides:

finalize in class Object

Throws:

Throwable - the Exception raised by this method

makeString

protected 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(Component component,
 MouseEvent event)

DOCUMENT ME!

Parameters:

component - DOCUMENT ME!

event - DOCUMENT ME!

handleMaskPopupMenu

public static void handleMaskPopupMenu(Component component,
 MouseEvent event)

Handles the popup menu for the Quick Mask buttons

Parameters:

component - DOCUMENT ME!

event - DOCUMENT ME!

handlePaintToMaskPopupMenu

protected void handlePaintToMaskPopupMenu(Component component,
 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 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:

OutOfMemoryError - if enough memory cannot be allocated for this method

initRGB

public static ModelRGB initRGB(ModelImage img)
                        throws 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:

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 FileFilter findFilter(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