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

All Implemented Interfaces:

ViewImageUpdateInterface, java.awt.event.ActionListener, java.awt.event.ComponentListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants
```
public class ViewJFrameColocalizationEM
extends ViewJFrameBase
implements javax.swing.event.ChangeListener, java.awt.event.ItemListener
```
This class produces a frame surrounding a 2D histogram with ellipses surrounding the most prominent clusters. Tool bar buttons are present for magnify, unmagnify, for generating a histogram LUT dialog, for generating a dialog to set brightness and contrast, and for switching between linear and log mode. Magnify will double the present magnification and Unmagnify will half the present magnification. Magnifications are only powers of 2.
The LUT dialog can be used to set colors and transfer functions of the LUT table used by the 2D histogram display.

The dialog box for brightness and contrast has brightness and contrast sliders, an Apply button, and a Cancel button. The brightness will add an offset ranging from -255 to 255 to every scaled red, green, and blue in the image. Contrast will multiply every original red, green, and blue value by a floating point number ranging from 0.1 to 10.0. Before apply is pressed, slider changes are only temporarily made to the currently displayed slice. If apply is pressed, these changes are permanently made to the histogram image. Pressing cancel keeps all the histogram image in its original state.

The file menu only has 1 simple function - a close ViewJFramColocalization structure function.

ViewJFrameColocalizationEM is called in AlgorithmColocalizationEM. ViewJFrameColocalizationEM calls ViewJComponentColocalizationEM

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, java.awt.Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  java.awt.Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`bottomPad`	DOCUMENT ME!
`private ViewJComponentColocalizationEM`	`componentImage`	DOCUMENT ME!
`private int`	`componentY`	DOCUMENT ME!
`private ViewJFrameBase`	`controlFrame`	DOCUMENT ME!
`private ViewControlsImage`	`controls`	DOCUMENT ME!
`private ModelImage`	`destImage`	The image containing the 2D histogram.
`private javax.swing.border.Border`	`etchedBorder`	DOCUMENT ME!
`private int[]`	`extents`	DOCUMENT ME!
`private java.awt.GridBagConstraints`	`gbcTP`	DOCUMENT ME!
`private double[]`	`halfMajor`	DOCUMENT ME!
`private double[]`	`halfMinor`	DOCUMENT ME!
`private ModelImage`	`imageA`	DOCUMENT ME!
`private ModelImage`	`imageB`	DOCUMENT ME!
`private float[]`	`imageBufferDest`	DOCUMENT ME!
`private javax.swing.JPanel`	`innerPanel`	DOCUMENT ME!
`private int`	`leftPad`	The spaces around the histogram bin area.
`private javax.swing.JToggleButton`	`logDisplayButton`	DOCUMENT ME!
`private boolean`	`logMagDisplay`	DOCUMENT ME!
`private ModelLUT`	`LUTa`	DOCUMENT ME!
`private ModelLUT`	`LUTdest`	The LUT for the 2D histogram.
`private double`	`max1`	Minimum and maximum buffer and secondBuffer areas.
`private double`	`max2`	Minimum and maximum buffer and secondBuffer areas.
`private double[][]`	`mean`	red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.
`private ViewMenuBuilder`	`menuObj`	DOCUMENT ME!
`private double`	`min1`	Minimum and maximum buffer and secondBuffer areas.
`private double`	`min2`	Minimum and maximum buffer and secondBuffer areas.
`private int`	`minimumHeight`	DOCUMENT ME!
`private int`	`minimumToolBarWidth`	DOCUMENT ME!
`private javax.swing.JMenuBar`	`openingMenuBar`	DOCUMENT ME!
`private int`	`origBrightness`	DOCUMENT ME!
`private float`	`origContrast`	red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.
`private int[]`	`paintBufferDest`	DOCUMENT ME!
`private int[]`	`pixBufferDest`	DOCUMENT ME!
`private javax.swing.border.Border`	`pressedBorder`	DOCUMENT ME!
`private javax.swing.border.Border`	`raisedBorder`	DOCUMENT ME!
`private ModelRGB`	`RGBTA`	DOCUMENT ME!
`private int`	`rightPad`	DOCUMENT ME!
`private double`	`scale1`	bin1 is generated from Math.round(scale1(buffer[i]-min1)) and bin2 is generated from Math.round(scale2(secondBuffer[i]-min2)).
`private double`	`scale2`	bin1 is generated from Math.round(scale1(buffer[i]-min1)) and bin2 is generated from Math.round(scale2(secondBuffer[i]-min2)).
`private javax.swing.JScrollPane`	`scrollPane`	DOCUMENT ME!
`private int`	`scrollPaneSize`	DOCUMENT ME!
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private int`	`structureY`	DOCUMENT ME!
`private double[]`	`theta`	DOCUMENT ME!
`private javax.swing.JToolBar`	`toolBar`	DOCUMENT ME!
`private int`	`topPad`	DOCUMENT ME!
`private javax.swing.JPanel`	`topPanel`	and innerPanel placed in scrollPane.
`private boolean`	`useBlue`	DOCUMENT ME!
`private boolean`	`useGreen`	DOCUMENT ME!
`private boolean`	`useRed`	DOCUMENT ME!
`private ViewUserInterface`	`userInterface`	DOCUMENT ME!
`private int`	`xScreen`	DOCUMENT ME!
`private int`	`yScreen`	DOCUMENT ME!
`private float`	`zoom`	DOCUMENT ME!

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

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

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

Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Constructor Summary

Constructors
Constructor	Description
`ViewJFrameColocalizationEM(ModelImage _imageA, ModelLUT _LUTa, ModelImage _imageB, ModelLUT _LUTb, ModelRGB _RGBTA, ModelImage destImage, ViewJFrameBase controlFrame, boolean useRed, boolean useGreen, boolean useBlue, double min1, double max1, double min2, double max2, double scale1, double scale2, int leftPad, int rightPad, int bottomPad, int topPad, double[][] mean, double[] halfMajor, double[] halfMinor, double[] theta)`	Makes a frame of the animated image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Calls various methods depending on the action.
`private javax.swing.JToolBar`	`buildColocalizeToolBar(java.awt.event.ActionListener al)`	Method to build the toolbar for the Animate frame.
`private void`	`buildMenu()`	This method builds a menu which contains the option Close Colocalization.
`private void`	`buildScrollPane()`	Make a scroll frame and puts an image component into it.
`void`	`cancelBrightness()`	Resets current slice's brightness and contrast to original.
`void`	`componentResized(java.awt.event.ComponentEvent event)`	Resizes frame and all components.
`void`	`dispose()`	Disposes of components and frame.
`ViewControlsImage`	`getControls()`	Get control widgets for frame.
`ModelImage`	`getImageA()`	Accessor that returns the reference to imageA.
`ModelImage`	`getImageB()`	Accessor that returns the reference to imageB.
`void`	`itemStateChanged(java.awt.event.ItemEvent event)`	Sets border painted or not painted depending on if the button was selected or deselected.
`private javax.swing.JButton`	`makeSeparator()`	Makes a separator for the use in the toolbars.
`void`	`removeControls()`	Does nothing.
`void`	`setActiveImage(int active)`	Does nothing.
`void`	`setAlphaBlend(int value)`	Does nothing.
`void`	`setBrightness(int brightness, float contrast)`	Sets the brightness and contrast of the component image.
`void`	`setControls()`	Does nothing.
`void`	`setEnabled(boolean flag)`	Does nothing.
`void`	`setImageB(ModelImage _imageB)`	Does nothing.
`void`	`setLUTdest(ModelLUT LUTdest)`	DOCUMENT ME!
`void`	`setPaintBitmapSwitch(boolean paintBitmapSwitch)`	Does nothing.
`void`	`setRGBTA(ModelRGB RGBT)`	Sets the RGB LUT table for ARGB image A.
`void`	`setRGBTB(ModelRGB RGBT)`	Sets the RGB LUT table for ARGB image B.
`void`	`setSlice(int slice)`	Does nothing.
`void`	`setTimeSlice(int slice)`	Does nothing.
`void`	`setTitle()`	Set the title of the frame with the image name and magnification.
`void`	`stateChanged(javax.swing.event.ChangeEvent e)`	Sets values based on knob along slider.
`protected boolean`	`testParameter(java.lang.String str, double minValue, double maxValue)`	Tests that the entered parameter is in range.
`void`	`updateFrame(float sX, float sY)`	Does nothing.
`boolean`	`updateImageExtents()`	Does nothing.
`boolean`	`updateImages()`	Does nothing.
`boolean`	`updateImages(boolean forceShow)`	This methods calls the componentImage's update method to redraw the screen.
`boolean`	`updateImages(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow, int interpMode)`	Does nothing.
`void`	`windowActivated(java.awt.event.WindowEvent event)`	Does nothing.
`void`	`windowClosed(java.awt.event.WindowEvent event)`	Does nothing.
`void`	`windowClosing(java.awt.event.WindowEvent event)`	Stops thread, calls close.
`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 gov.nih.mipav.view.ViewJFrameBase
about, buildLabelPanel, canCloseImageBAfterLoad, close, close, closeImageB, componentHidden, componentMoved, componentShown, finalize, getAlphaBlend, getDefaultLUTa, getDefaultLUTb, getDisplayMode, getImageNameA, getImageNameB, getLastState, getLUTa, getLUTb, getRGBTA, getRGBTB, getTriImg, getUserInterface, handleMaskPopupMenu, handlePaintToMaskPopupMenu, handleZoomPopupMenu, initExtents, initImageBuffer, initLUT, initNumSlices, initPixelBuffer, initResFactor, initResolutions, initRGB, initSlicePositions, initUnits, initZoom, loadAllVOIs, loadAllVOIsFrom, loadImage, loadLUT, loadLUTandTransferFunctionFrom, loadLUTandTransferFunctionFrom, makeString, newFrameBeenCreated, openVOI, openVOI, pickImageFile, save, save, save, saveAllVOIs, saveAllVOIsTo, saveLabels, saveLUT, saveLUTandTransferFunction, saveLUTandTransferFunction, saveLUTAs, saveLUTAs, saveVOI, saveVOIAs, saveVOIAs, saveVOIIntensities, saveVOIIntensitiesTo, setAbsPositionLabels, setEnableCloseImageBAfterLoad, setImageA, setLastState, setLinkedFrame, setLinkedTriFrame, setLUTa, setLUTb, setLUTs, setMessageText, setOpacityInfo, setpaintBitmap, setScannerPosition

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

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

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, 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

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - bottomPad
```
private int bottomPad
```
    DOCUMENT ME!
  - componentImage
```
private ViewJComponentColocalizationEM componentImage
```
    DOCUMENT ME!
  - componentY
```
private int componentY
```
    DOCUMENT ME!
  - controlFrame
```
private ViewJFrameBase controlFrame
```
    DOCUMENT ME!
  - controls
```
private ViewControlsImage controls
```
    DOCUMENT ME!
  - destImage
```
private ModelImage destImage
```
    The image containing the 2D histogram.
  - etchedBorder
```
private javax.swing.border.Border etchedBorder
```
    DOCUMENT ME!
  - extents
```
private int[] extents
```
    DOCUMENT ME!
  - gbcTP
```
private java.awt.GridBagConstraints gbcTP
```
    DOCUMENT ME!
  - halfMajor
```
private double[] halfMajor
```
    DOCUMENT ME!
  - halfMinor
```
private double[] halfMinor
```
    DOCUMENT ME!
  - imageA
```
private ModelImage imageA
```
    DOCUMENT ME!
  - imageB
```
private ModelImage imageB
```
    DOCUMENT ME!
  - imageBufferDest
```
private float[] imageBufferDest
```
    DOCUMENT ME!
  - innerPanel
```
private javax.swing.JPanel innerPanel
```
    DOCUMENT ME!
  - leftPad
```
private int leftPad
```
    The spaces around the histogram bin area.
  - logDisplayButton
```
private javax.swing.JToggleButton logDisplayButton
```
    DOCUMENT ME!
  - logMagDisplay
```
private boolean logMagDisplay
```
    DOCUMENT ME!
  - LUTa
```
private ModelLUT LUTa
```
    DOCUMENT ME!
  - LUTdest
```
private ModelLUT LUTdest
```
    The LUT for the 2D histogram.
  - mean
```
private double[][] mean
```
    red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.
  - menuObj
```
private ViewMenuBuilder menuObj
```
    DOCUMENT ME!
  - min1
```
private double min1
```
    Minimum and maximum buffer and secondBuffer areas.
  - max1
```
private double max1
```
    Minimum and maximum buffer and secondBuffer areas.
  - min2
```
private double min2
```
    Minimum and maximum buffer and secondBuffer areas.
  - max2
```
private double max2
```
    Minimum and maximum buffer and secondBuffer areas.
  - minimumHeight
```
private int minimumHeight
```
    DOCUMENT ME!
  - minimumToolBarWidth
```
private int minimumToolBarWidth
```
    DOCUMENT ME!
  - openingMenuBar
```
private javax.swing.JMenuBar openingMenuBar
```
    DOCUMENT ME!
  - origBrightness
```
private int origBrightness
```
    DOCUMENT ME!
  - origContrast
```
private float origContrast
```
    red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.
  - paintBufferDest
```
private int[] paintBufferDest
```
    DOCUMENT ME!
  - pixBufferDest
```
private int[] pixBufferDest
```
    DOCUMENT ME!
  - pressedBorder
```
private javax.swing.border.Border pressedBorder
```
    DOCUMENT ME!
  - raisedBorder
```
private javax.swing.border.Border raisedBorder
```
    DOCUMENT ME!
  - RGBTA
```
private ModelRGB RGBTA
```
    DOCUMENT ME!
  - rightPad
```
private int rightPad
```
    DOCUMENT ME!
  - scale1
```
private double scale1
```
    bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).
  - scale2
```
private double scale2
```
    bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).
  - scrollPane
```
private javax.swing.JScrollPane scrollPane
```
    DOCUMENT ME!
  - scrollPaneSize
```
private int scrollPaneSize
```
    DOCUMENT ME!
  - structureY
```
private int structureY
```
    DOCUMENT ME!
  - theta
```
private double[] theta
```
    DOCUMENT ME!
  - toolBar
```
private javax.swing.JToolBar toolBar
```
    DOCUMENT ME!
  - topPad
```
private int topPad
```
    DOCUMENT ME!
  - topPanel
```
private javax.swing.JPanel topPanel
```
    and innerPanel placed in scrollPane.
  - useBlue
```
private boolean useBlue
```
    DOCUMENT ME!
  - useGreen
```
private boolean useGreen
```
    DOCUMENT ME!
  - useRed
```
private boolean useRed
```
    DOCUMENT ME!
  - userInterface
```
private ViewUserInterface userInterface
```
    DOCUMENT ME!
  - xScreen
```
private int xScreen
```
    DOCUMENT ME!
  - yScreen
```
private int yScreen
```
    DOCUMENT ME!
  - zoom
```
private float zoom
```
    DOCUMENT ME!
- Constructor Detail
  - ViewJFrameColocalizationEM
```
public ViewJFrameColocalizationEM(ModelImage _imageA,
                                  ModelLUT _LUTa,
                                  ModelImage _imageB,
                                  ModelLUT _LUTb,
                                  ModelRGB _RGBTA,
                                  ModelImage destImage,
                                  ViewJFrameBase controlFrame,
                                  boolean useRed,
                                  boolean useGreen,
                                  boolean useBlue,
                                  double min1,
                                  double max1,
                                  double min2,
                                  double max2,
                                  double scale1,
                                  double scale2,
                                  int leftPad,
                                  int rightPad,
                                  int bottomPad,
                                  int topPad,
                                  double[][] mean,
                                  double[] halfMajor,
                                  double[] halfMinor,
                                  double[] theta)
```
    Makes a frame of the animated image.
    
    Parameters:
    
    _imageA - Model of imageA
    
    _LUTa - Model of LUT for image A
    
    _imageB - Model of imageB
    
    _LUTb - Model of LUT for image B
    
    _RGBTA - Model RGB LUT for color image (A) else null
    
    destImage - The destination image
    
    controlFrame - ViewJFrameBase passed to ViewJComponentColocalizationEM
    
    useRed - DOCUMENT ME!
    
    useGreen - DOCUMENT ME!
    
    useBlue - DOCUMENT ME!
    
    min1 - DOCUMENT ME!
    
    max1 - DOCUMENT ME!
    
    min2 - DOCUMENT ME!
    
    max2 - DOCUMENT ME!
    
    scale1 - DOCUMENT ME!
    
    scale2 - DOCUMENT ME!
    
    leftPad - DOCUMENT ME!
    
    rightPad - DOCUMENT ME!
    
    bottomPad - DOCUMENT ME!
    
    topPad - DOCUMENT ME!
    
    mean - DOCUMENT ME!
    
    halfMajor - DOCUMENT ME!
    
    halfMinor - DOCUMENT ME!
    
    theta - DOCUMENT ME!
- Method Detail
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Calls various methods depending on the action.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Specified by:
    
    actionPerformed in class ViewJFrameBase
    
    Parameters:
    
    event - event that triggered function
  - cancelBrightness
```
public void cancelBrightness()
```
    Resets current slice's brightness and contrast to original.
  - componentResized
```
public void componentResized(java.awt.event.ComponentEvent event)
```
    Resizes frame and all components.
    
    Specified by:
    
    componentResized in interface java.awt.event.ComponentListener
    
    Overrides:
    
    componentResized in class ViewJFrameBase
    
    Parameters:
    
    event - event that triggered function
  - dispose
```
public void dispose()
```
    Disposes of components and frame.
    
    Overrides:
    
    dispose in class java.awt.Window
  - getControls
```
public ViewControlsImage getControls()
```
    Get control widgets for frame.
    
    Specified by:
    
    getControls in class ViewJFrameBase
    
    Returns:
    
    controls
  - getImageA
```
public ModelImage getImageA()
```
    Accessor that returns the reference to imageA.
    
    Specified by:
    
    getImageA in class ViewJFrameBase
    
    Returns:
    
    image
  - getImageB
```
public ModelImage getImageB()
```
    Accessor that returns the reference to imageB.
    
    Specified by:
    
    getImageB in class ViewJFrameBase
    
    Returns:
    
    imageB
  - itemStateChanged
```
public void itemStateChanged(java.awt.event.ItemEvent event)
```
    Sets border painted or not painted depending on if the button was selected or deselected. Changes the currently selected script.
    
    Specified by:
    
    itemStateChanged in interface java.awt.event.ItemListener
    
    Parameters:
    
    event - Event that triggered this function.
  - removeControls
```
public void removeControls()
```
    Does nothing.
    
    Specified by:
    
    removeControls in class ViewJFrameBase
  - setActiveImage
```
public void setActiveImage(int active)
```
    Does nothing.
    
    Specified by:
    
    setActiveImage in class ViewJFrameBase
    
    Parameters:
    
    active - DOCUMENT ME!
  - setAlphaBlend
```
public void setAlphaBlend(int value)
```
    Does nothing.
    
    Specified by:
    
    setAlphaBlend in class ViewJFrameBase
    
    Parameters:
    
    value - DOCUMENT ME!
  - setBrightness
```
public void setBrightness(int brightness,
                          float contrast)
```
    Sets the brightness and contrast of the component image. Set all slices to have the new brightness and contrast. Results in createImage producing an Image img[slice] for every slice.
    
    Parameters:
    
    brightness - Brightness to set.
    
    contrast - Contrast to set.
  - setControls
```
public void setControls()
```
    Does nothing.
    
    Specified by:
    
    setControls in class ViewJFrameBase
  - setEnabled
```
public void setEnabled(boolean flag)
```
    Does nothing.
    
    Specified by:
    
    setEnabled in class ViewJFrameBase
    
    Parameters:
    
    flag - DOCUMENT ME!
  - setImageB
```
public void setImageB(ModelImage _imageB)
```
    Does nothing.
    
    Specified by:
    
    setImageB in class ViewJFrameBase
    
    Parameters:
    
    _imageB - DOCUMENT ME!
  - setLUTdest
```
public void setLUTdest(ModelLUT LUTdest)
```
    DOCUMENT ME!
    
    Parameters:
    
    LUTdest - DOCUMENT ME!
  - setPaintBitmapSwitch
```
public void setPaintBitmapSwitch(boolean paintBitmapSwitch)
```
    Does nothing.
    
    Specified by:
    
    setPaintBitmapSwitch in class ViewJFrameBase
    
    Parameters:
    
    paintBitmapSwitch - DOCUMENT ME!
  - setRGBTA
```
public void setRGBTA(ModelRGB RGBT)
```
    Sets the RGB LUT table for ARGB image A.
    
    Specified by:
    
    setRGBTA in class ViewJFrameBase
    
    Parameters:
    
    RGBT - the new RGB LUT to be applied to the image
  - setRGBTB
```
public void setRGBTB(ModelRGB RGBT)
```
    Sets the RGB LUT table for ARGB image B.
    
    Specified by:
    
    setRGBTB in class ViewJFrameBase
    
    Parameters:
    
    RGBT - the new RGB LUT to be applied to the image
  - setSlice
```
public void setSlice(int slice)
```
    Does nothing.
    
    Specified by:
    
    setSlice in interface ViewImageUpdateInterface
    
    Parameters:
    
    slice - DOCUMENT ME!
  - setTimeSlice
```
public void setTimeSlice(int slice)
```
    Does nothing.
    
    Specified by:
    
    setTimeSlice in interface ViewImageUpdateInterface
    
    Parameters:
    
    slice - DOCUMENT ME!
  - setTitle
```
public void setTitle()
```
    Set the title of the frame with the image name and magnification.
    
    Specified by:
    
    setTitle in class ViewJFrameBase
  - stateChanged
```
public void stateChanged(javax.swing.event.ChangeEvent e)
```
    Sets values based on knob along slider.
    
    Specified by:
    
    stateChanged in interface javax.swing.event.ChangeListener
    
    Overrides:
    
    stateChanged in class ViewJFrameBase
    
    Parameters:
    
    e - Event that triggered this function
  - updateFrame
```
public void updateFrame(float sX,
                        float sY)
```
    Does nothing.
    
    Parameters:
    
    sX - DOCUMENT ME!
    
    sY - DOCUMENT ME!
  - updateImageExtents
```
public boolean updateImageExtents()
```
    Does nothing.
    
    Specified by:
    
    updateImageExtents in interface ViewImageUpdateInterface
    
    Specified by:
    
    updateImageExtents in class ViewJFrameBase
    
    Returns:
    
    DOCUMENT ME!
    
    See Also:
    
    ViewImageUpdateInterface
  - updateImages
```
public final boolean updateImages()
```
    Does nothing.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Returns:
    
    DOCUMENT ME!
  - updateImages
```
public final boolean updateImages(boolean forceShow)
```
    This methods calls the componentImage's update method to redraw the screen. Without LUT changes.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Parameters:
    
    forceShow - unused parameter
    
    Returns:
    
    boolean confirming successful update
  - updateImages
```
public final boolean updateImages(ModelLUT LUTa,
                                  ModelLUT LUTb,
                                  boolean forceShow,
                                  int interpMode)
```
    Does nothing.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Parameters:
    
    LUTa - DOCUMENT ME!
    
    LUTb - DOCUMENT ME!
    
    forceShow - DOCUMENT ME!
    
    interpMode - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - windowActivated
```
public void windowActivated(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowActivated in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowActivated in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowClosed
```
public void windowClosed(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowClosed in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowClosed in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowClosing
```
public void windowClosing(java.awt.event.WindowEvent event)
```
    Stops thread, calls close.
    
    Specified by:
    
    windowClosing in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowClosing in class ViewJFrameBase
    
    Parameters:
    
    event - event that triggered function
  - windowDeactivated
```
public void windowDeactivated(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowDeactivated in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowDeactivated in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowDeiconified
```
public void windowDeiconified(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowDeiconified in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowDeiconified in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowIconified
```
public void windowIconified(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowIconified in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowIconified in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - windowOpened
```
public void windowOpened(java.awt.event.WindowEvent event)
```
    Does nothing.
    
    Specified by:
    
    windowOpened in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowOpened in class ViewJFrameBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - testParameter
```
protected boolean testParameter(java.lang.String str,
                                double minValue,
                                double maxValue)
```
    Tests that the entered parameter is in range.
    
    Parameters:
    
    str - the value entered by the user
    
    minValue - the minimum value this variable may be set to
    
    maxValue - the maximum value this variable may be set to
    
    Returns:
    
    boolean result of test
  - buildColocalizeToolBar
```
private javax.swing.JToolBar buildColocalizeToolBar(java.awt.event.ActionListener al)
```
    Method to build the toolbar for the Animate frame.
    
    Parameters:
    
    al - Action listener (this frame)
    
    Returns:
    
    The animation toolbar
  - buildMenu
```
private void buildMenu()
```
    This method builds a menu which contains the option Close Colocalization.
  - buildScrollPane
```
private void buildScrollPane()
```
    Make a scroll frame and puts an image component into it.
  - makeSeparator
```
private javax.swing.JButton makeSeparator()
```
    Makes a separator for the use in the toolbars.
    
    Returns:
    
    Separator button.

Class ViewJFrameColocalizationEM

Nested Class Summary

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

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

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

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

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

Field Summary

Fields inherited from class gov.nih.mipav.view.ViewJFrameBase

Fields inherited from class javax.swing.JFrame

Fields inherited from class java.awt.Frame

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface javax.swing.WindowConstants

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.ViewJFrameBase

Methods inherited from class javax.swing.JFrame

Methods inherited from class java.awt.Frame

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface java.awt.MenuContainer

Field Detail

serialVersionUID

bottomPad

componentImage

componentY

controlFrame

controls

destImage

etchedBorder

extents

gbcTP

halfMajor

halfMinor

imageA

imageB

imageBufferDest

innerPanel

leftPad

logDisplayButton

logMagDisplay

LUTa

LUTdest

mean

menuObj

min1

max1

min2

max2

minimumHeight

minimumToolBarWidth

openingMenuBar

origBrightness

origContrast

paintBufferDest

pixBufferDest

pressedBorder

raisedBorder

RGBTA

rightPad

scale1

scale2

scrollPane

scrollPaneSize

structureY

theta

toolBar

topPad

topPanel

useBlue

useGreen

useRed

userInterface

xScreen

yScreen

zoom

Constructor Detail