Package gov.nih.mipav.view.dialogs

Class JDialogNLNoiseReduction

    • Nested Class Summary

      • 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

    • 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, sets variables and calls algorithm.
      void algorithmPerformed​(AlgorithmBase algorithm)
      This method is required if the AlgorithmPerformed interface is implemented.
      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.
      ParameterTable createInputParameters()
      Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in setGUIFromParams()).
      ParameterTable createOutputParameters()
      Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
      protected void doPostAlgorithmActions()
      Store the result image in the script runner's image table now that the action execution is finished.
      ActionMetadata getActionMetadata()
      Return meta-information about this discoverable action for categorization and labeling purposes.
      java.lang.String getOutputImageName​(java.lang.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).
      ModelImage getResultImage()
      Accessor that returns the image.
      private void init()
      Initializes the GUI by creating the components, placing them in the dialog, and displaying them.
      boolean isActionComplete()
      Returns whether the action has successfully completed its execution.
      void setBt​(double bt)
      Accessor that sets the brightness threshold.
      private void setDefaults()
      Set the default values for the parameters.
      void setDisplayLocNew()
      Accessor that sets the display loc variable to new, so that a new image is created once the algorithm completes.
      void setDisplayLocReplace()
      Accessor that sets the display loc variable to replace, so the current image is replaced once the algorithm completes.
      protected void setGUIFromParams()
      Set the dialog GUI using the script parameters while running this algorithm as part of a script.
      void setImage25D​(boolean flag)
      Accessor that sets the slicing flag.
      void setMaskSD​(float maskSD)
      Accessor that sets the mask standard deviation (in the same units as the image).
      void setUseMedian​(boolean flag)
      Accessor that sets the useMedian flag.
      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 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

      • bt

        private double bt
        DOCUMENT ME!

      • destinationGroup

        private javax.swing.ButtonGroup destinationGroup
        DOCUMENT ME!

      • destinationPanel

        private javax.swing.JPanel destinationPanel
        DOCUMENT ME!

      • displayLoc

        private int displayLoc
        DOCUMENT ME!

      • image25D

        private boolean image25D
        DOCUMENT ME!

      • image25DCheckbox

        private javax.swing.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 javax.swing.JLabel labelMaskSD
        DOCUMENT ME!

      • labelThreshold

        private javax.swing.JLabel labelThreshold
        DOCUMENT ME!

      • maskSD

        private float maskSD
        DOCUMENT ME!

      • maximumThresholdDouble

        private double maximumThresholdDouble
        DOCUMENT ME!

      • defaultThresholdDouble

        private double defaultThresholdDouble
        DOCUMENT ME!

      • medianCheckbox

        private javax.swing.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 javax.swing.JRadioButton newImage
        DOCUMENT ME!

      • optionsPanel

        private javax.swing.JPanel optionsPanel
        DOCUMENT ME!

      • replaceImage

        private javax.swing.JRadioButton replaceImage
        DOCUMENT ME!

      • resultImage

        private ModelImage resultImage
        DOCUMENT ME!

      • textMaskSD

        private javax.swing.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 javax.swing.JTextField textThreshold
        DOCUMENT ME!

      • titles

        private java.lang.String[] titles
        DOCUMENT ME!

      • useMedian

        private boolean useMedian
        DOCUMENT ME!

    • Constructor Detail

      • JDialogNLNoiseReduction

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

      • JDialogNLNoiseReduction

        public JDialogNLNoiseReduction​(java.awt.Frame theParentFrame,
                               ModelImage im)
        Creates a new JDialogNLNoiseReduction object.
        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, sets variables and calls 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 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

      • 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 java.lang.String getOutputImageName​(java.lang.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.