Package gov.nih.mipav.view.dialogs

Class JDialogN4MRIBiasFieldCorrection

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.JDialogN4MRIBiasFieldCorrection
All Implemented Interfaces:
AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, ActionDiscovery, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants
public class JDialogN4MRIBiasFieldCorrection extends JDialogScriptableBase implements AlgorithmInterface, ActionDiscovery
Dialog to get user input, then call the algorithm.
See Also:

  • Field Details

    • autoThreshold

      private boolean autoThreshold
      DOCUMENT ME!

    • autoThresholdCheckbox

      private JCheckBox autoThresholdCheckbox
      DOCUMENT ME!

    • convertTomm

      private float convertTomm
      DOCUMENT ME!

    • createField

      private boolean createField
      DOCUMENT ME!

    • createFieldCheckbox

      private JCheckBox createFieldCheckbox
      DOCUMENT ME!

    • destExtents

      private int[] destExtents
      DOCUMENT ME!

    • endTol

      private double endTol
      DOCUMENT ME!

    • fieldDistance

      private float fieldDistance
      DOCUMENT ME!

    • fieldImage

      private ModelImage fieldImage
      DOCUMENT ME!

    • image

      private ModelImage image
      DOCUMENT ME!

    • kernelfwhm

      private double kernelfwhm
      DOCUMENT ME!

    • labelDistance

      private JLabel labelDistance
      DOCUMENT ME!

    • labelEndTol

      private JLabel labelEndTol
      DOCUMENT ME!

    • labelKernel

      private JLabel labelKernel
      DOCUMENT ME!

    • labelMaxIter

      private JLabel labelMaxIter
      DOCUMENT ME!

    • labelNoise

      private JLabel labelNoise
      DOCUMENT ME!

    • labelShrink

      private JLabel labelShrink
      DOCUMENT ME!

    • labelSignal

      private JLabel labelSignal
      DOCUMENT ME!

    • labelFittingLevels

      private JLabel labelFittingLevels

    • labelControlPoints

      private JLabel labelControlPoints

    • maxIter

      private int maxIter
      DOCUMENT ME!

    • N4Algo

      private AlgorithmN4MRIBiasFieldCorrectionFilter N4Algo
      DOCUMENT ME!

    • noise

      private double noise
      DOCUMENT ME!

    • orgResol

      private float[] orgResol
      DOCUMENT ME!

    • regionFlag

      private boolean regionFlag
      DOCUMENT ME!

    • resultImage

      private ModelImage resultImage
      DOCUMENT ME!

    • resXUnit

      private int resXUnit
      DOCUMENT ME!

    • resYUnit

      private int resYUnit
      DOCUMENT ME!

    • resZUnit

      private int resZUnit
      DOCUMENT ME!

    • shrink

      private float shrink
      DOCUMENT ME!

    • textDistance

      private JTextField textDistance
      DOCUMENT ME!

    • textEndTol

      private JTextField textEndTol
      DOCUMENT ME!

    • textKernel

      private JTextField textKernel
      DOCUMENT ME!

    • textMaxIter

      private JTextField textMaxIter
      DOCUMENT ME!

    • textNoise

      private JTextField textNoise
      DOCUMENT ME!

    • textShrink

      private JTextField textShrink
      DOCUMENT ME!

    • textSignal

      private JTextField textSignal
      DOCUMENT ME!

    • textFittingLevels

      private JTextField textFittingLevels

    • textControlPoints

      private JTextField textControlPoints

    • fittingLevels

      private int fittingLevels

    • controlPoints

      private int controlPoints

    • threshold

      private float threshold
      DOCUMENT ME!

    • confidenceImage

      private ModelImage confidenceImage

    • useScript

      private boolean useScript
      DOCUMENT ME!

    • VOIRegions

      private JRadioButton VOIRegions
      DOCUMENT ME!

    • wholeImage

      private JRadioButton wholeImage
      DOCUMENT ME!

  • Constructor Details

    • JDialogN4MRIBiasFieldCorrection

      public JDialogN4MRIBiasFieldCorrection()
      Empty constructor needed for dynamic instantiation (used during scripting).

    • JDialogN4MRIBiasFieldCorrection

      public JDialogN4MRIBiasFieldCorrection(Frame theParentFrame, ModelImage im)
      Create new dialog to set parameters for N4 MRI Bias Field Correction algorithm.
      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 algorithms 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.

    • setAutoFlag

      public void setAutoFlag(boolean flag)
      Accessor that sets the auto threshold flag.
      Parameters:
      flag - true indicates auto threshold, false otherwise.

    • setCreateField

      public void setCreateField(boolean flag)
      Accessor that sets the create field flag.
      Parameters:
      flag - true indicates create field image, false otherwise.

    • setEndTol

      public void setEndTol(double scale)
      Accessor that sets the end tol.
      Parameters:
      scale - Value to set end tol to.

    • setFieldDistance

      public void setFieldDistance(float scale)
      Accessor that sets the field distance.
      Parameters:
      scale - Value to set field distance to.

    • setKernel

      public void setKernel(double scale)
      Accessor that sets the kernel.
      Parameters:
      scale - Value to set kernel to.

    • setMaxIter

      public void setMaxIter(int max)
      Accessor that sets the max iterations.
      Parameters:
      max - The max iterations

    • setNoise

      public void setNoise(double scale)
      Accessor that sets the noise.
      Parameters:
      scale - Value to set noise to.

    • setFittingLevels

      public void setFittingLevels(int fittingLevels)
      Parameters:
      fittingLevels -

    • setControlPoints

      public void setControlPoints(int controlPoints)
      Parameters:
      controlPoints -

    • setRegionFlag

      public void setRegionFlag(boolean flag)
      Accessor that sets the region flag.
      Parameters:
      flag - true indicates the whole image is blurred, false indicates a region.

    • setShrink

      public void setShrink(float scale)
      Accessor that sets the shrink.
      Parameters:
      scale - Value to set shrink to.

    • setThreshold

      public void setThreshold(float scale)
      Accessor that sets the threshold.
      Parameters:
      scale - Value to set the threshold to.

    • callAlgorithm

      protected void callAlgorithm()
      Once all the necessary variables are set, call the N4 MRI Bias Field Correction algorithm.
      Specified by:
      callAlgorithm in class JDialogScriptableBase

    • doPostAlgorithmActions

      protected void doPostAlgorithmActions()
      Store the result image in the script runner's image table now that the action execution is finished.
      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.

    • init

      private void init()
      Sets up the GUI (panels, buttons, etc) and displays it on the screen.

    • initVars

      private void initVars()
      Initializes the variables (resolutions) needed for the algorithm.

    • 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.

    • getActionMetadata

      public ActionMetadata getActionMetadata()
      Return meta-information about this discoverable action for categorization and labeling purposes.
      Specified by:
      getActionMetadata in interface ActionDiscovery
      Returns:
      Metadata for this action.

    • createInputParameters

      public ParameterTable createInputParameters()
      Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in setGUIFromParams()).
      Specified by:
      createInputParameters in interface ActionDiscovery
      Returns:
      A parameter table listing the inputs of this algorithm.

    • createOutputParameters

      public ParameterTable createOutputParameters()
      Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
      Specified by:
      createOutputParameters in interface ActionDiscovery
      Returns:
      A parameter table listing the outputs of this algorithm.

    • getOutputImageName

      public String getOutputImageName(String imageParamName)
      Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).
      Specified by:
      getOutputImageName in interface ActionDiscovery
      Parameters:
      imageParamName - The output image parameter label for which to get the image name.
      Returns:
      The image name of the requested output image parameter label.

    • isActionComplete

      public boolean isActionComplete()
      Returns whether the action has successfully completed its execution.
      Specified by:
      isActionComplete in interface ActionDiscovery
      Returns:
      True, if the action is complete. False, if the action failed or is still running.