Package gov.nih.mipav.view.dialogs

Class JDialogColocalizationRegression

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, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, 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:

  • Field Details

    • serialVersionUID

      private static final long serialVersionUID
      Use serialVersionUID for interoperability.
      See Also:

    • 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 JLabel bin1Label
      DOCUMENT ME!

    • bin1Text

      private JTextField bin1Text
      DOCUMENT ME!

    • bin2

      private int bin2
      DOCUMENT ME!

    • bin2Label

      private JLabel bin2Label
      DOCUMENT ME!

    • bin2Text

      private JTextField bin2Text
      DOCUMENT ME!

    • blueCheckBox

      private JCheckBox blueCheckBox
      DOCUMENT ME!

    • bottomPad

      private int bottomPad
      DOCUMENT ME!

    • buffer

      private float[] buffer
      DOCUMENT ME!

    • colocalizationAlgo

      private AlgorithmColocalizationRegression colocalizationAlgo
      DOCUMENT ME!

    • colocCheckBox

      private JCheckBox colocCheckBox
      DOCUMENT ME!

    • colorsPresent

      private int colorsPresent
      DOCUMENT ME!

    • comboBoxCostFunct

      private 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 String firstName
      DOCUMENT ME!

    • greenCheckBox

      private JCheckBox greenCheckBox
      DOCUMENT ME!

    • imageComboBox

      private JComboBox imageComboBox
      DOCUMENT ME!

    • imageLength

      private int imageLength
      DOCUMENT ME!

    • labelCost

      private JLabel labelCost
      DOCUMENT ME!

    • labelImage

      private JLabel labelImage
      DOCUMENT ME!

    • leftPad

      private int leftPad
      DOCUMENT ME!

    • mask

      private BitSet mask
      DOCUMENT ME!

    • maskButton

      private JButton maskButton
      DOCUMENT ME!

    • maskFileDir

      private String maskFileDir
      DOCUMENT ME!

    • maskFileName

      private String maskFileName
      DOCUMENT ME!

    • maskImage

      private ModelImage maskImage
      DOCUMENT ME!

    • maskRadio

      private JRadioButton maskRadio
      DOCUMENT ME!

    • maskText

      private 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 JLabel point1Label
      DOCUMENT ME!

    • point1Text

      private JTextField point1Text
      DOCUMENT ME!

    • point2Label

      private JLabel point2Label
      DOCUMENT ME!

    • point2Text

      private JTextField point2Text
      DOCUMENT ME!

    • pointCalculation

      private boolean pointCalculation
      DOCUMENT ME!

    • pointCheckBox

      private JCheckBox pointCheckBox
      DOCUMENT ME!

    • possibleInt2Values

      private double possibleInt2Values
      DOCUMENT ME!

    • possibleIntValues

      private double possibleIntValues
      DOCUMENT ME!

    • redCheckBox

      private JCheckBox redCheckBox
      DOCUMENT ME!

    • regCheckBox

      private 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 JCheckBox secondIterationCheckBox
      DOCUMENT ME!

    • secondName

      private 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 JCheckBox VOICheckBox
      DOCUMENT ME!

    • VOIRegions

      private JRadioButton VOIRegions
      DOCUMENT ME!

    • wholeImage

      private JRadioButton wholeImage
      DOCUMENT ME!

    • xDim

      private int xDim
      DOCUMENT ME!

    • yDim

      private int yDim
      DOCUMENT ME!

    • zDim

      private int zDim
      DOCUMENT ME!

  • Constructor Details

    • 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(Frame theParentFrame, ModelImage im)
      Creates new dialog.
      Parameters:
      theParentFrame - Parent frame
      im - Source image

  • Method Details

    • actionPerformed

      public void actionPerformed(ActionEvent event)
      Closes dialog box when the OK button is pressed and calls the algorithm.
      Specified by:
      actionPerformed in interface 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(ItemEvent event)
      itemStateChanged.
      Specified by:
      itemStateChanged in interface 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(WindowEvent event)
      Disposes of error dialog, then frame. Sets cancelled to true.
      Specified by:
      windowClosing in interface 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 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.