Package gov.nih.mipav.view

Class ViewJComponentColocalizationRegression

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:

MouseListener, MouseMotionListener, ImageObserver, MenuContainer, Serializable, EventListener

public class ViewJComponentColocalizationRegression
extends ViewJComponentBase
implements MouseMotionListener, MouseListener

DOCUMENT ME!

See Also:

• Serialized Form

Nested Class Summary

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

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

Field Summary

Fields

Modifier and Type	Field	Description
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 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 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 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 final 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

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.
BitSet	getpaintBitmapDest()	Accessor that returns BitSet paintBitmap.
Dimension	getPreferredSize()	Size set to object size.
int	getred()	Accessor that returns int red.
Dimension	getSize(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(MouseEvent mouseEvent)	DOCUMENT ME!
void	mouseDragged(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(MouseEvent mouseEvent)	DOCUMENT ME!
void	mouseExited(MouseEvent mouseEvent)	DOCUMENT ME!
void	mouseMoved(MouseEvent mouseEvent)	DOCUMENT ME!
void	mousePressed(MouseEvent mouseEvent)	DOCUMENT ME!
void	mouseReleased(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(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(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(Graphics g)	Method to call paint without erasing background this reduces flicker!

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

disposeLocal, finalize, getImage, getInterpMode, getLastMouseX, getLastMouseY, getResolutionX, getResolutionY, getScaledX, getScaledY, getSelectedPaintColor, getShowMagIntensityEnabled, importImage, importImageB, LocalToScreen, makePaintBitmapBorder, makePaintImage, paintCursorBoxComponent, paintWindowComponent, paintWindowComponent, ScreenToLocal, setInterpolationMode, setResolutions, setShowSliceNumber, setSliceString, setTextColor, setZoomExact

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 Details

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 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 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 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 Details

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 Details

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 BitSet getpaintBitmapDest()

Accessor that returns BitSet paintBitmap.

Returns:

paintBitmap

getPreferredSize

public 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 Dimension getSize(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(MouseEvent mouseEvent)

DOCUMENT ME!

Specified by:

mouseClicked in interface MouseListener

Parameters:

mouseEvent - DOCUMENT ME!

mouseDragged

public void mouseDragged(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 MouseMotionListener

Parameters:

mouseEvent - DOCUMENT ME!

mouseEntered

public void mouseEntered(MouseEvent mouseEvent)

DOCUMENT ME!

Specified by:

mouseEntered in interface MouseListener

Parameters:

mouseEvent - DOCUMENT ME!

mouseExited

public void mouseExited(MouseEvent mouseEvent)

DOCUMENT ME!

Specified by:

mouseExited in interface MouseListener

Parameters:

mouseEvent - DOCUMENT ME!

mouseMoved

public void mouseMoved(MouseEvent mouseEvent)

DOCUMENT ME!

Specified by:

mouseMoved in interface MouseMotionListener

Parameters:

mouseEvent - DOCUMENT ME!

mousePressed

public void mousePressed(MouseEvent mouseEvent)

DOCUMENT ME!

Specified by:

mousePressed in interface MouseListener

Parameters:

mouseEvent - DOCUMENT ME!

mouseReleased

public void mouseReleased(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 MouseListener

Parameters:

mouseEvent - DOCUMENT ME!

paintComponent

public void paintComponent(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(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(Graphics g)

Method to call paint without erasing background this reduces flicker!

Overrides:

update in class ViewJComponentBase

Parameters:

g - Graphics handle