Class ViewJFrameColocalizationRegression

  • All Implemented Interfaces:
    ViewImageUpdateInterface, java.awt.event.ActionListener, java.awt.event.ComponentListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants

    public class ViewJFrameColocalizationRegression
    extends ViewJFrameBase
    implements javax.swing.event.ChangeListener, java.awt.event.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

        javax.swing.JFrame.AccessibleJFrame
      • Nested classes/interfaces inherited from class java.awt.Frame

        java.awt.Frame.AccessibleAWTFrame
      • Nested classes/interfaces inherited from class java.awt.Window

        java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type
      • Nested classes/interfaces inherited from class java.awt.Container

        java.awt.Container.AccessibleAWTContainer
      • Nested classes/interfaces inherited from class java.awt.Component

        java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
    • 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

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void actionPerformed​(java.awt.event.ActionEvent event)
      Calls various methods depending on the action.
      private void addStatusPanel​(java.awt.Component c, java.awt.GridBagConstraints gbc, int x, int y, int w, int h)
      Method that adds components to the control paenl.
      private javax.swing.JToolBar buildColocalizeToolBar​(java.awt.event.ActionListener al)
      Method to build the toolbar for the Animate frame.
      private void buildMenu()
      This method builds a menu which contains the option Close 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​(java.awt.event.ComponentEvent event)
      Resizes frame and all components.
      void dispose()
      Disposes of components and frame.
      ViewControlsImage getControls()
      Get control widgets for frame.
      ModelImage getImageA()
      Accessor that returns the reference to imageA.
      ModelImage getImageB()
      Accessor that returns the reference to imageB.
      void itemStateChanged​(java.awt.event.ItemEvent event)
      Sets border painted or not painted depending on if the button was selected or deselected.
      private javax.swing.JButton makeSeparator()
      Makes a separator for the use in the toolbars.
      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​(java.lang.String str1, java.lang.String str2, java.lang.String str3, java.lang.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​(javax.swing.event.ChangeEvent e)
      Sets values based on knob along slider.
      protected boolean testParameter​(java.lang.String str, double minValue, double maxValue)
      Tests that the entered parameter is in range.
      void updateFrame​(float sX, float sY)
      Does nothing.
      boolean updateImageExtents()
      Does nothing.
      boolean updateImages()
      Does nothing.
      boolean updateImages​(boolean forceShow)
      This methods calls the componentImage's update method to redraw the screen.
      boolean updateImages​(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow, int interpMode)
      Does nothing.
      void windowActivated​(java.awt.event.WindowEvent event)
      Does nothing.
      void windowClosed​(java.awt.event.WindowEvent event)
      Does nothing.
      void windowClosing​(java.awt.event.WindowEvent event)
      Stops thread, calls close.
      void windowDeactivated​(java.awt.event.WindowEvent event)
      Does nothing.
      void windowDeiconified​(java.awt.event.WindowEvent event)
      Does nothing.
      void windowIconified​(java.awt.event.WindowEvent event)
      Does nothing.
      void windowOpened​(java.awt.event.WindowEvent event)
      Does nothing.
      • Methods inherited from class javax.swing.JFrame

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

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

        addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFront
      • Methods inherited from class java.awt.Container

        add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree
      • Methods inherited from class java.awt.Component

        action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle
      • Methods inherited from class java.lang.Object

        clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
      • Methods inherited from interface java.awt.MenuContainer

        getFont, postEvent
    • Field Detail

      • serialVersionUID

        private static final long serialVersionUID
        Use serialVersionUID for interoperability.
        See Also:
        Constant Field Values
      • bottomPad

        private int bottomPad
        DOCUMENT ME!
      • colocIntensity1

        private float[] colocIntensity1
        DOCUMENT ME!
      • colocIntensity2

        private float[] colocIntensity2
        DOCUMENT ME!
      • colocSize

        private float[] colocSize
        DOCUMENT ME!
      • componentY

        private int componentY
        DOCUMENT ME!
      • cpGBC

        private java.awt.GridBagConstraints cpGBC
        DOCUMENT ME!
      • cpGBL

        private java.awt.GridBagLayout cpGBL
        DOCUMENT ME!
      • dataLine1

        private java.lang.String dataLine1
        DOCUMENT ME!
      • dataLine2

        private java.lang.String dataLine2
        DOCUMENT ME!
      • destImage

        private ModelImage destImage
        The image containing the 2D histogram.
      • doSecondIteration

        private boolean doSecondIteration
        DOCUMENT ME!
      • etchedBorder

        private javax.swing.border.Border etchedBorder
        DOCUMENT ME!
      • extents

        private int[] extents
        DOCUMENT ME!
      • freeRangeButton

        private javax.swing.JToggleButton freeRangeButton
        DOCUMENT ME!
      • freeRangeMode

        private boolean freeRangeMode
        DOCUMENT ME!
      • gbcTP

        private java.awt.GridBagConstraints gbcTP
        DOCUMENT ME!
      • haveFreeRangeThreshold

        private boolean[] haveFreeRangeThreshold
        true for pixels with calculated freeRangeRThreshold values.
      • haveThreshold

        private boolean[] haveThreshold
        DOCUMENT ME!
      • imageBufferDest

        private float[] imageBufferDest
        DOCUMENT ME!
      • innerPanel

        private javax.swing.JPanel innerPanel
        DOCUMENT ME!
      • labelCurrent

        private javax.swing.JLabel labelCurrent
        DOCUMENT ME!
      • labelCurrentColoc

        private javax.swing.JLabel labelCurrentColoc
        private JLabel labelLineFunction;.
      • labelCurrentIntensity1

        private javax.swing.JLabel labelCurrentIntensity1
        DOCUMENT ME!
      • labelCurrentIntensity2

        private javax.swing.JLabel labelCurrentIntensity2
        DOCUMENT ME!
      • labelLinearCorrelation

        private javax.swing.JLabel labelLinearCorrelation
        DOCUMENT ME!
      • labelPValue

        private javax.swing.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 javax.swing.JToggleButton logDisplayButton
        DOCUMENT ME!
      • logMagDisplay

        private boolean logMagDisplay
        DOCUMENT ME!
      • LUTa

        private ModelLUT LUTa
        DOCUMENT ME!
      • LUTdest

        private ModelLUT LUTdest
        The LUT for the 2D histogram.
      • 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 java.text.NumberFormat nf
        DOCUMENT ME!
      • nVOI

        private int nVOI
        DOCUMENT ME!
      • offset

        private float offset
        DOCUMENT ME!
      • openingMenuBar

        private javax.swing.JMenuBar openingMenuBar
        DOCUMENT ME!
      • origBrightness

        private int origBrightness
        DOCUMENT ME!
      • origContrast

        private float origContrast
        red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.
      • 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 javax.swing.border.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 javax.swing.border.Border raisedBorder
        DOCUMENT ME!
      • regionLinesDisplay

        private boolean regionLinesDisplay
        DOCUMENT ME!
      • regionLinesDisplayButton

        private javax.swing.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 javax.swing.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 javax.swing.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 javax.swing.JToolBar toolBar
        DOCUMENT ME!
      • topPad

        private int topPad
        DOCUMENT ME!
      • topPanel

        private javax.swing.JPanel topPanel
        and innerPanel placed in scrollPane.
      • useBlue

        private boolean useBlue
        DOCUMENT ME!
      • useGreen

        private boolean useGreen
        DOCUMENT ME!
      • useRed

        private boolean useRed
        DOCUMENT ME!
      • 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 Detail

      • 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 Detail

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent event)
        Calls various methods depending on the action.
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener
        Specified by:
        actionPerformed in class ViewJFrameBase
        Parameters:
        event - event that triggered function
      • cancelBrightness

        public void cancelBrightness()
        Resets current slice's brightness and contrast to original.
      • componentResized

        public void componentResized​(java.awt.event.ComponentEvent event)
        Resizes frame and all components.
        Specified by:
        componentResized in interface java.awt.event.ComponentListener
        Overrides:
        componentResized in class ViewJFrameBase
        Parameters:
        event - event that triggered function
      • dispose

        public void dispose()
        Disposes of components and frame.
        Overrides:
        dispose in class java.awt.Window
      • itemStateChanged

        public void itemStateChanged​(java.awt.event.ItemEvent event)
        Sets border painted or not painted depending on if the button was selected or deselected. Changes the currently selected script.
        Specified by:
        itemStateChanged in interface java.awt.event.ItemListener
        Parameters:
        event - Event that triggered this function.
      • 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!
      • 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.
      • setCurrentLabels

        public void setCurrentLabels​(java.lang.String str1,
                                     java.lang.String str2,
                                     java.lang.String str3,
                                     java.lang.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!
      • 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
      • setTitle

        public void setTitle()
        Set the title of the frame with the image name and magnification.
        Specified by:
        setTitle in class ViewJFrameBase
      • stateChanged

        public void stateChanged​(javax.swing.event.ChangeEvent e)
        Sets values based on knob along slider.
        Specified by:
        stateChanged in interface javax.swing.event.ChangeListener
        Overrides:
        stateChanged in class ViewJFrameBase
        Parameters:
        e - Event that triggered this function
      • updateFrame

        public void updateFrame​(float sX,
                                float sY)
        Does nothing.
        Parameters:
        sX - DOCUMENT ME!
        sY - DOCUMENT ME!
      • updateImages

        public final boolean updateImages​(boolean forceShow)
        This methods calls the componentImage's update method to redraw the screen. Without LUT changes.
        Specified by:
        updateImages in interface ViewImageUpdateInterface
        Parameters:
        forceShow - unused parameter
        Returns:
        boolean confirming successful update
      • updateImages

        public final boolean updateImages​(ModelLUT LUTa,
                                          ModelLUT LUTb,
                                          boolean forceShow,
                                          int interpMode)
        Does nothing.
        Specified by:
        updateImages in interface ViewImageUpdateInterface
        Parameters:
        LUTa - DOCUMENT ME!
        LUTb - DOCUMENT ME!
        forceShow - DOCUMENT ME!
        interpMode - DOCUMENT ME!
        Returns:
        DOCUMENT ME!
      • windowActivated

        public void windowActivated​(java.awt.event.WindowEvent event)
        Does nothing.
        Specified by:
        windowActivated in interface java.awt.event.WindowListener
        Overrides:
        windowActivated in class ViewJFrameBase
        Parameters:
        event - DOCUMENT ME!
      • windowClosed

        public void windowClosed​(java.awt.event.WindowEvent event)
        Does nothing.
        Specified by:
        windowClosed in interface java.awt.event.WindowListener
        Overrides:
        windowClosed in class ViewJFrameBase
        Parameters:
        event - DOCUMENT ME!
      • windowClosing

        public void windowClosing​(java.awt.event.WindowEvent event)
        Stops thread, calls close.
        Specified by:
        windowClosing in interface java.awt.event.WindowListener
        Overrides:
        windowClosing in class ViewJFrameBase
        Parameters:
        event - event that triggered function
      • windowDeactivated

        public void windowDeactivated​(java.awt.event.WindowEvent event)
        Does nothing.
        Specified by:
        windowDeactivated in interface java.awt.event.WindowListener
        Overrides:
        windowDeactivated in class ViewJFrameBase
        Parameters:
        event - DOCUMENT ME!
      • windowDeiconified

        public void windowDeiconified​(java.awt.event.WindowEvent event)
        Does nothing.
        Specified by:
        windowDeiconified in interface java.awt.event.WindowListener
        Overrides:
        windowDeiconified in class ViewJFrameBase
        Parameters:
        event - DOCUMENT ME!
      • windowIconified

        public void windowIconified​(java.awt.event.WindowEvent event)
        Does nothing.
        Specified by:
        windowIconified in interface java.awt.event.WindowListener
        Overrides:
        windowIconified in class ViewJFrameBase
        Parameters:
        event - DOCUMENT ME!
      • windowOpened

        public void windowOpened​(java.awt.event.WindowEvent event)
        Does nothing.
        Specified by:
        windowOpened in interface java.awt.event.WindowListener
        Overrides:
        windowOpened in class ViewJFrameBase
        Parameters:
        event - DOCUMENT ME!
      • testParameter

        protected boolean testParameter​(java.lang.String str,
                                        double minValue,
                                        double maxValue)
        Tests that the entered parameter is in range.
        Parameters:
        str - the value entered by the user
        minValue - the minimum value this variable may be set to
        maxValue - the maximum value this variable may be set to
        Returns:
        boolean result of test
      • addStatusPanel

        private void addStatusPanel​(java.awt.Component c,
                                    java.awt.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 javax.swing.JToolBar buildColocalizeToolBar​(java.awt.event.ActionListener al)
        Method to build the toolbar for the Animate frame.
        Parameters:
        al - Action listener (this frame)
        Returns:
        The animation toolbar
      • buildMenu

        private void buildMenu()
        This method builds a menu which contains the option Close 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 javax.swing.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.