Package gov.nih.mipav.view.renderer.WildMagic.ProstateFramework

Class JDialogProstateExtractCEFeature

  • All Implemented Interfaces:
    AlgorithmInterface, 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 JDialogProstateExtractCEFeature
extends JDialogBase
implements AlgorithmInterface
    After the 3D images convert to 2D slices ( 512x512 ), this class picks the 2D slices, extracts the Coherence Enhanced diffusion based features, and saves those features with linear SVM readable file formats. User specifies the 2D slices saved directory as input, and the same directory as the output. The class automatically apply the following steps, 1) picks those slices, cropped region according to central prostate gland. 2) apply Coherence Enhanced filter to each cropped slice. 3) Save the Hurst index and Haralick features of each 2D slice to corresponding directory. Those saved CE features will be used to create linear SVM models. Also, for test cases, this class functions as the pre-processing steps to save CE features before automatic segmentation.
    Author:
    Ruida Cheng
    See Also:
    Serialized Form

    • 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)
      Action performed handler for this dialog.
      void algorithmPerformed​(AlgorithmBase algorithm)
      This method is required if the AlgorithmPerformed interface is implemented.
      void buildKeyImagePanel()
      Build the panel.
      private void calculateCoherenceEnhancingDiffusion()
      From the cropped images, apply Coherence Enhanced Diffusion filter to each 2D slices.
      private void calculateNumberFeatures()
      Calculate number of features being saved.
      void callAlgorithm()
      Driver to do automatic feature extraction.
      void cropKeyImages()
      Crop the central prostate gland region from the 512x512 slices.
      void disposeLocal()
      dispose memory.
      void extractFeatures()
      Extract CE features.
      void init()
      Dialog GUI initialization.
      void printImages()
      debuger for file names read.
      private void processDir​(java.io.File dir)
      Process directory, save the image names and voi names.
      void readFiles()
      read 2D slices directory.
      private void readKeyImageDir()
      Read 2D slices.
      private void recordSaveImageDir()
      Record the save 2D slice features directory.
      Features[] saveFeatureSpaceValue​(ModelImage resultImage, ModelImage classificationImage, ModelImage keyImage, ModelImage srcImage, int sliceNumber)
      Save CE features to user specified directory.
      private void traverse​(java.io.File dir)
      Traverse the 2D slices directory.

      • 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

      • radioButtonSVMBinary

        private javax.swing.JRadioButton radioButtonSVMBinary
        SVM option button.

      • radioButtonSVMMulticlass

        private javax.swing.JRadioButton radioButtonSVMMulticlass

      • svmTrainingBinary

        private boolean svmTrainingBinary
        flag to indicate is SVM training with binary class or multi-class.

      • boxYmin

        private int boxYmin
        cropped image boundary.

      • boxYmax

        private int boxYmax
        cropped image boundary.

      • boxXmin

        private int boxXmin

      • boxXmax

        private int boxXmax

      • xBounds

        private int[] xBounds
        x dimension bounds

      • yBounds

        private int[] yBounds
        y dimension bound

      • zBounds

        private int[] zBounds
        z dimension bound

      • imageIntensityFilter

        private boolean imageIntensityFilter
        image intensity.

      • coherenceEnhancingDiffusionFilter

        private boolean coherenceEnhancingDiffusionFilter
        Coherence Enhancing Diffusion filter.

      • regisotropicDiffusionFilter

        private boolean regisotropicDiffusionFilter
        Anisotropic Diffusion filter.

      • IHN3CorrectionFilter

        private boolean IHN3CorrectionFilter
        Inhomogeneity N3 correction.

      • modeFilter

        private boolean modeFilter
        Haralick mode filter.

      • meanFilter

        private boolean meanFilter
        Haralick mean filter.

      • medianFilter

        private boolean medianFilter
        Haralick median filter.

      • invertFilter

        private boolean invertFilter
        Haralick invert filter.

      • haralickFilter

        private boolean haralickFilter
        haralick filter.

      • gaborFilter

        private boolean gaborFilter
        gabor filter.

      • hurstFilter

        private boolean hurstFilter
        Hurst index.

      • waveletFilter

        private boolean waveletFilter
        Wavelet filter.

      • gaussianFilter

        private boolean gaussianFilter
        gussian filter.

      • gmFilter

        private boolean gmFilter
        gradient magnitude filter.

      • numberFeatures

        private int numberFeatures
        number features being saved.

      • haralickFeatureNumber

        private int haralickFeatureNumber
        Haralick feature numbers.

      • labelKeyImage

        private javax.swing.JLabel labelKeyImage
        2D Slices key image directory.

      • textFieldKeyImage

        private javax.swing.JTextField textFieldKeyImage

      • buttonKeyImage

        private javax.swing.JButton buttonKeyImage

      • imageSelectionPanel

        private javax.swing.JPanel imageSelectionPanel
        2D slices image selection panel.

      • keyImageChooser

        private javax.swing.JFileChooser keyImageChooser
        2D slice images file chooser.

      • keyImageDirectory

        private java.lang.String keyImageDirectory
        2D slices image directory.

      • axisList

        private javax.swing.JComboBox axisList
        axis region.

      • labelAxis

        private javax.swing.JLabel labelAxis

      • Axial

        private static int Axial

      • Saggital

        private static int Saggital

      • Coronal

        private static int Coronal

      • axis

        private int axis

      • waveletFeatureNumber

        private int waveletFeatureNumber
        wavelet feature number.

      • keyImageVector

        private java.util.Vector<java.lang.String> keyImageVector
        key images names vector.

      • keyImages

        private java.util.Vector<ModelImage> keyImages
        key images vector.

      • keyImageVOIVector

        private java.util.Vector<java.lang.String> keyImageVOIVector
        key image VOI names vector.

      • keyImageVOIs

        private java.util.Vector<VOI[]> keyImageVOIs
        key image VOIs vector.

      • cropKeyImages

        private java.util.Vector<ModelImage> cropKeyImages
        cropped key image, crop from 512x512 to central prostate gland region.

      • cropKeyImagesCE

        private java.util.Vector<java.util.Vector<ModelImage>> cropKeyImagesCE
        cropped CE image vector.

      • labelSaveImage

        private javax.swing.JLabel labelSaveImage
        Save features directory.

      • textFieldSaveImage

        private javax.swing.JTextField textFieldSaveImage

      • buttonSaveImage

        private javax.swing.JButton buttonSaveImage

      • saveImageChooser

        private javax.swing.JFileChooser saveImageChooser
        Saved features directory.

      • saveImageDirectory

        private java.lang.String saveImageDirectory

    • Constructor Detail

      • JDialogProstateExtractCEFeature

        public JDialogProstateExtractCEFeature​(java.awt.Frame theParentFrame)
        Constructor.
        Parameters:
        theParentFrame -

    • Method Detail

      • disposeLocal

        public void disposeLocal()
        dispose memory.

      • calculateNumberFeatures

        private void calculateNumberFeatures()
        Calculate number of features being saved. Currently, only Hurst index and Haralick features being used.

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent event)
        Action performed handler for this dialog.
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener
        Overrides:
        actionPerformed in class JDialogBase

      • recordSaveImageDir

        private void recordSaveImageDir()
        Record the save 2D slice features directory.

      • readKeyImageDir

        private void readKeyImageDir()
        Read 2D slices.

      • printImages

        public void printImages()
        debuger for file names read.

      • traverse

        private void traverse​(java.io.File dir)
        Traverse the 2D slices directory.
        Parameters:
        dir -

      • processDir

        private void processDir​(java.io.File dir)
        Process directory, save the image names and voi names.
        Parameters:
        dir -

      • 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.

      • callAlgorithm

        public void callAlgorithm()
        Driver to do automatic feature extraction.

      • calculateCoherenceEnhancingDiffusion

        private void calculateCoherenceEnhancingDiffusion()
        From the cropped images, apply Coherence Enhanced Diffusion filter to each 2D slices.

      • cropKeyImages

        public void cropKeyImages()
        Crop the central prostate gland region from the 512x512 slices.

      • readFiles

        public void readFiles()
        read 2D slices directory.

      • extractFeatures

        public void extractFeatures()
        Extract CE features.

      • saveFeatureSpaceValue

        public Features[] saveFeatureSpaceValue​(ModelImage resultImage,
                                        ModelImage classificationImage,
                                        ModelImage keyImage,
                                        ModelImage srcImage,
                                        int sliceNumber)
        Save CE features to user specified directory.
        Parameters:
        resultImage - result image from feature extraction algorithm.
        classificationImage - corresponding class +1 or -1.
        keyImage - cropped key image
        srcImage - corresponding src image
        sliceNumber - slice number
        Returns:
        Feature vectors for the 2D slices.

      • init

        public void init()
        Dialog GUI initialization.

      • buildKeyImagePanel

        public void buildKeyImagePanel()
        Build the panel.