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

Class JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale

  • 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 JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale
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/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 actionPerformed 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.
      private ModelImage calculateCoherenceEnhancingDiffusion​(ModelImage inImage)  
      ModelImage calculateTransform​(ModelImage image)  
      void callAlgorithm()
      Driver function to read image and VOIs, and convert each 3D image to 2D slices.
      void cropKeyImages()
      Crop key images.
      void crossValidationTest()  
      void crossValidationTrain()  
      static boolean deleteDir​(java.io.File dir)
      Debugger to test dir deletion.
      void disposeLocal()
      dispose memory
      private void generateBoundaryContours​(VOIBase srcContour, ModelImage targetImageSlice)
      Convert VOI from one contour to two contours
      void init()
      Initial panel
      void loadFiles()
      load image files and voi files
      static void pause()  
      void printImages()
      Debugger for test the image and VOis reading.
      private void processDir_folder_1​(java.io.File dir)  
      private void processDir_folder_2​(java.io.File dir)  
      private void processDir_folder_3​(java.io.File dir)  
      private void processDir_folder_4​(java.io.File dir)  
      private void processDir_folder_5​(java.io.File dir)  
      void readFile()  
      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 runCED()  
      void runMask()  
      void runTransform()  
      void saveImages()  
      void saveImages​(java.lang.String key, int[] index, java.lang.String folderName, java.util.Hashtable<java.lang.String,​ModelImage> whichTable)  
      void saveImagesTest​(java.lang.String key, int[] index, java.lang.String folderName)  
      private void savePNGfile​(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, boolean isMask)  
      private void savePNGfile​(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)  
      void saveTestedImages()  
      void smoothVOI60​(ModelImage maskImage, ModelImage resultImage)
      Smooth VOIs to 60 points.
      void sortKeyImage_1()  
      void sortKeyImage_2()  
      void sortKeyImage_3()  
      void sortKeyImage_4()  
      void sortKeyImage_5()  
      private void traverse_DicomLayer​(java.io.File lastLayer, java.lang.String hashID)  
      private void traverse_firstLayer​(java.io.File firstDir, java.lang.String child)  
      private void traverse_folder_2​(java.io.File dir)  
      private void traverse_folder_3​(java.io.File dir)  
      private void traverse_folder_4​(java.io.File dir)  
      private void traverse_folder_5​(java.io.File dir)  
      private void traverse_Layer​(java.io.File dir)  
      private void traverse_scanLayer​(java.io.File secondLayer, java.lang.String hashID)  
      private void traverse_secondLayer​(java.io.File firstLayer, java.lang.String hashID)  
      private void traverse_T2Layer​(java.io.File T2Layer, java.lang.String hashID)  
      private void traverse_thirdLayer​(java.io.File secondLayer, java.lang.String hashID)  
      private void traverse_voiLayer​(java.io.File secondLayer, java.lang.String hashID)  

      • 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

      • keyImages

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

      • keyImageVOIs

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

      • keyImageVector1

        private java.util.Vector<java.lang.String> keyImageVector1

      • keyImageVOIVector1

        private java.util.Vector<java.lang.String> keyImageVOIVector1

      • keyImageVector2

        private java.util.Vector<java.lang.String> keyImageVector2

      • keyImageVOIVector2

        private java.util.Vector<java.lang.String> keyImageVOIVector2

      • keyImageVector3

        private java.util.Vector<java.lang.String> keyImageVector3

      • keyImageVOIVector3

        private java.util.Vector<java.lang.String> keyImageVOIVector3

      • keyImageVector4

        private java.util.Vector<java.lang.String> keyImageVector4

      • keyImageVOIVector4

        private java.util.Vector<java.lang.String> keyImageVOIVector4

      • keyImageVector5

        private java.util.Vector<java.lang.String> keyImageVector5

      • keyImageVOIVector5

        private java.util.Vector<java.lang.String> keyImageVOIVector5

      • 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

      • imageNameHashtable

        java.util.Hashtable<java.lang.String,​java.util.Vector<java.lang.String>> imageNameHashtable

      • voiNameHashtable

        java.util.Hashtable<java.lang.String,​java.util.Vector<java.lang.String>> voiNameHashtable

      • imageHashtable

        java.util.Hashtable<java.lang.String,​ModelImage> imageHashtable

      • cedTable

        java.util.Hashtable<java.lang.String,​ModelImage> cedTable

      • voiTable

        java.util.Hashtable<java.lang.String,​ModelImage> voiTable

      • scaleImageTable

        java.util.Hashtable<java.lang.String,​ModelImage> scaleImageTable

      • scaleCedTable

        java.util.Hashtable<java.lang.String,​ModelImage> scaleCedTable

      • scaleVoiTable

        java.util.Hashtable<java.lang.String,​ModelImage> scaleVoiTable

      • voiHashtable

        java.util.Hashtable<java.lang.String,​VOI> voiHashtable

    • Constructor Detail

      • JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale

        public JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale​(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 actionPerformed 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.

      • traverse_Layer

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

      • traverse_firstLayer

        private void traverse_firstLayer​(java.io.File firstDir,
                                 java.lang.String child)

      • traverse_secondLayer

        private void traverse_secondLayer​(java.io.File firstLayer,
                                  java.lang.String hashID)

      • traverse_thirdLayer

        private void traverse_thirdLayer​(java.io.File secondLayer,
                                 java.lang.String hashID)

      • traverse_scanLayer

        private void traverse_scanLayer​(java.io.File secondLayer,
                                java.lang.String hashID)

      • traverse_T2Layer

        private void traverse_T2Layer​(java.io.File T2Layer,
                              java.lang.String hashID)

      • traverse_DicomLayer

        private void traverse_DicomLayer​(java.io.File lastLayer,
                                 java.lang.String hashID)

      • traverse_voiLayer

        private void traverse_voiLayer​(java.io.File secondLayer,
                               java.lang.String hashID)

      • processDir_folder_1

        private void processDir_folder_1​(java.io.File dir)

      • sortKeyImage_1

        public void sortKeyImage_1()

      • traverse_folder_2

        private void traverse_folder_2​(java.io.File dir)

      • processDir_folder_2

        private void processDir_folder_2​(java.io.File dir)

      • sortKeyImage_2

        public void sortKeyImage_2()

      • traverse_folder_3

        private void traverse_folder_3​(java.io.File dir)

      • processDir_folder_3

        private void processDir_folder_3​(java.io.File dir)

      • sortKeyImage_3

        public void sortKeyImage_3()

      • traverse_folder_4

        private void traverse_folder_4​(java.io.File dir)

      • processDir_folder_4

        private void processDir_folder_4​(java.io.File dir)

      • sortKeyImage_4

        public void sortKeyImage_4()

      • traverse_folder_5

        private void traverse_folder_5​(java.io.File dir)

      • processDir_folder_5

        private void processDir_folder_5​(java.io.File dir)

      • sortKeyImage_5

        public void sortKeyImage_5()

      • printImages

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

      • 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.

      • runMask

        public void runMask()

      • runCED

        public void runCED()

      • runTransform

        public void runTransform()

      • calculateCoherenceEnhancingDiffusion

        private ModelImage calculateCoherenceEnhancingDiffusion​(ModelImage inImage)

      • saveTestedImages

        public void saveTestedImages()

      • crossValidationTest

        public void crossValidationTest()

      • crossValidationTrain

        public void crossValidationTrain()

      • saveImages

        public void saveImages()

      • savePNGfile

        private void savePNGfile​(java.lang.String dirName,
                         java.lang.String fileName,
                         ModelImage srcImage,
                         float minIntensity,
                         float maxIntensity,
                         int xDim,
                         int yDim,
                         boolean isMask)

      • saveImages

        public void saveImages​(java.lang.String key,
                       int[] index,
                       java.lang.String folderName,
                       java.util.Hashtable<java.lang.String,​ModelImage> whichTable)

      • saveImagesTest

        public void saveImagesTest​(java.lang.String key,
                           int[] index,
                           java.lang.String folderName)

      • savePNGfile

        private void savePNGfile​(java.lang.String dirName,
                         java.lang.String fileName,
                         ModelImage srcImage,
                         float minIntensity,
                         float maxIntensity,
                         boolean isMask)

      • 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:

      • readFile

        public void readFile()

      • pause

        public static void pause()

      • init

        public void init()
        Initial panel

      • buildKeyImagePanel

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