visad.bio
Class VisBio

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by java.awt.Window
              extended by java.awt.Frame
                  extended by javax.swing.JFrame
                      extended by visad.util.GUIFrame
                          extended by visad.bio.VisBio
All Implemented Interfaces:
java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class VisBio
extends GUIFrame
implements javax.swing.event.ChangeListener

VisBio is a multi-purpose biological analysis tool. It provides multi-dimensional visualization of an image or stack of images across time, arbitrary slicing of the data, and measurement tools for computing distances between data points.

See Also:
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
 
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
protected static boolean ALLOW_3D
          Flag for enabling or disabling Java3D, for debugging.
protected static java.lang.String TITLE
          Application title.
protected static java.lang.String[] TOOL_PANELS
          Tool panel names.
protected static java.lang.String VERSION
          Application version.
 
Fields inherited from class visad.util.GUIFrame
hash, heavy, menubar
 
Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, 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 javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
VisBio()
          Constructs a new instance of VisBio.
 
Method Summary
 void editUndo()
          Undoes the last action taken.
 void fileExit()
          Exits the application.
 void fileExport()
          Exports the current dataset as specified by the user.
 void fileImport()
          Loads a data series specified by the user.
 void fileOptions()
          Displays the VisBio options dialog box.
 void fileRestore()
          Restores the current state from a text file specified by the user.
 void fileSave()
          Saves the current state to a text file specified by the user.
 void fileSnap()
          Saves a snapshot of the displays to a file specified by the user.
 void helpAbout()
          Brings up the help window on the About tab.
 void helpAlign()
          Brings up the help window on the Align tab.
 void helpColor()
          Brings up the help window on the Color tab.
 void helpMeasure()
          Brings up the help window on the Measure tab.
 void helpOverview()
          Brings up the help window on the Overview tab.
 void helpQuickTime()
          Brings up the help window on the QuickTime tab.
 void helpView()
          Brings up the help window on the View tab.
static void main(java.lang.String[] args)
          Launches the VisBio GUI.
 void resetZoom(boolean threeD)
          Restores a display's zoom to the original value.
 void set2D(boolean twoD)
          Toggles the visibility of the 2-D display.
 void set3D(boolean threeD)
          Toggles the visibility of the 3-D display.
 void setAspect(double x, double y, double z)
          Adjusts the aspect ratio of the displays.
 void setFloating(boolean floating)
          Sets whether control panels are separate, floating windows.
 void setImageColors(int brightness, int contrast, int model, boolean composite, RealType r, RealType g, RealType b)
          Updates image color table to match the given values.
 void setPreview(boolean preview)
          Toggles the visibility of the preview displays.
 void setVolume(boolean volume)
          Toggles the 3-D display between image stack and volume render modes.
 void setZoom(boolean threeD, double scale)
          Zooms a display by the given amount.
 void stateChanged(javax.swing.event.ChangeEvent e)
          Listens for file series widget changes.
 void windowAlign()
          Displays or switches to the Align tool panel.
 void windowColor()
          Displays or switches to the Color tool panel.
 void windowMeasure()
          Displays or switches to the Measure tool panel.
 void windowView()
          Displays or switches to the View tool panel.
 
Methods inherited from class visad.util.GUIFrame
actionPerformed, addMenuItem, addMenuItem, addMenuItem, addMenuSeparator, addSubMenu, addSubMenu, addSubMenu, getMenu, getMenuItem
 
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, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated
 
Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOwnedWindows, getOwner, getOwnerlessWindows, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, 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, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, 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, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, 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, isOpaque, 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, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Field Detail

TITLE

protected static final java.lang.String TITLE
Application title.

See Also:
Constant Field Values

VERSION

protected static final java.lang.String VERSION
Application version.

See Also:
Constant Field Values

ALLOW_3D

protected static final boolean ALLOW_3D
Flag for enabling or disabling Java3D, for debugging.

See Also:
Constant Field Values

TOOL_PANELS

protected static final java.lang.String[] TOOL_PANELS
Tool panel names.

Constructor Detail

VisBio

public VisBio()
       throws VisADException,
              java.rmi.RemoteException
Constructs a new instance of VisBio.

Throws:
VisADException
java.rmi.RemoteException
Method Detail

set2D

public void set2D(boolean twoD)
Toggles the visibility of the 2-D display.


set3D

public void set3D(boolean threeD)
Toggles the visibility of the 3-D display.


setPreview

public void setPreview(boolean preview)
Toggles the visibility of the preview displays.


setZoom

public void setZoom(boolean threeD,
                    double scale)
Zooms a display by the given amount.


resetZoom

public void resetZoom(boolean threeD)
Restores a display's zoom to the original value.


setFloating

public void setFloating(boolean floating)
Sets whether control panels are separate, floating windows.


setVolume

public void setVolume(boolean volume)
Toggles the 3-D display between image stack and volume render modes.


setAspect

public void setAspect(double x,
                      double y,
                      double z)
Adjusts the aspect ratio of the displays.


setImageColors

public void setImageColors(int brightness,
                           int contrast,
                           int model,
                           boolean composite,
                           RealType r,
                           RealType g,
                           RealType b)
Updates image color table to match the given values.


fileImport

public void fileImport()
Loads a data series specified by the user.


fileExport

public void fileExport()
Exports the current dataset as specified by the user.


fileRestore

public void fileRestore()
Restores the current state from a text file specified by the user.


fileSave

public void fileSave()
Saves the current state to a text file specified by the user.


fileSnap

public void fileSnap()
Saves a snapshot of the displays to a file specified by the user.


fileOptions

public void fileOptions()
Displays the VisBio options dialog box.


fileExit

public void fileExit()
Exits the application.


editUndo

public void editUndo()
Undoes the last action taken.


windowView

public void windowView()
Displays or switches to the View tool panel.


windowColor

public void windowColor()
Displays or switches to the Color tool panel.


windowAlign

public void windowAlign()
Displays or switches to the Align tool panel.


windowMeasure

public void windowMeasure()
Displays or switches to the Measure tool panel.


helpOverview

public void helpOverview()
Brings up the help window on the Overview tab.


helpQuickTime

public void helpQuickTime()
Brings up the help window on the QuickTime tab.


helpView

public void helpView()
Brings up the help window on the View tab.


helpColor

public void helpColor()
Brings up the help window on the Color tab.


helpAlign

public void helpAlign()
Brings up the help window on the Align tab.


helpMeasure

public void helpMeasure()
Brings up the help window on the Measure tab.


helpAbout

public void helpAbout()
Brings up the help window on the About tab.


stateChanged

public void stateChanged(javax.swing.event.ChangeEvent e)
Listens for file series widget changes.

Specified by:
stateChanged in interface javax.swing.event.ChangeListener

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception
Launches the VisBio GUI.

Throws:
java.lang.Exception