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

Class JDialogProstateCheckPngFile

  • 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 JDialogProstateCheckPngFile
extends JDialogBase
implements AlgorithmInterface
    This class convert the 3D images to 2D slices based atlas. Users specify the 3D prostate images dir, and output 2D slices based dir, the algorithm auto convert each 3D image to 2D slices with corresponding VOIs. Each saved VOIs is 2-contour based VOI, which is used to build the Active Appearance Model (AAM).
    Author:
    Ruida Cheng
    See Also:
    Serialized Form

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      (package private) class  JDialogProstateCheckPngFile.ImageAttributes  

      • 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 Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void actionPerformed​(java.awt.event.ActionEvent event)
      Dialog local handler.
      void algorithmPerformed​(AlgorithmBase algorithm)
      This method is required if the AlgorithmPerformed interface is implemented.
      void buildKeyImagePanel()
      Panel contains both the 3D image dir and saved 2D slices atlas dir.
      void callAlgorithm()
      Driver function to read image and VOIs, and convert each 3D image to 2D slices.
      void createTestingPatches()  
      void createTrainingPatches()  
      void cropKeyImages()
      Crop key images.
      static boolean deleteDir​(java.io.File dir)
      Debugger to test dir deletion.
      void disposeLocal()
      dispose memory
      (package private) void extractTable()  
      private void generateBoundaryContours​(VOIBase srcContour, ModelImage targetImageSlice)
      Convert VOI from one contour to two contours
      void init()
      Initial panel
      private void initTable()  
      void loadFiles()
      load image files and voi files
      static void pause()
      Pauses the display until the user hits enter.
      void printImages()
      Debugger for test the image and VOis reading.
      private void processDirLevel1​(java.io.File dir, int index)  
      private void processDirSingleImage​(java.io.File dir)
      Process the dir, read image and corresponding VOI file names.
      void readFiles()
      Read image and VOIs file names.
      private void readKeyImageDir()
      Read 3D images atlas directory.
      private void recordSaveImageDir()
      Let user specify the saved 2D slices atlas, record the save directory.
      private void rotateToStartingPoint_leftMost​(float[] xPts, float[] yPts, int xDim, int yDim)  
      private void rotateToStartingPoint_yMid​(float[] xPts, float[] yPts, int xDim, int yDim)
      Re-oriented the starting and ending VOIs.
      void saveImages()
      Save the 2D slices and VOIs to user specified dir.
      private void scaleDown​(ModelImage image)  
      void smoothVOI128​(ModelImage maskImage, ModelImage resultImage)  
      void smoothVOI30​(ModelImage maskImage, ModelImage resultImage)  
      void smoothVOI60​(ModelImage maskImage, ModelImage resultImage)
      Smooth VOIs to 60 points.
      void testingPatches​(ModelImage keyImage, int i, int startSliceIndex, int endSliceIndex, float minIntensity, float maxIntensity, boolean train, java.io.BufferedWriter outStream)  
      void trainingPatches​(ModelImage keyImage, int i, int startSliceIndex, int endSliceIndex, float minIntensity, float maxIntensity, boolean train)  
      private void traverse​(java.io.File dir)
      Recursively traverse the image directory.
      private void traverseCurrent​(java.io.File dir)  
      private void traverseLevel1​(java.io.File dir, int index)  

      • 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

      • boxYmin

        private int boxYmin
        bounding box for crop the image. Currently set from 0 to 512, the orginal image slice size.

      • boxYmax

        private int boxYmax
        bounding box for crop the image. Currently set from 0 to 512, the orginal image slice size.

      • boxXmin

        private int boxXmin

      • boxXmax

        private int boxXmax

      • xBounds

        private int[] xBounds
        X cropped region bounds.

      • yBounds

        private int[] yBounds
        Y cropped region bounds.

      • zBounds

        private int[] zBounds
        Z cropped region bound.

      • cropImage

        private ModelImage cropImage
        result cropped image.

      • labelKeyImage

        private javax.swing.JLabel labelKeyImage
        key image directory.

      • textFieldKeyImage

        private javax.swing.JTextField textFieldKeyImage

      • buttonKeyImage

        private javax.swing.JButton buttonKeyImage

      • imageSelectionPanel

        private javax.swing.JPanel imageSelectionPanel

      • keyImageChooser

        private javax.swing.JFileChooser keyImageChooser
        key images variables.

      • keyImageDirectory

        private java.lang.String keyImageDirectory

      • axisList

        private javax.swing.JComboBox axisList

      • 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

      • keyImageVector

        private java.util.Vector<java.lang.String> keyImageVector
        image vector to hold the image names.

      • keyImages

        private java.util.Vector<ModelImage> keyImages
        image vector to hold the actual images.

      • keyImageVOIVector

        private java.util.Vector<java.lang.String> keyImageVOIVector
        voi vector to hold the VOI names.

      • keyImageVOIVectorAAM

        private java.util.Vector<java.lang.String> keyImageVOIVectorAAM

      • keyImageVOIs

        private java.util.Vector<VOI[]> keyImageVOIs
        voi vector to hold the actual vois.

      • cropKeyImages

        private java.util.Vector<ModelImage> cropKeyImages
        cropped key image vector.

      • labelSaveImage

        private javax.swing.JLabel labelSaveImage
        saved 2D slices atlas dir.

      • textFieldSaveImage

        private javax.swing.JTextField textFieldSaveImage

      • buttonSaveImage

        private javax.swing.JButton buttonSaveImage

      • saveImageChooser

        private javax.swing.JFileChooser saveImageChooser

      • saveImageDirectory

        private java.lang.String saveImageDirectory

      • globalCounter

        private int globalCounter

    • Constructor Detail

      • JDialogProstateCheckPngFile

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

    • Method Detail

      • disposeLocal

        public void disposeLocal()
        dispose memory

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent event)
        Dialog local handler.
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener
        Overrides:
        actionPerformed in class JDialogBase

      • recordSaveImageDir

        private void recordSaveImageDir()
        Let user specify the saved 2D slices atlas, record the save directory.

      • readKeyImageDir

        private void readKeyImageDir()
        Read 3D images atlas directory.

      • printImages

        public void printImages()
        Debugger for test the image and VOis reading.

      • traverse

        private void traverse​(java.io.File dir)
        Recursively traverse the image directory.
        Parameters:
        dir - image dir.

      • traverseCurrent

        private void traverseCurrent​(java.io.File dir)

      • traverseLevel1

        private void traverseLevel1​(java.io.File dir,
                            int index)

      • pause

        public static void pause()
        Pauses the display until the user hits enter.

      • initTable

        private void initTable()

      • processDirLevel1

        private void processDirLevel1​(java.io.File dir,
                              int index)

      • extractTable

        void extractTable()

      • processDirSingleImage

        private void processDirSingleImage​(java.io.File dir)
        Process the dir, read image and corresponding VOI file names.
        Parameters:
        dir - 3D atlas image 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 function to read image and VOIs, and convert each 3D image to 2D slices.

      • createTestingPatches

        public void createTestingPatches()

      • scaleDown

        private void scaleDown​(ModelImage image)

      • createTrainingPatches

        public void createTrainingPatches()

      • testingPatches

        public void testingPatches​(ModelImage keyImage,
                           int i,
                           int startSliceIndex,
                           int endSliceIndex,
                           float minIntensity,
                           float maxIntensity,
                           boolean train,
                           java.io.BufferedWriter outStream)

      • trainingPatches

        public void trainingPatches​(ModelImage keyImage,
                            int i,
                            int startSliceIndex,
                            int endSliceIndex,
                            float minIntensity,
                            float maxIntensity,
                            boolean train)

      • saveImages

        public void saveImages()
        Save the 2D slices and VOIs to user specified dir.

      • rotateToStartingPoint_yMid

        private void rotateToStartingPoint_yMid​(float[] xPts,
                                        float[] yPts,
                                        int xDim,
                                        int yDim)
        Re-oriented the starting and ending VOIs.
        Parameters:
        xPts - voi x coordinate
        yPts - voi y coordinate
        xDim - image x dimension
        yDim - image y dimension

      • rotateToStartingPoint_leftMost

        private void rotateToStartingPoint_leftMost​(float[] xPts,
                                            float[] yPts,
                                            int xDim,
                                            int yDim)

      • smoothVOI60

        public void smoothVOI60​(ModelImage maskImage,
                        ModelImage resultImage)
        Smooth VOIs to 60 points.
        Parameters:
        maskImage -
        resultImage -

      • generateBoundaryContours

        private void generateBoundaryContours​(VOIBase srcContour,
                                      ModelImage targetImageSlice)
        Convert VOI from one contour to two contours
        Parameters:
        srcContour - single VOI contour
        targetImageSlice - target 2D image slice

      • cropKeyImages

        public void cropKeyImages()
        Crop key images.

      • loadFiles

        public void loadFiles()
        load image files and voi files

      • deleteDir

        public static boolean deleteDir​(java.io.File dir)
        Debugger to test dir deletion.
        Parameters:
        dir -
        Returns:

      • readFiles

        public void readFiles()
        Read image and VOIs file names.

      • init

        public void init()
        Initial panel

      • buildKeyImagePanel

        public void buildKeyImagePanel()
        Panel contains both the 3D image dir and saved 2D slices atlas dir.