java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Dialog
      - javax.swing.JDialog
        
        gov.nih.mipav.view.dialogs.JDialogBase
        
        gov.nih.mipav.view.dialogs.JDialogScriptableBase
        
        gov.nih.mipav.view.dialogs.JDialogColocalizationRegression

All Implemented Interfaces:

AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, java.awt.event.ActionListener, java.awt.event.FocusListener, 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.RootPaneContainer, javax.swing.WindowConstants
```
public class JDialogColocalizationRegression
extends JDialogScriptableBase
implements AlgorithmInterface
```
Dialog to get user input Calculate Pearson's correlation coefficient Calculate P value for this correlation coefficient Identify colocalized pixels Algorithms are executed in their own thread.

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase
  JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction
- Nested classes/interfaces inherited from class javax.swing.JDialog
  javax.swing.JDialog.AccessibleJDialog
- Nested classes/interfaces inherited from class java.awt.Dialog
  java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType
- Nested classes/interfaces inherited from class java.awt.Window
  java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  java.awt.Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field	Description
`private float`	`background1`	DOCUMENT ME!
`private float`	`background2`	DOCUMENT ME!
`private int`	`bin1`	DOCUMENT ME!
`private javax.swing.JLabel`	`bin1Label`	DOCUMENT ME!
`private javax.swing.JTextField`	`bin1Text`	DOCUMENT ME!
`private int`	`bin2`	DOCUMENT ME!
`private javax.swing.JLabel`	`bin2Label`	DOCUMENT ME!
`private javax.swing.JTextField`	`bin2Text`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`blueCheckBox`	DOCUMENT ME!
`private int`	`bottomPad`	DOCUMENT ME!
`private float[]`	`buffer`	DOCUMENT ME!
`private AlgorithmColocalizationRegression`	`colocalizationAlgo`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`colocCheckBox`	DOCUMENT ME!
`private int`	`colorsPresent`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxCostFunct`	DOCUMENT ME!
`private ViewJComponentEditImage`	`componentImage1`	DOCUMENT ME!
`private ViewJComponentEditImage`	`componentImage2`	DOCUMENT ME!
`private int`	`cost`	DOCUMENT ME!
`private boolean`	`doColocWithThresholds`	DOCUMENT ME!
`private boolean`	`doSecondIteration`	DOCUMENT ME!
`private boolean`	`doVOISubtraction`	DOCUMENT ME!
`private boolean`	`entireImage`	DOCUMENT ME!
`private ModelImage`	`firstImage`	DOCUMENT ME!
`private java.lang.String`	`firstName`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`greenCheckBox`	DOCUMENT ME!
`private javax.swing.JComboBox`	`imageComboBox`	DOCUMENT ME!
`private int`	`imageLength`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelCost`	DOCUMENT ME!
`private javax.swing.JLabel`	`labelImage`	DOCUMENT ME!
`private int`	`leftPad`	DOCUMENT ME!
`private java.util.BitSet`	`mask`	DOCUMENT ME!
`private javax.swing.JButton`	`maskButton`	DOCUMENT ME!
`private java.lang.String`	`maskFileDir`	DOCUMENT ME!
`private java.lang.String`	`maskFileName`	DOCUMENT ME!
`private ModelImage`	`maskImage`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`maskRadio`	DOCUMENT ME!
`private javax.swing.JTextField`	`maskText`	DOCUMENT ME!
`private double`	`maxB`	DOCUMENT ME!
`private double`	`maxG`	DOCUMENT ME!
`private double`	`maxR`	DOCUMENT ME!
`private double`	`minB`	DOCUMENT ME!
`private double`	`minG`	DOCUMENT ME!
`private double`	`minR`	DOCUMENT ME!
`private int`	`nBoundingVOIs`	DOCUMENT ME!
`(package private) float`	`point1`	DOCUMENT ME!
`private javax.swing.JLabel`	`point1Label`	DOCUMENT ME!
`private javax.swing.JTextField`	`point1Text`	DOCUMENT ME!
`(package private) float`	`point2`	DOCUMENT ME!
`private javax.swing.JLabel`	`point2Label`	DOCUMENT ME!
`private javax.swing.JTextField`	`point2Text`	DOCUMENT ME!
`private boolean`	`pointCalculation`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`pointCheckBox`	DOCUMENT ME!
`private double`	`possibleInt2Values`	DOCUMENT ME!
`private double`	`possibleIntValues`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`redCheckBox`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`regCheckBox`	DOCUMENT ME!
`private boolean`	`register`	DOCUMENT ME!
`private ModelImage`	`resultImage`	DOCUMENT ME!
`private int`	`rightPad`	DOCUMENT ME!
`private ModelImage`	`secondImage`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`secondIterationCheckBox`	DOCUMENT ME!
`private java.lang.String`	`secondName`	DOCUMENT ME!
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private int`	`topPad`	DOCUMENT ME!
`private ViewUserInterface`	`UI`	DOCUMENT ME!
`private boolean`	`useBlue`	DOCUMENT ME!
`private boolean`	`useGreen`	DOCUMENT ME!
`private boolean`	`useRed`	DOCUMENT ME!
`private javax.swing.JCheckBox`	`VOICheckBox`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`VOIRegions`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`wholeImage`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private int`	`zDim`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase
displayInNewFrame, isComplete, scriptParameters

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase
applyButton, bar, cancelButton, cancelFlag, closeButton, HELP, helpButton, mainDialogPanel, NEW, OKButton, parentFrame, progressBar, REPLACE, runInSeparateThread, runningScriptFlag, runQuiet, serif12, serif12B, voiManager

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

Fields inherited from class java.awt.Dialog
DEFAULT_MODALITY_TYPE

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
`JDialogColocalizationRegression()`	Empty constructor needed for dynamic instantiation (used during scripting).
`JDialogColocalizationRegression(ModelImage firstImage)`	Creates a new JDialogColocalizationRegression object.
`JDialogColocalizationRegression(java.awt.Frame theParentFrame, ModelImage im)`	Creates new dialog.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Closes dialog box when the OK button is pressed and calls the algorithm.
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	This method is required if the AlgorithmPerformed interface is implemented.
`private javax.swing.JComboBox`	`buildComboBox(ModelImage image)`	Builds a list of images.
`protected void`	`callAlgorithm()`	DOCUMENT ME!
`protected void`	`doPostAlgorithmActions()`	Used to perform actions after the execution of the algorithm is completed (e.g., put the result image in the image table).
`ModelImage`	`getResultImage()`	Accessor that returns the image.
`private void`	`init()`	Initializes GUI components and displays dialog.
`void`	`itemStateChanged(java.awt.event.ItemEvent event)`	itemStateChanged.
`void`	`setBackground1(float background1)`	DOCUMENT ME!
`void`	`setBackground2(float background2)`	DOCUMENT ME!
`void`	`setBin1(int bin1)`	DOCUMENT ME!
`void`	`setBin2(int bin2)`	DOCUMENT ME!
`void`	`setBottomPad(int bottomPad)`	DOCUMENT ME!
`void`	`setCost(int cost)`	DOCUMENT ME!
`void`	`setDoColocWithThresholds(boolean doColocWithThresholds)`	DOCUMENT ME!
`void`	`setDoSecondIteration(boolean doSecondIteration)`	DOCUMENT ME!
`void`	`setDoVOISubtraction(boolean doVOISubtraction)`	DOCUMENT ME!
`void`	`setEntireImage(boolean entireImage)`	DOCUMENT ME!
`protected void`	`setGUIFromParams()`	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
`void`	`setLeftPad(int leftPad)`	DOCUMENT ME!
`void`	`setPoint1(float point1)`	DOCUMENT ME!
`void`	`setPoint2(float point2)`	DOCUMENT ME!
`void`	`setPointCalculation(boolean pointCalculation)`	DOCUMENT ME!
`void`	`setRegister(boolean register)`	DOCUMENT ME!
`void`	`setRightPad(int rightPad)`	DOCUMENT ME!
`void`	`setSecondImage(ModelImage secondImage)`	DOCUMENT ME!
`void`	`setTopPad(int topPad)`	DOCUMENT ME!
`private boolean`	`setupMask()`	DOCUMENT ME!
`boolean`	`setupMaskImage(ModelImage im)`	DOCUMENT ME!
`void`	`setUseBlue(boolean useBlue)`	DOCUMENT ME!
`void`	`setUseGreen(boolean useGreen)`	DOCUMENT ME!
`void`	`setUseRed(boolean useRed)`	DOCUMENT ME!
`private boolean`	`setVariables()`	Use the GUI results to set up the variables needed to run the algorithm.
`protected void`	`storeParamsFromGUI()`	Record the parameters just used to run this algorithm in a script.
`void`	`windowClosing(java.awt.event.WindowEvent event)`	Disposes of error dialog, then frame.

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase
getDialogActionString, insertScriptLine, isComplete, scriptRun, setComplete

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase
buildApplyButton, buildButtons, buildCancelButton, buildCancelButton, buildCloseButton, buildHelpButton, buildImageComboBox, buildOKButton, buildOKButton, buildOKCancelButtons, buildTitledBorder, buildTitledBorder, createLabel, createProgressBar, createProgressBar, createTextField, focusGained, focusLost, getDialogName, isCancelled, isQuietRunning, isRunInSeparateThread, isScriptRunning, loadDefaults, loadDefaults, makeImageName, makeString, openNewFrame, saveDefaults, saveDefaults, setLeftHandSystem, setQuietRunning, setScriptRunning, setSeparateThread, setVisible, setVisible, setVisibleMenuBar, setVisibleStandard, setVOIManager, setWCSystem, testParameter, testParameterMin, updateFFTFileInfo, updateFileInfo, updateFileInfoOtherModality, updateFileInfoStatic, updateFileInfoStatic, updateFileTypeInfo, updateFileTypeInfo, windowActivated, windowClosed, windowDeactivated, windowDeiconified, windowIconified, windowOpened

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

Methods inherited from class java.awt.Dialog
addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, 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, remove, 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, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

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

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - point1
```
float point1
```
    DOCUMENT ME!
  - point2
```
float point2
```
    DOCUMENT ME!
  - background1
```
private float background1
```
    DOCUMENT ME!
  - background2
```
private float background2
```
    DOCUMENT ME!
  - bin1
```
private int bin1
```
    DOCUMENT ME!
  - bin1Label
```
private javax.swing.JLabel bin1Label
```
    DOCUMENT ME!
  - bin1Text
```
private javax.swing.JTextField bin1Text
```
    DOCUMENT ME!
  - bin2
```
private int bin2
```
    DOCUMENT ME!
  - bin2Label
```
private javax.swing.JLabel bin2Label
```
    DOCUMENT ME!
  - bin2Text
```
private javax.swing.JTextField bin2Text
```
    DOCUMENT ME!
  - blueCheckBox
```
private javax.swing.JCheckBox blueCheckBox
```
    DOCUMENT ME!
  - bottomPad
```
private int bottomPad
```
    DOCUMENT ME!
  - buffer
```
private float[] buffer
```
    DOCUMENT ME!
  - colocalizationAlgo
```
private AlgorithmColocalizationRegression colocalizationAlgo
```
    DOCUMENT ME!
  - colocCheckBox
```
private javax.swing.JCheckBox colocCheckBox
```
    DOCUMENT ME!
  - colorsPresent
```
private int colorsPresent
```
    DOCUMENT ME!
  - comboBoxCostFunct
```
private javax.swing.JComboBox comboBoxCostFunct
```
    DOCUMENT ME!
  - componentImage1
```
private ViewJComponentEditImage componentImage1
```
    DOCUMENT ME!
  - componentImage2
```
private ViewJComponentEditImage componentImage2
```
    DOCUMENT ME!
  - cost
```
private int cost
```
    DOCUMENT ME!
  - doColocWithThresholds
```
private boolean doColocWithThresholds
```
    DOCUMENT ME!
  - doSecondIteration
```
private boolean doSecondIteration
```
    DOCUMENT ME!
  - doVOISubtraction
```
private boolean doVOISubtraction
```
    DOCUMENT ME!
  - entireImage
```
private boolean entireImage
```
    DOCUMENT ME!
  - firstImage
```
private ModelImage firstImage
```
    DOCUMENT ME!
  - firstName
```
private java.lang.String firstName
```
    DOCUMENT ME!
  - greenCheckBox
```
private javax.swing.JCheckBox greenCheckBox
```
    DOCUMENT ME!
  - imageComboBox
```
private javax.swing.JComboBox imageComboBox
```
    DOCUMENT ME!
  - imageLength
```
private int imageLength
```
    DOCUMENT ME!
  - labelCost
```
private javax.swing.JLabel labelCost
```
    DOCUMENT ME!
  - labelImage
```
private javax.swing.JLabel labelImage
```
    DOCUMENT ME!
  - leftPad
```
private int leftPad
```
    DOCUMENT ME!
  - mask
```
private java.util.BitSet mask
```
    DOCUMENT ME!
  - maskButton
```
private javax.swing.JButton maskButton
```
    DOCUMENT ME!
  - maskFileDir
```
private java.lang.String maskFileDir
```
    DOCUMENT ME!
  - maskFileName
```
private java.lang.String maskFileName
```
    DOCUMENT ME!
  - maskImage
```
private ModelImage maskImage
```
    DOCUMENT ME!
  - maskRadio
```
private javax.swing.JRadioButton maskRadio
```
    DOCUMENT ME!
  - maskText
```
private javax.swing.JTextField maskText
```
    DOCUMENT ME!
  - maxR
```
private double maxR
```
    DOCUMENT ME!
  - maxG
```
private double maxG
```
    DOCUMENT ME!
  - maxB
```
private double maxB
```
    DOCUMENT ME!
  - minR
```
private double minR
```
    DOCUMENT ME!
  - minG
```
private double minG
```
    DOCUMENT ME!
  - minB
```
private double minB
```
    DOCUMENT ME!
  - nBoundingVOIs
```
private int nBoundingVOIs
```
    DOCUMENT ME!
  - point1Label
```
private javax.swing.JLabel point1Label
```
    DOCUMENT ME!
  - point1Text
```
private javax.swing.JTextField point1Text
```
    DOCUMENT ME!
  - point2Label
```
private javax.swing.JLabel point2Label
```
    DOCUMENT ME!
  - point2Text
```
private javax.swing.JTextField point2Text
```
    DOCUMENT ME!
  - pointCalculation
```
private boolean pointCalculation
```
    DOCUMENT ME!
  - pointCheckBox
```
private javax.swing.JCheckBox pointCheckBox
```
    DOCUMENT ME!
  - possibleInt2Values
```
private double possibleInt2Values
```
    DOCUMENT ME!
  - possibleIntValues
```
private double possibleIntValues
```
    DOCUMENT ME!
  - redCheckBox
```
private javax.swing.JCheckBox redCheckBox
```
    DOCUMENT ME!
  - regCheckBox
```
private javax.swing.JCheckBox regCheckBox
```
    DOCUMENT ME!
  - register
```
private boolean register
```
    DOCUMENT ME!
  - resultImage
```
private ModelImage resultImage
```
    DOCUMENT ME!
  - rightPad
```
private int rightPad
```
    DOCUMENT ME!
  - secondImage
```
private ModelImage secondImage
```
    DOCUMENT ME!
  - secondIterationCheckBox
```
private javax.swing.JCheckBox secondIterationCheckBox
```
    DOCUMENT ME!
  - secondName
```
private java.lang.String secondName
```
    DOCUMENT ME!
  - topPad
```
private int topPad
```
    DOCUMENT ME!
  - UI
```
private ViewUserInterface UI
```
    DOCUMENT ME!
  - useBlue
```
private boolean useBlue
```
    DOCUMENT ME!
  - useGreen
```
private boolean useGreen
```
    DOCUMENT ME!
  - useRed
```
private boolean useRed
```
    DOCUMENT ME!
  - VOICheckBox
```
private javax.swing.JCheckBox VOICheckBox
```
    DOCUMENT ME!
  - VOIRegions
```
private javax.swing.JRadioButton VOIRegions
```
    DOCUMENT ME!
  - wholeImage
```
private javax.swing.JRadioButton wholeImage
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - zDim
```
private int zDim
```
    DOCUMENT ME!
- Constructor Detail
  - JDialogColocalizationRegression
```
public JDialogColocalizationRegression()
```
    Empty constructor needed for dynamic instantiation (used during scripting).
  - JDialogColocalizationRegression
```
public JDialogColocalizationRegression(ModelImage firstImage)
```
    Creates a new JDialogColocalizationRegression object.
    
    Parameters:
    
    firstImage - DOCUMENT ME!
  - JDialogColocalizationRegression
```
public JDialogColocalizationRegression(java.awt.Frame theParentFrame,
                                       ModelImage im)
```
    Creates new dialog.
    
    Parameters:
    
    theParentFrame - Parent frame
    
    im - Source image
- Method Detail
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Closes dialog box when the OK button is pressed and calls the algorithm.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Overrides:
    
    actionPerformed in class JDialogBase
    
    Parameters:
    
    event - Event that triggers function.
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    This method is required if the AlgorithmPerformed interface is implemented. It is called by the algorithm when it has completed or failed to to complete, so that the dialog can be display the result image and/or clean up.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - Algorithm that caused the event.
  - getResultImage
```
public ModelImage getResultImage()
```
    Accessor that returns the image.
    
    Returns:
    
    The result image.
  - itemStateChanged
```
public void itemStateChanged(java.awt.event.ItemEvent event)
```
    itemStateChanged.
    
    Specified by:
    
    itemStateChanged in interface java.awt.event.ItemListener
    
    Overrides:
    
    itemStateChanged in class JDialogBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - setBackground1
```
public void setBackground1(float background1)
```
    DOCUMENT ME!
    
    Parameters:
    
    background1 - DOCUMENT ME!
  - setBackground2
```
public void setBackground2(float background2)
```
    DOCUMENT ME!
    
    Parameters:
    
    background2 - DOCUMENT ME!
  - setBin1
```
public void setBin1(int bin1)
```
    DOCUMENT ME!
    
    Parameters:
    
    bin1 - DOCUMENT ME!
  - setBin2
```
public void setBin2(int bin2)
```
    DOCUMENT ME!
    
    Parameters:
    
    bin2 - DOCUMENT ME!
  - setBottomPad
```
public void setBottomPad(int bottomPad)
```
    DOCUMENT ME!
    
    Parameters:
    
    bottomPad - DOCUMENT ME!
  - setCost
```
public void setCost(int cost)
```
    DOCUMENT ME!
    
    Parameters:
    
    cost - DOCUMENT ME!
  - setDoColocWithThresholds
```
public void setDoColocWithThresholds(boolean doColocWithThresholds)
```
    DOCUMENT ME!
    
    Parameters:
    
    doColocWithThresholds - DOCUMENT ME!
  - setDoSecondIteration
```
public void setDoSecondIteration(boolean doSecondIteration)
```
    DOCUMENT ME!
    
    Parameters:
    
    doSecondIteration - DOCUMENT ME!
  - setDoVOISubtraction
```
public void setDoVOISubtraction(boolean doVOISubtraction)
```
    DOCUMENT ME!
    
    Parameters:
    
    doVOISubtraction - DOCUMENT ME!
  - setEntireImage
```
public void setEntireImage(boolean entireImage)
```
    DOCUMENT ME!
    
    Parameters:
    
    entireImage - DOCUMENT ME!
  - setLeftPad
```
public void setLeftPad(int leftPad)
```
    DOCUMENT ME!
    
    Parameters:
    
    leftPad - DOCUMENT ME!
  - setPoint1
```
public void setPoint1(float point1)
```
    DOCUMENT ME!
    
    Parameters:
    
    point1 - DOCUMENT ME!
  - setPoint2
```
public void setPoint2(float point2)
```
    DOCUMENT ME!
    
    Parameters:
    
    point2 - DOCUMENT ME!
  - setPointCalculation
```
public void setPointCalculation(boolean pointCalculation)
```
    DOCUMENT ME!
    
    Parameters:
    
    pointCalculation - DOCUMENT ME!
  - setRegister
```
public void setRegister(boolean register)
```
    DOCUMENT ME!
    
    Parameters:
    
    register - DOCUMENT ME!
  - setRightPad
```
public void setRightPad(int rightPad)
```
    DOCUMENT ME!
    
    Parameters:
    
    rightPad - DOCUMENT ME!
  - setSecondImage
```
public void setSecondImage(ModelImage secondImage)
```
    DOCUMENT ME!
    
    Parameters:
    
    secondImage - DOCUMENT ME!
  - setTopPad
```
public void setTopPad(int topPad)
```
    DOCUMENT ME!
    
    Parameters:
    
    topPad - DOCUMENT ME!
  - setupMaskImage
```
public boolean setupMaskImage(ModelImage im)
```
    DOCUMENT ME!
    
    Parameters:
    
    im - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - setUseBlue
```
public void setUseBlue(boolean useBlue)
```
    DOCUMENT ME!
    
    Parameters:
    
    useBlue - DOCUMENT ME!
  - setUseGreen
```
public void setUseGreen(boolean useGreen)
```
    DOCUMENT ME!
    
    Parameters:
    
    useGreen - DOCUMENT ME!
  - setUseRed
```
public void setUseRed(boolean useRed)
```
    DOCUMENT ME!
    
    Parameters:
    
    useRed - DOCUMENT ME!
  - windowClosing
```
public void windowClosing(java.awt.event.WindowEvent event)
```
    Disposes of error dialog, then frame. Sets cancelled to true.
    
    Specified by:
    
    windowClosing in interface java.awt.event.WindowListener
    
    Overrides:
    
    windowClosing in class JDialogBase
    
    Parameters:
    
    event - DOCUMENT ME!
  - callAlgorithm
```
protected void callAlgorithm()
```
    DOCUMENT ME!
    
    Specified by:
    
    callAlgorithm in class JDialogScriptableBase
  - doPostAlgorithmActions
```
protected void doPostAlgorithmActions()
```
    Used to perform actions after the execution of the algorithm is completed (e.g., put the result image in the image table). Defaults to no action, override to actually have it do something.
    
    Overrides:
    
    doPostAlgorithmActions in class JDialogScriptableBase
  - setGUIFromParams
```
protected void setGUIFromParams()
```
    Set the dialog GUI using the script parameters while running this algorithm as part of a script.
    
    Specified by:
    
    setGUIFromParams in class JDialogScriptableBase
  - storeParamsFromGUI
```
protected void storeParamsFromGUI()
                           throws ParserException
```
    Record the parameters just used to run this algorithm in a script.
    
    Specified by:
    
    storeParamsFromGUI in class JDialogScriptableBase
    
    Throws:
    
    ParserException - If there is a problem creating/recording the new parameters.
  - buildComboBox
```
private javax.swing.JComboBox buildComboBox(ModelImage image)
```
    Builds a list of images. Returns combobox. List must be all color or all black and white.
    
    Parameters:
    
    image - DOCUMENT ME!
    
    Returns:
    
    Newly created combo box.
  - init
```
private void init()
```
    Initializes GUI components and displays dialog.
  - setupMask
```
private boolean setupMask()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - setVariables
```
private boolean setVariables()
```
    Use the GUI results to set up the variables needed to run the algorithm.
    
    Returns:
    
    true if parameters set successfully, false otherwise.

Class JDialogColocalizationRegression

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase

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

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

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

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

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

Field Summary

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Fields inherited from class javax.swing.JDialog

Fields inherited from class java.awt.Dialog

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface javax.swing.WindowConstants

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Methods inherited from class javax.swing.JDialog

Methods inherited from class java.awt.Dialog

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

point1

point2

background1

background2

bin1

bin1Label

bin1Text

bin2

bin2Label

bin2Text

blueCheckBox

bottomPad

buffer

colocalizationAlgo

colocCheckBox

colorsPresent

comboBoxCostFunct

componentImage1

componentImage2

cost

doColocWithThresholds

doSecondIteration

doVOISubtraction

entireImage

firstImage

firstName

greenCheckBox

imageComboBox

imageLength

labelCost

labelImage

leftPad

mask

maskButton

maskFileDir

maskFileName

maskImage

maskRadio

maskText

maxR

maxG

maxB

minR

minG

minB

nBoundingVOIs

point1Label

point1Text

point2Label

point2Text

pointCalculation

pointCheckBox