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.JDialogColocalizationEM

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 JDialogColocalizationEM
extends JDialogScriptableBase
implements AlgorithmInterface
```
Dialog to get user input 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 javax.swing.JRadioButton`	`andButton`	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 AlgorithmColocalizationEM`	`colocalizationAlgo`	DOCUMENT ME!
`private int`	`colorsPresent`	DOCUMENT ME!
`private javax.swing.JComboBox`	`comboBoxCostFunct`	DOCUMENT ME!
`private int`	`cost`	DOCUMENT ME!
`private boolean`	`doOr`	DOCUMENT ME!
`private boolean`	`entireImage`	DOCUMENT ME!
`private ModelImage`	`firstImage`	DOCUMENT ME!
`private javax.swing.JLabel`	`gaussianLabel`	DOCUMENT ME!
`private int`	`gaussians`	DOCUMENT ME!
`private javax.swing.JTextField`	`gaussianText`	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`	`iterationLabel`	DOCUMENT ME!
`private int`	`iterations`	DOCUMENT ME!
`private javax.swing.JTextField`	`iterationText`	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 double`	`maxB`	DOCUMENT ME!
`private double`	`maxBV`	DOCUMENT ME!
`private double`	`maxG`	DOCUMENT ME!
`private double`	`maxGV`	DOCUMENT ME!
`private double`	`maxR`	DOCUMENT ME!
`private double`	`maxRV`	DOCUMENT ME!
`private double`	`maxV`	DOCUMENT ME!
`private double`	`minB`	DOCUMENT ME!
`private double`	`minBV`	DOCUMENT ME!
`private double`	`minG`	DOCUMENT ME!
`private double`	`minGV`	DOCUMENT ME!
`private double`	`minR`	DOCUMENT ME!
`private double`	`minRV`	DOCUMENT ME!
`private double`	`minV`	DOCUMENT ME!
`private int`	`nBoundingVOIs`	DOCUMENT ME!
`private javax.swing.JRadioButton`	`orButton`	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 double`	`secondMaxV`	DOCUMENT ME!
`private double`	`secondMinV`	DOCUMENT ME!
`private java.lang.String`	`secondName`	DOCUMENT ME!
`private ModelImage`	`segImage`	Class segmentation shown.
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private float`	`threshold1`	DOCUMENT ME!
`private javax.swing.JLabel`	`threshold1Label`	DOCUMENT ME!
`private javax.swing.JTextField`	`threshold1Text`	DOCUMENT ME!
`private float`	`threshold2`	DOCUMENT ME!
`private javax.swing.JLabel`	`threshold2Label`	DOCUMENT ME!
`private javax.swing.JTextField`	`threshold2Text`	DOCUMENT ME!
`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.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
`JDialogColocalizationEM()`	Empty constructor needed for dynamic instantiation (used during scripting).
`JDialogColocalizationEM(ModelImage firstImage)`	Creates a new JDialogColocalizationEM object.
`JDialogColocalizationEM(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.
`ModelImage`	`getSegImage()`	Accessor that returns the image.
`private void`	`init()`	Initializes GUI components and displays dialog.
`void`	`itemStateChanged(java.awt.event.ItemEvent event)`	itemStateChanged.
`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`	`setDoOr(boolean doOr)`	DOCUMENT ME!
`void`	`setEntireImage(boolean entireImage)`	DOCUMENT ME!
`void`	`setGaussians(int gaussians)`	DOCUMENT ME!
`protected void`	`setGUIFromParams()`	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
`void`	`setIterations(int iterations)`	DOCUMENT ME!
`void`	`setLeftPad(int leftPad)`	DOCUMENT ME!
`void`	`setRegister(boolean register)`	DOCUMENT ME!
`void`	`setRightPad(int rightPad)`	DOCUMENT ME!
`void`	`setSecondImage(ModelImage secondImage)`	DOCUMENT ME!
`void`	`setThreshold1(float threshold1)`	DOCUMENT ME!
`void`	`setThreshold2(float threshold2)`	DOCUMENT ME!
`void`	`setTopPad(int topPad)`	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.

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, windowClosing, 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
  - andButton
```
private javax.swing.JRadioButton andButton
```
    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 AlgorithmColocalizationEM colocalizationAlgo
```
    DOCUMENT ME!
  - colorsPresent
```
private int colorsPresent
```
    DOCUMENT ME!
  - comboBoxCostFunct
```
private javax.swing.JComboBox comboBoxCostFunct
```
    DOCUMENT ME!
  - cost
```
private int cost
```
    DOCUMENT ME!
  - doOr
```
private boolean doOr
```
    DOCUMENT ME!
  - entireImage
```
private boolean entireImage
```
    DOCUMENT ME!
  - firstImage
```
private ModelImage firstImage
```
    DOCUMENT ME!
  - gaussianLabel
```
private javax.swing.JLabel gaussianLabel
```
    DOCUMENT ME!
  - gaussians
```
private int gaussians
```
    DOCUMENT ME!
  - gaussianText
```
private javax.swing.JTextField gaussianText
```
    DOCUMENT ME!
  - greenCheckBox
```
private javax.swing.JCheckBox greenCheckBox
```
    DOCUMENT ME!
  - imageComboBox
```
private javax.swing.JComboBox imageComboBox
```
    DOCUMENT ME!
  - imageLength
```
private int imageLength
```
    DOCUMENT ME!
  - iterationLabel
```
private javax.swing.JLabel iterationLabel
```
    DOCUMENT ME!
  - iterations
```
private int iterations
```
    DOCUMENT ME!
  - iterationText
```
private javax.swing.JTextField iterationText
```
    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!
  - maxR
```
private double maxR
```
    DOCUMENT ME!
  - maxG
```
private double maxG
```
    DOCUMENT ME!
  - maxB
```
private double maxB
```
    DOCUMENT ME!
  - maxRV
```
private double maxRV
```
    DOCUMENT ME!
  - maxGV
```
private double maxGV
```
    DOCUMENT ME!
  - maxBV
```
private double maxBV
```
    DOCUMENT ME!
  - minR
```
private double minR
```
    DOCUMENT ME!
  - minG
```
private double minG
```
    DOCUMENT ME!
  - minB
```
private double minB
```
    DOCUMENT ME!
  - minRV
```
private double minRV
```
    DOCUMENT ME!
  - minGV
```
private double minGV
```
    DOCUMENT ME!
  - minBV
```
private double minBV
```
    DOCUMENT ME!
  - minV
```
private double minV
```
    DOCUMENT ME!
  - maxV
```
private double maxV
```
    DOCUMENT ME!
  - nBoundingVOIs
```
private int nBoundingVOIs
```
    DOCUMENT ME!
  - orButton
```
private javax.swing.JRadioButton orButton
```
    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!
  - secondMinV
```
private double secondMinV
```
    DOCUMENT ME!
  - secondMaxV
```
private double secondMaxV
```
    DOCUMENT ME!
  - secondName
```
private java.lang.String secondName
```
    DOCUMENT ME!
  - segImage
```
private ModelImage segImage
```
    Class segmentation shown.
  - threshold1
```
private float threshold1
```
    DOCUMENT ME!
  - threshold1Label
```
private javax.swing.JLabel threshold1Label
```
    DOCUMENT ME!
  - threshold1Text
```
private javax.swing.JTextField threshold1Text
```
    DOCUMENT ME!
  - threshold2
```
private float threshold2
```
    DOCUMENT ME!
  - threshold2Label
```
private javax.swing.JLabel threshold2Label
```
    DOCUMENT ME!
  - threshold2Text
```
private javax.swing.JTextField threshold2Text
```
    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!
  - 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
  - JDialogColocalizationEM
```
public JDialogColocalizationEM()
```
    Empty constructor needed for dynamic instantiation (used during scripting).
  - JDialogColocalizationEM
```
public JDialogColocalizationEM(ModelImage firstImage)
```
    Creates a new JDialogColocalizationEM object.
    
    Parameters:
    
    firstImage - DOCUMENT ME!
  - JDialogColocalizationEM
```
public JDialogColocalizationEM(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.
  - getSegImage
```
public ModelImage getSegImage()
```
    Accessor that returns the image.
    
    Returns:
    
    The segmented 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!
  - 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!
  - setDoOr
```
public void setDoOr(boolean doOr)
```
    DOCUMENT ME!
    
    Parameters:
    
    doOr - DOCUMENT ME!
  - setEntireImage
```
public void setEntireImage(boolean entireImage)
```
    DOCUMENT ME!
    
    Parameters:
    
    entireImage - DOCUMENT ME!
  - setGaussians
```
public void setGaussians(int gaussians)
```
    DOCUMENT ME!
    
    Parameters:
    
    gaussians - DOCUMENT ME!
  - setIterations
```
public void setIterations(int iterations)
```
    DOCUMENT ME!
    
    Parameters:
    
    iterations - DOCUMENT ME!
  - setLeftPad
```
public void setLeftPad(int leftPad)
```
    DOCUMENT ME!
    
    Parameters:
    
    leftPad - 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!
  - setThreshold1
```
public void setThreshold1(float threshold1)
```
    DOCUMENT ME!
    
    Parameters:
    
    threshold1 - DOCUMENT ME!
  - setThreshold2
```
public void setThreshold2(float threshold2)
```
    DOCUMENT ME!
    
    Parameters:
    
    threshold2 - DOCUMENT ME!
  - setTopPad
```
public void setTopPad(int topPad)
```
    DOCUMENT ME!
    
    Parameters:
    
    topPad - 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!
  - 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.
  - 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 JDialogColocalizationEM

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

andButton

bin1

bin1Label

bin1Text

bin2

bin2Label

bin2Text

blueCheckBox

bottomPad

buffer

colocalizationAlgo

colorsPresent

comboBoxCostFunct

cost

doOr

entireImage

firstImage

gaussianLabel

gaussians

gaussianText

greenCheckBox

imageComboBox

imageLength

iterationLabel

iterations

iterationText

labelCost

labelImage

leftPad

mask

maxR

maxG

maxB

maxRV

maxGV

maxBV

minR

minG

minB

minRV

minGV

minBV

minV

maxV

nBoundingVOIs

orButton

possibleInt2Values

possibleIntValues

redCheckBox

regCheckBox

register

resultImage