Package gov.nih.mipav.view

Class ViewJFrameColocalizationRegression

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.ViewJFrameColocalizationRegression

All Implemented Interfaces:

ViewImageUpdateInterface, ActionListener, ComponentListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, ChangeListener, RootPaneContainer, WindowConstants

public class ViewJFrameColocalizationRegression
extends ViewJFrameBase
implements ChangeListener, ItemListener

This class produces a frame surrounding a 2D histogram with a orthogonal least squares regression line and a threshold point that slides along the line. In free range mode this VOI point may be taken off the line. Optional region lines that go horizontally to the right and vertically to the top from the threshold point may be selected with the region button. Tool bar buttons are present for reset, magnify, unmagnify, for generating a histogram LUT dialog, for generating a dialog to set brightness and contrast, for switching between linear and log mode, for whether or not horizontal and vertical region lines are included, for taking the histogram frame into and out of free range mode, and for outputting statistics for each slice in a 3D image. Reset returns the sliding point to its initial position - the point on the line just above the point where the first negative or zero linear correlation coefficient is present. 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 ViewJFrameColocalization structure function. The help menu only has 1 simple function - an about colocalization function.

ViewJFrameColocalizationRegression is called in AlgorithmColocalizationRegression. ViewJFrameColocalizationRegression calls ViewJComponentColocalizationRegression

See Also:

• Serialized Form

Nested Class Summary

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

JFrame.AccessibleJFrame

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

Frame.AccessibleAWTFrame

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

Window.AccessibleAWTWindow, Window.Type

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

Container.AccessibleAWTContainer

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

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

Field Summary

Fields

Modifier and Type	Field	Description
private AlgorithmColocalizationRegression	alg	DOCUMENT ME!
private int	bottomPad	DOCUMENT ME!
private float[]	colocIntensity1	DOCUMENT ME!
private float[]	colocIntensity2	DOCUMENT ME!
private float[]	colocSize	DOCUMENT ME!
private ViewJComponentColocalizationRegression	componentImage	DOCUMENT ME!
private int	componentY	DOCUMENT ME!
private ViewJFrameBase	controlFrame	DOCUMENT ME!
private ViewControlsImage	controls	DOCUMENT ME!
private GridBagConstraints	cpGBC	DOCUMENT ME!
private GridBagLayout	cpGBL	DOCUMENT ME!
private String	dataLine1	DOCUMENT ME!
private String	dataLine2	DOCUMENT ME!
private ModelImage	destImage	The image containing the 2D histogram.
private boolean	doSecondIteration	DOCUMENT ME!
private Border	etchedBorder	DOCUMENT ME!
private int[]	extents	DOCUMENT ME!
private JToggleButton	freeRangeButton	DOCUMENT ME!
private boolean	freeRangeMode	DOCUMENT ME!
private GridBagConstraints	gbcTP	DOCUMENT ME!
private boolean[]	haveFreeRangeThreshold	true for pixels with calculated freeRangeRThreshold values.
private boolean[]	haveThreshold	DOCUMENT ME!
private ModelImage	imageA	DOCUMENT ME!
private ModelImage	imageB	DOCUMENT ME!
private float[]	imageBufferDest	DOCUMENT ME!
private JPanel	innerPanel	DOCUMENT ME!
private JLabel	labelCurrent	DOCUMENT ME!
private JLabel	labelCurrentColoc	private JLabel labelLineFunction;.
private JLabel	labelCurrentIntensity1	DOCUMENT ME!
private JLabel	labelCurrentIntensity2	DOCUMENT ME!
private JLabel	labelLinearCorrelation	DOCUMENT ME!
private JLabel	labelPValue	DOCUMENT ME!
private int	leftPad	The spaces around the histogram bin area.
private float	linearCorrelation	The linear correlation coefficient for all points with either buffer[i] >= threshold1 or secondBuffer[i] >= threshold2.
private double	lineMax1	The endpoints of the line segment in (buffer,secondBuffer) values.
private double	lineMax2	The endpoints of the line segment in (buffer,secondBuffer) values.
private double	lineMin1	The endpoints of the line segment in (buffer,secondBuffer) values.
private double	lineMin2	The endpoints of the line segment in (buffer,secondBuffer) values.
private 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 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 NumberFormat	nf	DOCUMENT ME!
private int	nVOI	DOCUMENT ME!
private float	offset	DOCUMENT ME!
private 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	originalX	DOCUMENT ME!
private int	originalY	DOCUMENT ME!
private int[]	paintBufferDest	DOCUMENT ME!
private int[]	pixBufferDest	DOCUMENT ME!
private boolean	pointCalculation	DOCUMENT ME!
private VOI	pointVOI	DOCUMENT ME!
private Border	pressedBorder	DOCUMENT ME!
private float	PValue	statistic giving the portion of images generated with randomly scrambled blocks of pixels having a linear correlation coefficient less than that of the actual image.
private Border	raisedBorder	DOCUMENT ME!
private boolean	regionLinesDisplay	DOCUMENT ME!
private JToggleButton	regionLinesDisplayButton	DOCUMENT ME!
private ModelRGB	RGBTA	set to give 6 digits to the right of the decimal.
private int	rightPad	DOCUMENT ME!
private float[]	rThreshold	The linear correlation coefficients for all pixels with values either below color1 for buffer or below a*color1 + b for secondBuffer.
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 JScrollPane	scrollPane	DOCUMENT ME!
private int	scrollPaneSize	DOCUMENT ME!
private static final long	serialVersionUID	Use serialVersionUID for interoperability.
private float	slope	The slope and offset of the total least squares line.
private JPanel	statusPanel	DOCUMENT ME!
private int	structureY	DOCUMENT ME!
private boolean	thresholdOn1	If true, the matrix of linear correlation coefficients is taken along color 1 at unity spacings.
private JToolBar	toolBar	DOCUMENT ME!
private int	topPad	DOCUMENT ME!
private 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 ViewVOIVector	VOIs	red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.
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

ViewJFrameColocalizationRegression(AlgorithmColocalizationRegression alg, ModelImage _imageA, ModelLUT _LUTa, ModelImage _imageB, ModelLUT _LUTb, ModelRGB _RGBTA, ModelImage destImage, ViewJFrameBase controlFrame, boolean useRed, boolean useGreen, boolean useBlue, float slope, float offset, float linearCorrelation, float PValue, 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 leftPad, int rightPad, int bottomPad, int topPad, boolean doSecondIteration, boolean pointCalculation)

Makes a frame of the colocalization histogram.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent event)	Calls various methods depending on the action.
private void	addStatusPanel(Component c, GridBagConstraints gbc, int x, int y, int w, int h)	Method that adds components to the control paenl.
private JToolBar	buildColocalizeToolBar(ActionListener al)	Method to build the toolbar for the Animate frame.
private void	buildMenu()	This method builds a menu which contains the option Close ColocalizationRegression.
private void	buildScrollPane()	Make a scroll frame and puts an image component into it.
private void	buildStatusPanel()	Panel that builds the status display panel.
void	cancelBrightness()	Resets current slice's brightness and contrast to original.
void	componentResized(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(ItemEvent event)	Sets border painted or not painted depending on if the button was selected or deselected.
private JButton	makeSeparator()	Makes a separator for the use in the toolbars.
private void	modifyStatusPanel()	Panel that builds the status display panel.
void	passFreeRangeArrays(boolean[] haveFreeRangeThreshold, float[] freeRangeRThreshold, float[] freeRangeColocSize, float[] freeRangeColocIntensity1, float[] freeRangeColocIntensity2)	Passes arrays needed in free range mode.
void	pointCalculate()	DOCUMENT ME!
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	setCurrentLabels(String str1, String str2, String str3, String str4)	DOCUMENT ME!
void	setEnabled(boolean flag)	Does nothing.
void	setImageB(ModelImage _imageB)	Does nothing.
void	setLUTdest(ModelLUT LUTdest)	DOCUMENT ME!
void	setNewVar(float slope, float offset, float linearCorrelation, float PValue, 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)	Modifies a frame of the colocalization histogram after mouseRelased has indicated the contour VOI in the source image has been moved.
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(ChangeEvent e)	Sets values based on knob along slider.
protected boolean	testParameter(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.
final boolean	updateImages()	Does nothing.
final boolean	updateImages(boolean forceShow)	This methods calls the componentImage's update method to redraw the screen.
final boolean	updateImages(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow, int interpMode)	Does nothing.
void	windowActivated(WindowEvent event)	Does nothing.
void	windowClosed(WindowEvent event)	Does nothing.
void	windowClosing(WindowEvent event)	Stops thread, calls close.
void	windowDeactivated(WindowEvent event)	Does nothing.
void	windowDeiconified(WindowEvent event)	Does nothing.
void	windowIconified(WindowEvent event)	Does nothing.
void	windowOpened(WindowEvent event)	Does nothing.

Methods inherited from class 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 Details

serialVersionUID

private static final long serialVersionUID

Use serialVersionUID for interoperability.

See Also:

• Constant Field Values

alg

private AlgorithmColocalizationRegression alg

DOCUMENT ME!

bottomPad

private int bottomPad

DOCUMENT ME!

colocIntensity1

private float[] colocIntensity1

DOCUMENT ME!

colocIntensity2

private float[] colocIntensity2

DOCUMENT ME!

colocSize

private float[] colocSize

DOCUMENT ME!

componentImage

private ViewJComponentColocalizationRegression componentImage

DOCUMENT ME!

componentY

private int componentY

DOCUMENT ME!

controlFrame

private ViewJFrameBase controlFrame

DOCUMENT ME!

controls

private ViewControlsImage controls

DOCUMENT ME!

cpGBC

private GridBagConstraints cpGBC

DOCUMENT ME!

cpGBL

private GridBagLayout cpGBL

DOCUMENT ME!

dataLine1

private String dataLine1

DOCUMENT ME!

dataLine2

private String dataLine2

DOCUMENT ME!

destImage

private ModelImage destImage

The image containing the 2D histogram.

doSecondIteration

private boolean doSecondIteration

DOCUMENT ME!

etchedBorder

private Border etchedBorder

DOCUMENT ME!

extents

private int[] extents

DOCUMENT ME!

freeRangeButton

private JToggleButton freeRangeButton

DOCUMENT ME!

freeRangeMode

private boolean freeRangeMode

DOCUMENT ME!

gbcTP

private GridBagConstraints gbcTP

DOCUMENT ME!

haveFreeRangeThreshold

private boolean[] haveFreeRangeThreshold

true for pixels with calculated freeRangeRThreshold values.

haveThreshold

private boolean[] haveThreshold

DOCUMENT ME!

imageA

private ModelImage imageA

DOCUMENT ME!

imageB

private ModelImage imageB

DOCUMENT ME!

imageBufferDest

private float[] imageBufferDest

DOCUMENT ME!

innerPanel

private JPanel innerPanel

DOCUMENT ME!

labelCurrent

private JLabel labelCurrent

DOCUMENT ME!

labelCurrentColoc

private JLabel labelCurrentColoc

private JLabel labelLineFunction;.

labelCurrentIntensity1

private JLabel labelCurrentIntensity1

DOCUMENT ME!

labelCurrentIntensity2

private JLabel labelCurrentIntensity2

DOCUMENT ME!

labelLinearCorrelation

private JLabel labelLinearCorrelation

DOCUMENT ME!

labelPValue

private JLabel labelPValue

DOCUMENT ME!

leftPad

private int leftPad

The spaces around the histogram bin area.

linearCorrelation

private float linearCorrelation

The linear correlation coefficient for all points with either buffer[i] >= threshold1 or secondBuffer[i] >= threshold2.

lineMin1

private double lineMin1

The endpoints of the line segment in (buffer,secondBuffer) values.

lineMax1

private double lineMax1

The endpoints of the line segment in (buffer,secondBuffer) values.

lineMin2

private double lineMin2

The endpoints of the line segment in (buffer,secondBuffer) values.

lineMax2

private double lineMax2

The endpoints of the line segment in (buffer,secondBuffer) values.

logDisplayButton

private 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.

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!

nf

private NumberFormat nf

DOCUMENT ME!

nVOI

private int nVOI

DOCUMENT ME!

offset

private float offset

DOCUMENT ME!

openingMenuBar

private 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.

originalX

private int originalX

DOCUMENT ME!

originalY

private int originalY

DOCUMENT ME!

paintBufferDest

private int[] paintBufferDest

DOCUMENT ME!

pixBufferDest

private int[] pixBufferDest

DOCUMENT ME!

pointCalculation

private boolean pointCalculation

DOCUMENT ME!

pointVOI

private VOI pointVOI

DOCUMENT ME!

pressedBorder

private Border pressedBorder

DOCUMENT ME!

PValue

private float PValue

statistic giving the portion of images generated with randomly scrambled blocks of pixels having a linear correlation coefficient less than that of the actual image.

raisedBorder

private Border raisedBorder

DOCUMENT ME!

regionLinesDisplay

private boolean regionLinesDisplay

DOCUMENT ME!

regionLinesDisplayButton

private JToggleButton regionLinesDisplayButton

DOCUMENT ME!

RGBTA

private ModelRGB RGBTA

set to give 6 digits to the right of the decimal.

rightPad

private int rightPad

DOCUMENT ME!

rThreshold

private float[] rThreshold

The linear correlation coefficients for all pixels with values either below color1 for buffer or below a*color1 + b for secondBuffer.

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 JScrollPane scrollPane

DOCUMENT ME!

scrollPaneSize

private int scrollPaneSize

DOCUMENT ME!

slope

private float slope

The slope and offset of the total least squares line.

statusPanel

private JPanel statusPanel

DOCUMENT ME!

structureY

private int structureY

DOCUMENT ME!

thresholdOn1

private boolean thresholdOn1

If true, the matrix of linear correlation coefficients is taken along color 1 at unity spacings. If false, along color 2.

toolBar

private JToolBar toolBar

DOCUMENT ME!

topPad

private int topPad

DOCUMENT ME!

topPanel

private 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!

VOIs

private ViewVOIVector VOIs

red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.

xScreen

private int xScreen

DOCUMENT ME!

yScreen

private int yScreen

DOCUMENT ME!

zoom

private float zoom

DOCUMENT ME!

Constructor Details

ViewJFrameColocalizationRegression

public ViewJFrameColocalizationRegression(AlgorithmColocalizationRegression alg,
 ModelImage _imageA,
 ModelLUT _LUTa,
 ModelImage _imageB,
 ModelLUT _LUTb,
 ModelRGB _RGBTA,
 ModelImage destImage,
 ViewJFrameBase controlFrame,
 boolean useRed,
 boolean useGreen,
 boolean useBlue,
 float slope,
 float offset,
 float linearCorrelation,
 float PValue,
 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 leftPad,
 int rightPad,
 int bottomPad,
 int topPad,
 boolean doSecondIteration,
 boolean pointCalculation)

Makes a frame of the colocalization histogram.

Parameters:

alg - AlgorithmColocalizationRegression parent

_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 ViewJComponentColocalizationRegression

useRed - DOCUMENT ME!

useGreen - DOCUMENT ME!

useBlue - DOCUMENT ME!

slope - DOCUMENT ME!

offset - DOCUMENT ME!

linearCorrelation - DOCUMENT ME!

PValue - 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!

leftPad - DOCUMENT ME!

rightPad - DOCUMENT ME!

bottomPad - DOCUMENT ME!

topPad - DOCUMENT ME!

doSecondIteration - DOCUMENT ME!

pointCalculation - DOCUMENT ME!

Method Details

actionPerformed

public void actionPerformed(ActionEvent event)

Calls various methods depending on the action.

Specified by:

actionPerformed in interface 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(ComponentEvent event)

Resizes frame and all components.

Specified by:

componentResized in interface 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 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(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 ItemListener

Parameters:

event - Event that triggered this function.

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!

freeRangeColocIntensity2 -

pointCalculate

public void pointCalculate()

DOCUMENT ME!

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

setCurrentLabels

public void setCurrentLabels(String str1,
 String str2,
 String str3,
 String str4)

DOCUMENT ME!

Parameters:

str1 - DOCUMENT ME!

str2 - DOCUMENT ME!

str3 - DOCUMENT ME!

str4 - DOCUMENT ME!

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!

setNewVar

public void setNewVar(float slope,
 float offset,
 float linearCorrelation,
 float PValue,
 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)

Modifies a frame of the colocalization histogram after mouseRelased has indicated the contour VOI in the source image has been moved.

Parameters:

slope - DOCUMENT ME!

offset - DOCUMENT ME!

linearCorrelation - DOCUMENT ME!

PValue - 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!

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(ChangeEvent e)

Sets values based on knob along slider.

Specified by:

stateChanged in interface 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(WindowEvent event)

Does nothing.

Specified by:

windowActivated in interface WindowListener

Overrides:

windowActivated in class ViewJFrameBase

Parameters:

event - DOCUMENT ME!

windowClosed

public void windowClosed(WindowEvent event)

Does nothing.

Specified by:

windowClosed in interface WindowListener

Overrides:

windowClosed in class ViewJFrameBase

Parameters:

event - DOCUMENT ME!

windowClosing

public void windowClosing(WindowEvent event)

Stops thread, calls close.

Specified by:

windowClosing in interface WindowListener

Overrides:

windowClosing in class ViewJFrameBase

Parameters:

event - event that triggered function

windowDeactivated

public void windowDeactivated(WindowEvent event)

Does nothing.

Specified by:

windowDeactivated in interface WindowListener

Overrides:

windowDeactivated in class ViewJFrameBase

Parameters:

event - DOCUMENT ME!

windowDeiconified

public void windowDeiconified(WindowEvent event)

Does nothing.

Specified by:

windowDeiconified in interface WindowListener

Overrides:

windowDeiconified in class ViewJFrameBase

Parameters:

event - DOCUMENT ME!

windowIconified

public void windowIconified(WindowEvent event)

Does nothing.

Specified by:

windowIconified in interface WindowListener

Overrides:

windowIconified in class ViewJFrameBase

Parameters:

event - DOCUMENT ME!

windowOpened

public void windowOpened(WindowEvent event)

Does nothing.

Specified by:

windowOpened in interface WindowListener

Overrides:

windowOpened in class ViewJFrameBase

Parameters:

event - DOCUMENT ME!

testParameter

protected boolean testParameter(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

addStatusPanel

private void addStatusPanel(Component c,
 GridBagConstraints gbc,
 int x,
 int y,
 int w,
 int h)

Method that adds components to the control paenl.

Parameters:

c - component added to the control panel

gbc - GridBagConstraints of added component

x - grdix location

y - gridy location

w - gridwidth

h - gridheight

buildColocalizeToolBar

private JToolBar buildColocalizeToolBar(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 ColocalizationRegression.

buildScrollPane

private void buildScrollPane()

Make a scroll frame and puts an image component into it.

buildStatusPanel

private void buildStatusPanel()

Panel that builds the status display panel.

makeSeparator

private JButton makeSeparator()

Makes a separator for the use in the toolbars.

Returns:

Separator button.

modifyStatusPanel

private void modifyStatusPanel()

Panel that builds the status display panel.