Package gov.nih.mipav.view.dialogs

Class JDialogNLNoiseReduction

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.JDialogNLNoiseReduction
All Implemented Interfaces:
AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, ActionDiscovery, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants
public class JDialogNLNoiseReduction extends JDialogScriptableBase implements AlgorithmInterface, ActionDiscovery, ScriptableActionInterface
Dialog to get user input, then call the algorithm. The user has the option to generate a new image or replace the source image. The program called performs nonlinear noise reduction on 2D and 3D black and white images. It does this by only averaging a voxel with local voxels which have similar intensity. Algorithms are executed in their own thread.
See Also:

  • Field Details

    • serialVersionUID

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

    • bt

      private double bt
      DOCUMENT ME!

    • destinationGroup

      private ButtonGroup destinationGroup
      DOCUMENT ME!

    • destinationPanel

      private JPanel destinationPanel
      DOCUMENT ME!

    • displayLoc

      private int displayLoc
      DOCUMENT ME!

    • image

      private ModelImage image
      DOCUMENT ME!

    • image25D

      private boolean image25D
      DOCUMENT ME!

    • image25DCheckbox

      private JCheckBox image25DCheckbox
      of similar brightness voxels is empty, a local median filter is used. This allows the correction of impulse ("salt-and-pepper") noise. If false, when no neighborhood is found, the original intensity of the voxel of interest remains unchanged.

    • labelMaskSD

      private JLabel labelMaskSD
      DOCUMENT ME!

    • labelThreshold

      private JLabel labelThreshold
      DOCUMENT ME!

    • maskSD

      private float maskSD
      DOCUMENT ME!

    • maximumThresholdDouble

      private double maximumThresholdDouble
      DOCUMENT ME!

    • defaultThresholdDouble

      private double defaultThresholdDouble
      DOCUMENT ME!

    • medianCheckbox

      private JCheckBox medianCheckbox
      The mask is basically Gaussian with standard deviation in image units - e.g. mm set by the user. However, for a small, fast, flat response with a 3x3 or 3x3x3 voxel mask, set maskSD to 0.

    • minimumThreshold

      private long minimumThreshold
      DOCUMENT ME!

    • maximumThreshold

      private long maximumThreshold
      DOCUMENT ME!

    • defaultThreshold

      private long defaultThreshold
      DOCUMENT ME!

    • newImage

      private JRadioButton newImage
      DOCUMENT ME!

    • nlnrAlgo

      private AlgorithmNLNoiseReduction nlnrAlgo
      DOCUMENT ME!

    • optionsPanel

      private JPanel optionsPanel
      DOCUMENT ME!

    • replaceImage

      private JRadioButton replaceImage
      DOCUMENT ME!

    • resultImage

      private ModelImage resultImage
      DOCUMENT ME!

    • textMaskSD

      private JTextField textMaskSD
      discriminate between noise and the underlying image. Ideally, the value should be set greater than the noise level and less than the contrast of the underlying image. Edges of contrast smaller than this threshold will tend to be blurred whereas those of greater contrast will not be.

    • textThreshold

      private JTextField textThreshold
      DOCUMENT ME!

    • titles

      private String[] titles
      DOCUMENT ME!

    • useMedian

      private boolean useMedian
      DOCUMENT ME!

    • userInterface

      private ViewUserInterface userInterface
      DOCUMENT ME!

  • Constructor Details

    • JDialogNLNoiseReduction

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

    • JDialogNLNoiseReduction

      public JDialogNLNoiseReduction(Frame theParentFrame, ModelImage im)
      Creates a new JDialogNLNoiseReduction object.
      Parameters:
      theParentFrame - Parent frame.
      im - Source image.

  • Method Details

    • actionPerformed

      public void actionPerformed(ActionEvent event)
      Closes dialog box when the OK button is pressed, sets variables and calls 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.

    • setBt

      public void setBt(double bt)
      Accessor that sets the brightness threshold.
      Parameters:
      bt - the brightness threshold. (values between 0.0 and (image.getMax()-image.getMin())).

    • setDisplayLocNew

      public void setDisplayLocNew()
      Accessor that sets the display loc variable to new, so that a new image is created once the algorithm completes.

    • setDisplayLocReplace

      public void setDisplayLocReplace()
      Accessor that sets the display loc variable to replace, so the current image is replaced once the algorithm completes.

    • setImage25D

      public void setImage25D(boolean flag)
      Accessor that sets the slicing flag.
      Parameters:
      flag - true indicates slices should be blurred independently.

    • setMaskSD

      public void setMaskSD(float maskSD)
      Accessor that sets the mask standard deviation (in the same units as the image).
      Parameters:
      maskSD - the maskSD. (values between 0.0 and max float).

    • setUseMedian

      public void setUseMedian(boolean flag)
      Accessor that sets the useMedian flag.
      Parameters:
      flag - true indicates useMedian should be processed.

    • callAlgorithm

      protected void callAlgorithm()
      Once all the necessary variables are set, call the Gaussian Blur algorithm based on what type of image this is and whether or not there is a separate destination image.
      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()
      Initializes the GUI by creating the components, placing them in the dialog, and displaying them.

    • setDefaults

      private void setDefaults()
      Set the default values for the parameters.

    • 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.