java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - javax.swing.JComponent
    - - gov.nih.mipav.view.ViewJComponentBase
      - gov.nih.mipav.view.ViewJComponentColocalizationRegression

All Implemented Interfaces:

java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener
```
public class ViewJComponentColocalizationRegression
extends ViewJComponentBase
implements java.awt.event.MouseMotionListener, java.awt.event.MouseListener
```
DOCUMENT ME!

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class javax.swing.JComponent
  javax.swing.JComponent.AccessibleJComponent
- 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 AlgorithmColocalizationRegression`	`alg`	DOCUMENT ME!
`private int`	`bin1`	DOCUMENT ME!
`private int`	`bin2`	DOCUMENT ME!
`private int`	`blue`	DOCUMENT ME!
`private int`	`bottomPad`	DOCUMENT ME!
`private int`	`brightness`	DOCUMENT ME!
`private float[]`	`colocIntensity1`	DOCUMENT ME!
`private float[]`	`colocIntensity2`	DOCUMENT ME!
`private float[]`	`colocSize`	DOCUMENT ME!
`private float`	`contrast`	DOCUMENT ME!
`private ModelImage`	`destImage`	DOCUMENT ME!
`private boolean`	`doSecondIteration`	DOCUMENT ME!
`private ViewJComponentEditImage`	`editImageFrameA`	DOCUMENT ME!
`private ViewJComponentEditImage`	`editImageFrameB`	DOCUMENT ME!
`private float`	`firstIndex`	DOCUMENT ME!
`protected ViewJFrameBase`	`frame`	frame - frame where the component image is displayed.
`private float[]`	`freeRangeColocIntensity1`	DOCUMENT ME!
`private float[]`	`freeRangeColocIntensity2`	DOCUMENT ME!
`private float[]`	`freeRangeColocSize`	DOCUMENT ME!
`private boolean`	`freeRangeMode`	DOCUMENT ME!
`private float[]`	`freeRangeRThreshold`	DOCUMENT ME!
`private int`	`green`	DOCUMENT ME!
`private boolean`	`haveFiltered`	DOCUMENT ME!
`private boolean[]`	`haveFreeRangeThreshold`	DOCUMENT ME!
`private boolean[]`	`haveThreshold`	DOCUMENT ME!
`protected ModelImage`	`imageA`	imageA - model for image A.
`protected ModelImage`	`imageB`	imageB - model for image B.
`private float[]`	`imageBufferDest`	DOCUMENT ME!
`private java.awt.Image`	`imgDest`	DOCUMENT ME!
`protected int`	`interpMode`	DOCUMENT ME!
`private int`	`leftPad`	DOCUMENT ME!
`private float`	`linearCorrelation`	DOCUMENT ME!
`private int`	`lineMin`	DOCUMENT ME!
`private double`	`lineOffset`	DOCUMENT ME!
`private double`	`lineSlope`	DOCUMENT ME!
`private VOI`	`lineVOI`	DOCUMENT ME!
`private ViewJFrameColocalizationRegression`	`localizeFrame`	DOCUMENT ME!
`private boolean`	`logMagDisplay`	DOCUMENT ME!
`private int[]`	`lutBufferRemappedDest`	DOCUMENT ME!
`private ModelLUT`	`LUTdest`	LUTa - lookup table for destImage.
`private double`	`max1`	DOCUMENT ME!
`private double`	`max2`	DOCUMENT ME!
`private double`	`maximumx`	DOCUMENT ME!
`private java.awt.image.MemoryImageSource`	`memImageDest`	DOCUMENT ME!
`private double`	`min1`	DOCUMENT ME!
`private double`	`min2`	DOCUMENT ME!
`private double`	`minimumx`	DOCUMENT ME!
`private int`	`nVOI`	DOCUMENT ME!
`float`	`OPACITY`	Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
`private float`	`originalLineOffset`	DOCUMENT ME!
`private float`	`originalLineSlope`	DOCUMENT ME!
`private java.util.BitSet`	`paintBitmapDest`	Buffer used to indicate if the pixel location is painted (true) or unpainted (false).
`private int[]`	`paintBufferDest`	Buffer that displays the combined paintBitmap and pixBuffer buffers.
`private int[]`	`pixBufferDest`	Buffer used to store ARGB images of the image presently being displayed.
`private VOI`	`pointVOI`	DOCUMENT ME!
`private int`	`red`	DOCUMENT ME!
`private boolean`	`regionLinesDisplay`	DOCUMENT ME!
`private float`	`resX`	DOCUMENT ME!
`private float`	`resY`	DOCUMENT ME!
`protected ModelRGB`	`RGBTA`	true if selected red, green, blue components present in RGB image.
`protected ModelRGB`	`RGBTB`	DOCUMENT ME!
`private int`	`rightPad`	DOCUMENT ME!
`private float[]`	`rThreshold`	DOCUMENT ME!
`private double`	`scale1`	DOCUMENT ME!
`private double`	`scale2`	DOCUMENT ME!
`private float`	`secondIndex`	DOCUMENT ME!
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private int`	`tDim`	Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
`private boolean`	`thresholdOn1`	DOCUMENT ME!
`private int`	`topPad`	DOCUMENT ME!
`private boolean`	`useBlue`	DOCUMENT ME!
`private boolean`	`useGreen`	DOCUMENT ME!
`private boolean`	`useRed`	DOCUMENT ME!
`private ViewUserInterface`	`userInterface`	DOCUMENT ME!
`private ViewVOIVector`	`VOIs`	DOCUMENT ME!
`private float[]`	`xArray`	DOCUMENT ME!
`private double`	`xdiff`	DOCUMENT ME!
`private int`	`xDim`	Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
`private float[]`	`yArray`	DOCUMENT ME!
`private double`	`ydiff`	DOCUMENT ME!
`private int`	`yDim`	Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
`private float[]`	`zArray`	DOCUMENT ME!
`private int`	`zDim`	Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
`private float`	`zoomX`	DOCUMENT ME!
`private float`	`zoomY`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.view.ViewJComponentBase
ANNOTATION, BOTH, CENTER_VOI, CUBE_BOUNDS, DEFAULT, DELETE_POINT, DROPPER_PAINT, ELLIPSE, ERASER_PAINT, IMAGE_A, IMAGE_B, imageDim, img, imgB, INTERPOLATE_A, INTERPOLATE_B, INTERPOLATE_BOTH, lastMouseX, lastMouseY, LEVELSET, LINE, LIVEWIRE, MAG_REGION, memImageA, memImageB, MOVE, MOVE_INTERSECTION_POINT, MOVE_POINT, MOVE_VOIPOINT, NEAREST_BOTH, NEW_POINT, NEW_VOI, OUT_OF_BOUNDS, PAINT_CAN, PAINT_VASC, PAINT_VOI, POINT_VOI, POLYLINE, POLYLINE_SLICE_VOI, PROBE, PROTRACTOR, QUICK_LUT, RECTANGLE, RECTANGLE3D, resolutionX, resolutionY, RETRACE, ROTATE, SELECT, showSliceNumber, sliceString, SMOOTH, SPLIT_VOI, textColor, TRANSLATE, VOI_3D, WAND, WIN_REGION, ZOOMING_IN, ZOOMING_OUT

Fields inherited from class javax.swing.JComponent
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component
accessibleContext, 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

Constructor Summary

Constructors
Constructor	Description
ViewJComponentColocalizationRegression(AlgorithmColocalizationRegression alg, ViewJFrameBase _frame, ViewJFrameColocalizationRegression localizeFrame, ModelImage _imageA, ModelImage _imageB, ModelImage destImage, ModelLUT LUTdest, float[] imageBufferDest, boolean useRed, boolean useGreen, boolean useBlue, float originalLineSlope, float originalLineOffset, boolean[] haveThreshold, float[] rThreshold, float[] colocSize, float[] colocIntensity1, float[] colocIntensity2, double min1, double max1, double min2, double max2, double scale1, double scale2, double lineMin1, double lineMax1, double lineMin2, double lineMax2, boolean thresholdOn1, int[] pixBufferDest, int[] paintBufferDest, float zoom, int[] extents, boolean logMagDisplay, boolean regionLinesDisplay, int leftPad, int rightPad, int bottomPad, int topPad, boolean doSecondIteration, float linearCorrelation, ViewUserInterface userInterface)	Constructor: ImageA and ImageB are expected to be of the same dimensionality !!

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`buildImageDestObject(ModelLUT _LUTdest, boolean forceShow)`	Shows the 2D histogram image.
`void`	`dispose(boolean gcFlag)`	Sets all variables to null, disposes, and garbage collects.
`void`	`finalizeLocal()`	Clean up some resources!
`int`	`getblue()`	Accessor that returns int blue.
`int`	`getgreen()`	Accessor that returns int green.
`ModelImage`	`getImageA()`	Accessor that returns the imageA.
`ModelImage`	`getImageB()`	Accessor that returns the imageB.
`float`	`getOPACITY()`	Accessor that returns float OPACITY.
`java.util.BitSet`	`getpaintBitmapDest()`	Accessor that returns BitSet paintBitmap.
`java.awt.Dimension`	`getPreferredSize()`	Size set to object size.
`int`	`getred()`	Accessor that returns int red.
`java.awt.Dimension`	`getSize(java.awt.Dimension wh)`	Gets the size of the object taking into account the zoom.
`float`	`getZoomX()`	Magnification in the x - dimension.
`float`	`getZoomY()`	Magnification in the y - dimension.
`void`	`importImageDest(int[] data)`	Creates a Image object form an array of ints that have been formatted (packed) properly (i.e. aRGB)
`void`	`mouseClicked(java.awt.event.MouseEvent mouseEvent)`	DOCUMENT ME!
`void`	`mouseDragged(java.awt.event.MouseEvent mouseEvent)`	mouseDragged only updates the histogram display header when the mouse passes over a point for which the linear correlation coefficient and colocalizations have already been calculated.
`void`	`mouseEntered(java.awt.event.MouseEvent mouseEvent)`	DOCUMENT ME!
`void`	`mouseExited(java.awt.event.MouseEvent mouseEvent)`	DOCUMENT ME!
`void`	`mouseMoved(java.awt.event.MouseEvent mouseEvent)`	DOCUMENT ME!
`void`	`mousePressed(java.awt.event.MouseEvent mouseEvent)`	DOCUMENT ME!
`void`	`mouseReleased(java.awt.event.MouseEvent mouseEvent)`	If the correlation coefficient and colocalizations have not already been calculated at the mouse release point, then a call to AlgorithmColocalizationRegression calculates them.
`void`	`paintComponent(java.awt.Graphics g)`	Paints the image and border.
`void`	`passFreeRangeArrays(boolean[] haveFreeRangeThreshold, float[] freeRangeRThreshold, float[] freeRangeColocSize, float[] freeRangeColocIntensity1, float[] freeRangeColocIntensity2)`	Passes arrays needed in free range mode.
`void`	`setBrightness(int brightness, float contrast)`	Method to set the brightness and contrast of the animate images.
`void`	`setFreeRangeMode(boolean freeRangeMode)`	Accessor that sets freeRangeMode.
`void`	`setLogMagDisplay(boolean logMagDisplay)`	DOCUMENT ME!
`void`	`setNewVar(float originalLineSlope, float originalLineOffset, boolean[] haveThreshold, float[] rThreshold, float[] colocSize, float[] colocIntensity1, float[] colocIntensity2, double min1, double max1, double min2, double max2, double scale1, double scale2, double lineMin1, double lineMax1, double lineMin2, double lineMax2, boolean thresholdOn1, float linearCorrelation)`	Modifies component after mouseReleased in contour VOI indicating that the VOI has been moved.
`void`	`setPaintMaskDest(java.util.BitSet mask)`	Accessor that sets the paint mask.
`void`	`setPosition(int xS, int yS)`	DOCUMENT ME!
`void`	`setRegionLinesDisplay(boolean regionLinesDisplay)`	DOCUMENT ME!
`void`	`setRGBTA(ModelRGB RGBT)`	Sets the RGB table for the ARGB image A.
`void`	`setRGBTB(ModelRGB RGBT)`	Sets the RGB table for the ARGB image B.
`void`	`setZoom(float zX, float zY)`	Sets the magnification in both x and y directions.
`void`	`update()`	Method to call paint without erasing background this reduces flicker!
`void`	`update(java.awt.Graphics g)`	Method to call paint without erasing background this reduces flicker!

Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getUI, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateUI

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getAccessibleContext, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

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

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - OPACITY
```
public float OPACITY
```
    Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
  - frame
```
protected ViewJFrameBase frame
```
    frame - frame where the component image is displayed.
  - imageA
```
protected ModelImage imageA
```
    imageA - model for image A.
  - imageB
```
protected ModelImage imageB
```
    imageB - model for image B.
  - interpMode
```
protected int interpMode
```
    DOCUMENT ME!
  - RGBTA
```
protected ModelRGB RGBTA
```
    true if selected red, green, blue components present in RGB image.
  - RGBTB
```
protected ModelRGB RGBTB
```
    DOCUMENT ME!
  - alg
```
private AlgorithmColocalizationRegression alg
```
    DOCUMENT ME!
  - bin1
```
private int bin1
```
    DOCUMENT ME!
  - bin2
```
private int bin2
```
    DOCUMENT ME!
  - bottomPad
```
private int bottomPad
```
    DOCUMENT ME!
  - brightness
```
private int brightness
```
    DOCUMENT ME!
  - colocIntensity1
```
private float[] colocIntensity1
```
    DOCUMENT ME!
  - colocIntensity2
```
private float[] colocIntensity2
```
    DOCUMENT ME!
  - colocSize
```
private float[] colocSize
```
    DOCUMENT ME!
  - contrast
```
private float contrast
```
    DOCUMENT ME!
  - destImage
```
private ModelImage destImage
```
    DOCUMENT ME!
  - doSecondIteration
```
private boolean doSecondIteration
```
    DOCUMENT ME!
  - editImageFrameA
```
private ViewJComponentEditImage editImageFrameA
```
    DOCUMENT ME!
  - editImageFrameB
```
private ViewJComponentEditImage editImageFrameB
```
    DOCUMENT ME!
  - firstIndex
```
private float firstIndex
```
    DOCUMENT ME!
  - freeRangeColocIntensity1
```
private float[] freeRangeColocIntensity1
```
    DOCUMENT ME!
  - freeRangeColocIntensity2
```
private float[] freeRangeColocIntensity2
```
    DOCUMENT ME!
  - freeRangeColocSize
```
private float[] freeRangeColocSize
```
    DOCUMENT ME!
  - freeRangeMode
```
private boolean freeRangeMode
```
    DOCUMENT ME!
  - freeRangeRThreshold
```
private float[] freeRangeRThreshold
```
    DOCUMENT ME!
  - haveFiltered
```
private boolean haveFiltered
```
    DOCUMENT ME!
  - haveFreeRangeThreshold
```
private boolean[] haveFreeRangeThreshold
```
    DOCUMENT ME!
  - haveThreshold
```
private boolean[] haveThreshold
```
    DOCUMENT ME!
  - imageBufferDest
```
private float[] imageBufferDest
```
    DOCUMENT ME!
  - imgDest
```
private java.awt.Image imgDest
```
    DOCUMENT ME!
  - leftPad
```
private int leftPad
```
    DOCUMENT ME!
  - linearCorrelation
```
private float linearCorrelation
```
    DOCUMENT ME!
  - lineMin
```
private int lineMin
```
    DOCUMENT ME!
  - lineOffset
```
private double lineOffset
```
    DOCUMENT ME!
  - lineSlope
```
private double lineSlope
```
    DOCUMENT ME!
  - lineVOI
```
private VOI lineVOI
```
    DOCUMENT ME!
  - localizeFrame
```
private ViewJFrameColocalizationRegression localizeFrame
```
    DOCUMENT ME!
  - logMagDisplay
```
private boolean logMagDisplay
```
    DOCUMENT ME!
  - lutBufferRemappedDest
```
private int[] lutBufferRemappedDest
```
    DOCUMENT ME!
  - LUTdest
```
private ModelLUT LUTdest
```
    LUTa - lookup table for destImage.
  - memImageDest
```
private java.awt.image.MemoryImageSource memImageDest
```
    DOCUMENT ME!
  - min1
```
private double min1
```
    DOCUMENT ME!
  - max1
```
private double max1
```
    DOCUMENT ME!
  - min2
```
private double min2
```
    DOCUMENT ME!
  - max2
```
private double max2
```
    DOCUMENT ME!
  - minimumx
```
private double minimumx
```
    DOCUMENT ME!
  - maximumx
```
private double maximumx
```
    DOCUMENT ME!
  - nVOI
```
private int nVOI
```
    DOCUMENT ME!
  - originalLineOffset
```
private float originalLineOffset
```
    DOCUMENT ME!
  - originalLineSlope
```
private float originalLineSlope
```
    DOCUMENT ME!
  - paintBitmapDest
```
private java.util.BitSet paintBitmapDest
```
    Buffer used to indicate if the pixel location is painted (true) or unpainted (false).
  - paintBufferDest
```
private int[] paintBufferDest
```
    Buffer that displays the combined paintBitmap and pixBuffer buffers.
  - pixBufferDest
```
private int[] pixBufferDest
```
    Buffer used to store ARGB images of the image presently being displayed.
  - pointVOI
```
private VOI pointVOI
```
    DOCUMENT ME!
  - red
```
private int red
```
    DOCUMENT ME!
  - green
```
private int green
```
    DOCUMENT ME!
  - blue
```
private int blue
```
    DOCUMENT ME!
  - regionLinesDisplay
```
private boolean regionLinesDisplay
```
    DOCUMENT ME!
  - resX
```
private float resX
```
    DOCUMENT ME!
  - resY
```
private float resY
```
    DOCUMENT ME!
  - rightPad
```
private int rightPad
```
    DOCUMENT ME!
  - rThreshold
```
private float[] rThreshold
```
    DOCUMENT ME!
  - scale1
```
private double scale1
```
    DOCUMENT ME!
  - scale2
```
private double scale2
```
    DOCUMENT ME!
  - secondIndex
```
private float secondIndex
```
    DOCUMENT ME!
  - thresholdOn1
```
private boolean thresholdOn1
```
    DOCUMENT ME!
  - topPad
```
private int topPad
```
    DOCUMENT ME!
  - useBlue
```
private boolean useBlue
```
    DOCUMENT ME!
  - useGreen
```
private boolean useGreen
```
    DOCUMENT ME!
  - useRed
```
private boolean useRed
```
    DOCUMENT ME!
  - userInterface
```
private ViewUserInterface userInterface
```
    DOCUMENT ME!
  - VOIs
```
private ViewVOIVector VOIs
```
    DOCUMENT ME!
  - xArray
```
private float[] xArray
```
    DOCUMENT ME!
  - xdiff
```
private double xdiff
```
    DOCUMENT ME!
  - ydiff
```
private double ydiff
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
  - yDim
```
private int yDim
```
    Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
  - zDim
```
private int zDim
```
    Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
  - tDim
```
private int tDim
```
    Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
  - yArray
```
private float[] yArray
```
    DOCUMENT ME!
  - zArray
```
private float[] zArray
```
    DOCUMENT ME!
  - zoomX
```
private float zoomX
```
    DOCUMENT ME!
  - zoomY
```
private float zoomY
```
    DOCUMENT ME!
- Constructor Detail
  - ViewJComponentColocalizationRegression
```
public ViewJComponentColocalizationRegression(AlgorithmColocalizationRegression alg,
                                              ViewJFrameBase _frame,
                                              ViewJFrameColocalizationRegression localizeFrame,
                                              ModelImage _imageA,
                                              ModelImage _imageB,
                                              ModelImage destImage,
                                              ModelLUT LUTdest,
                                              float[] imageBufferDest,
                                              boolean useRed,
                                              boolean useGreen,
                                              boolean useBlue,
                                              float originalLineSlope,
                                              float originalLineOffset,
                                              boolean[] haveThreshold,
                                              float[] rThreshold,
                                              float[] colocSize,
                                              float[] colocIntensity1,
                                              float[] colocIntensity2,
                                              double min1,
                                              double max1,
                                              double min2,
                                              double max2,
                                              double scale1,
                                              double scale2,
                                              double lineMin1,
                                              double lineMax1,
                                              double lineMin2,
                                              double lineMax2,
                                              boolean thresholdOn1,
                                              int[] pixBufferDest,
                                              int[] paintBufferDest,
                                              float zoom,
                                              int[] extents,
                                              boolean logMagDisplay,
                                              boolean regionLinesDisplay,
                                              int leftPad,
                                              int rightPad,
                                              int bottomPad,
                                              int topPad,
                                              boolean doSecondIteration,
                                              float linearCorrelation,
                                              ViewUserInterface userInterface)
```
    Constructor: ImageA and ImageB are expected to be of the same dimensionality !!
    
    Parameters:
    
    alg - AlgorithmColocalizationRegression parent
    
    _frame - frame where the controls are obtained
    
    localizeFrame - frame where 2D histogram is displayed
    
    _imageA - Model of the image that will be displayed
    
    _imageB - Model of the image that will be displayed
    
    destImage - Image with histogram information
    
    LUTdest - LUT used to display destImage
    
    imageBufferDest - storage buffer used to display destImage
    
    useRed - DOCUMENT ME!
    
    useGreen - DOCUMENT ME!
    
    useBlue - DOCUMENT ME!
    
    originalLineSlope - DOCUMENT ME!
    
    originalLineOffset - DOCUMENT ME!
    
    haveThreshold - DOCUMENT ME!
    
    rThreshold - DOCUMENT ME!
    
    colocSize - DOCUMENT ME!
    
    colocIntensity1 - DOCUMENT ME!
    
    colocIntensity2 - DOCUMENT ME!
    
    min1 - DOCUMENT ME!
    
    max1 - DOCUMENT ME!
    
    min2 - DOCUMENT ME!
    
    max2 - DOCUMENT ME!
    
    scale1 - DOCUMENT ME!
    
    scale2 - DOCUMENT ME!
    
    lineMin1 - DOCUMENT ME!
    
    lineMax1 - DOCUMENT ME!
    
    lineMin2 - DOCUMENT ME!
    
    lineMax2 - DOCUMENT ME!
    
    thresholdOn1 - DOCUMENT ME!
    
    pixBufferDest - storage buffer used to build a displayable image
    
    paintBufferDest - DOCUMENT ME!
    
    zoom - initial magnification of image
    
    extents - initial display dimensions of the image
    
    logMagDisplay - display log magnitude of image
    
    regionLinesDisplay - DOCUMENT ME!
    
    leftPad - DOCUMENT ME!
    
    rightPad - DOCUMENT ME!
    
    bottomPad - DOCUMENT ME!
    
    topPad - DOCUMENT ME!
    
    doSecondIteration - DOCUMENT ME!
    
    linearCorrelation - DOCUMENT ME!
    
    userInterface - DOCUMENT ME!
- Method Detail
  - buildImageDestObject
```
public boolean buildImageDestObject(ModelLUT _LUTdest,
                                    boolean forceShow)
```
    Shows the 2D histogram image.
    
    Parameters:
    
    _LUTdest - LUTdest - to change to new LUT for imageA else null
    
    forceShow - forces this method to import image and recalculate java image
    
    Returns:
    
    boolean to indicate if the show was successful
  - dispose
```
public void dispose(boolean gcFlag)
```
    Sets all variables to null, disposes, and garbage collects.
    
    Overrides:
    
    dispose in class ViewJComponentBase
    
    Parameters:
    
    gcFlag - if true garbage collector should be called.
  - finalizeLocal
```
public void finalizeLocal()
```
    Clean up some resources!
  - getblue
```
public int getblue()
```
    Accessor that returns int blue.
    
    Returns:
    
    blue
  - getgreen
```
public int getgreen()
```
    Accessor that returns int green.
    
    Returns:
    
    green
  - getImageA
```
public ModelImage getImageA()
```
    Accessor that returns the imageA.
    
    Returns:
    
    imageA
  - getImageB
```
public ModelImage getImageB()
```
    Accessor that returns the imageB.
    
    Returns:
    
    imageB
  - getOPACITY
```
public float getOPACITY()
```
    Accessor that returns float OPACITY.
    
    Returns:
    
    OPACITY
  - getpaintBitmapDest
```
public java.util.BitSet getpaintBitmapDest()
```
    Accessor that returns BitSet paintBitmap.
    
    Returns:
    
    paintBitmap
  - getPreferredSize
```
public java.awt.Dimension getPreferredSize()
```
    Size set to object size.
    
    Overrides:
    
    getPreferredSize in class ViewJComponentBase
    
    Returns:
    
    dimension with the size
  - getred
```
public int getred()
```
    Accessor that returns int red.
    
    Returns:
    
    red
  - getSize
```
public java.awt.Dimension getSize(java.awt.Dimension wh)
```
    Gets the size of the object taking into account the zoom.
    
    Overrides:
    
    getSize in class ViewJComponentBase
    
    Parameters:
    
    wh - dimension
    
    Returns:
    
    dimension with the size
  - getZoomX
```
public float getZoomX()
```
    Magnification in the x - dimension.
    
    Overrides:
    
    getZoomX in class ViewJComponentBase
    
    Returns:
    
    magnificaiton in the x - dimension
  - getZoomY
```
public float getZoomY()
```
    Magnification in the y - dimension.
    
    Overrides:
    
    getZoomY in class ViewJComponentBase
    
    Returns:
    
    magnificaiton in the y - dimension
  - importImageDest
```
public void importImageDest(int[] data)
```
    Creates a Image object form an array of ints that have been formatted (packed) properly (i.e. aRGB)
    
    Parameters:
    
    data - Data (image) to be displayed that has been formatted (packed) properly (i.e. aRGB)
  - mouseClicked
```
public void mouseClicked(java.awt.event.MouseEvent mouseEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseClicked in interface java.awt.event.MouseListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - mouseDragged
```
public void mouseDragged(java.awt.event.MouseEvent mouseEvent)
```
    mouseDragged only updates the histogram display header when the mouse passes over a point for which the linear correlation coefficient and colocalizations have already been calculated.
    
    Specified by:
    
    mouseDragged in interface java.awt.event.MouseMotionListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - mouseEntered
```
public void mouseEntered(java.awt.event.MouseEvent mouseEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseEntered in interface java.awt.event.MouseListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - mouseExited
```
public void mouseExited(java.awt.event.MouseEvent mouseEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseExited in interface java.awt.event.MouseListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - mouseMoved
```
public void mouseMoved(java.awt.event.MouseEvent mouseEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseMoved in interface java.awt.event.MouseMotionListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - mousePressed
```
public void mousePressed(java.awt.event.MouseEvent mouseEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mousePressed in interface java.awt.event.MouseListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - mouseReleased
```
public void mouseReleased(java.awt.event.MouseEvent mouseEvent)
```
    If the correlation coefficient and colocalizations have not already been calculated at the mouse release point, then a call to AlgorithmColocalizationRegression calculates them.
    
    Specified by:
    
    mouseReleased in interface java.awt.event.MouseListener
    
    Parameters:
    
    mouseEvent - DOCUMENT ME!
  - paintComponent
```
public void paintComponent(java.awt.Graphics g)
```
    Paints the image and border.
    
    Overrides:
    
    paintComponent in class ViewJComponentBase
    
    Parameters:
    
    g - Graphics handle
  - passFreeRangeArrays
```
public void passFreeRangeArrays(boolean[] haveFreeRangeThreshold,
                                float[] freeRangeRThreshold,
                                float[] freeRangeColocSize,
                                float[] freeRangeColocIntensity1,
                                float[] freeRangeColocIntensity2)
```
    Passes arrays needed in free range mode.
    
    Parameters:
    
    haveFreeRangeThreshold - DOCUMENT ME!
    
    freeRangeRThreshold - DOCUMENT ME!
    
    freeRangeColocSize - DOCUMENT ME!
    
    freeRangeColocIntensity1 - DOCUMENT ME!
    
    freeRangeColocIntensity2 - DOCUMENT ME!
  - setBrightness
```
public void setBrightness(int brightness,
                          float contrast)
```
    Method to set the brightness and contrast of the animate images.
    
    Parameters:
    
    brightness - int going from -255 to 255
    
    contrast - float scale factor
  - setFreeRangeMode
```
public void setFreeRangeMode(boolean freeRangeMode)
```
    Accessor that sets freeRangeMode.
    
    Parameters:
    
    freeRangeMode - DOCUMENT ME!
  - setLogMagDisplay
```
public void setLogMagDisplay(boolean logMagDisplay)
```
    DOCUMENT ME!
    
    Parameters:
    
    logMagDisplay - DOCUMENT ME!
  - setNewVar
```
public void setNewVar(float originalLineSlope,
                      float originalLineOffset,
                      boolean[] haveThreshold,
                      float[] rThreshold,
                      float[] colocSize,
                      float[] colocIntensity1,
                      float[] colocIntensity2,
                      double min1,
                      double max1,
                      double min2,
                      double max2,
                      double scale1,
                      double scale2,
                      double lineMin1,
                      double lineMax1,
                      double lineMin2,
                      double lineMax2,
                      boolean thresholdOn1,
                      float linearCorrelation)
```
    Modifies component after mouseReleased in contour VOI indicating that the VOI has been moved.
    
    Parameters:
    
    originalLineSlope - DOCUMENT ME!
    
    originalLineOffset - DOCUMENT ME!
    
    haveThreshold - DOCUMENT ME!
    
    rThreshold - DOCUMENT ME!
    
    colocSize - DOCUMENT ME!
    
    colocIntensity1 - DOCUMENT ME!
    
    colocIntensity2 - DOCUMENT ME!
    
    min1 - DOCUMENT ME!
    
    max1 - DOCUMENT ME!
    
    min2 - DOCUMENT ME!
    
    max2 - DOCUMENT ME!
    
    scale1 - DOCUMENT ME!
    
    scale2 - DOCUMENT ME!
    
    lineMin1 - DOCUMENT ME!
    
    lineMax1 - DOCUMENT ME!
    
    lineMin2 - DOCUMENT ME!
    
    lineMax2 - DOCUMENT ME!
    
    thresholdOn1 - DOCUMENT ME!
    
    linearCorrelation - DOCUMENT ME!
  - setPaintMaskDest
```
public void setPaintMaskDest(java.util.BitSet mask)
```
    Accessor that sets the paint mask.
    
    Parameters:
    
    mask - DOCUMENT ME!
  - setPosition
```
public void setPosition(int xS,
                        int yS)
```
    DOCUMENT ME!
    
    Parameters:
    
    xS - DOCUMENT ME!
    
    yS - DOCUMENT ME!
  - setRegionLinesDisplay
```
public void setRegionLinesDisplay(boolean regionLinesDisplay)
```
    DOCUMENT ME!
    
    Parameters:
    
    regionLinesDisplay - DOCUMENT ME!
  - setRGBTA
```
public void setRGBTA(ModelRGB RGBT)
```
    Sets the RGB table for the ARGB image A.
    
    Parameters:
    
    RGBT - RGB table
  - setRGBTB
```
public void setRGBTB(ModelRGB RGBT)
```
    Sets the RGB table for the ARGB image B.
    
    Parameters:
    
    RGBT - RGB table
  - setZoom
```
public void setZoom(float zX,
                    float zY)
```
    Sets the magnification in both x and y directions.
    
    Overrides:
    
    setZoom in class ViewJComponentBase
    
    Parameters:
    
    zX - zoom in the x direction
    
    zY - zoom in the y direction
  - update
```
public void update()
```
    Method to call paint without erasing background this reduces flicker!
  - update
```
public void update(java.awt.Graphics g)
```
    Method to call paint without erasing background this reduces flicker!
    
    Overrides:
    
    update in class ViewJComponentBase
    
    Parameters:
    
    g - Graphics handle

Class ViewJComponentColocalizationRegression

Nested Class Summary

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

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.ViewJComponentBase

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

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

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

OPACITY

frame

imageA

imageB

interpMode

RGBTA

RGBTB

alg

bin1

bin2

bottomPad

brightness

colocIntensity1

colocIntensity2

colocSize

contrast

destImage

doSecondIteration

editImageFrameA

editImageFrameB

firstIndex

freeRangeColocIntensity1

freeRangeColocIntensity2

freeRangeColocSize

freeRangeMode

freeRangeRThreshold

haveFiltered

haveFreeRangeThreshold

haveThreshold

imageBufferDest

imgDest

leftPad

linearCorrelation

lineMin

lineOffset

lineSlope

lineVOI

localizeFrame

logMagDisplay

lutBufferRemappedDest

LUTdest

memImageDest

min1

max1

min2

max2

minimumx

maximumx

nVOI

originalLineOffset

originalLineSlope

paintBitmapDest

paintBufferDest

pixBufferDest

pointVOI

red

green

blue

regionLinesDisplay

resX

resY