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

Class JDialogProstateSPIEcancerChallenge

  • 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 JDialogProstateSPIEcancerChallenge
extends JDialogBase
implements AlgorithmInterface
    This class is for ProstateX 2017 MICCAI challenge. We use NIH data to train the HED model. Both MRI and CED (png) slices generated from the axial NIH data will be used to train the deep learning model. This class are the basic image processing and extraction steps for preprocessing. This class is used for MICCAI prostateX 2017 challenge test cases. IMPORTANT!!! Steps: 1) transform the image to x, y isotropic resolution images 2) Crop the center part with 25% deduction from each image boundary 3) Normalized the image intensity in range [0, 1000] 4) Run Coherence Enhance Diffusion (CED) against the MRI image to enhance the boundary. 5) Extract MRI, CED slice with corresponding binary masks, saving them in 2D PNG files.
    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)  
      ModelImage calculateTransform_dim_fixed​(ModelImage image)  
      ModelImage calculateTransform_resol_fix​(ModelImage image)  
      void callAlgorithm()
      Driver function to read image and VOIs, and convert each 3D image to 2D slices.
      private ModelImage cropImage​(ModelImage image)  
      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
      void disposeMemory()  
      ModelImage histoEqual​(ModelImage image)  
      void init()
      Initial panel
      void loadFiles()
      load image files and voi files
      static void pause()  
      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.
      void runCED()  
      void runCrop()  
      void runMask()  
      void runScaleIntensity()  
      void runTransform()  
      void saveImages()  
      void saveImages​(int key, int[] index, java.lang.String folderName, java.util.Hashtable<java.lang.Integer,​ModelImage> whichTable)  
      void saveImagesTest​(int key, int[] index, java.lang.String folderName)  
      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()  
      ModelImage scaleIntensity​(ModelImage image)  
      void smoothVOI60​(ModelImage maskImage, ModelImage resultImage)
      Smooth VOIs to 60 points.
      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_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)  

      • 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.

      • imageSelectionPanel

        private javax.swing.JPanel imageSelectionPanel

      • keyImages

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

      • keyImageVector1

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

      • 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.Integer,​ModelImage> imageHashtable

      • cedTable

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

      • scaleImageTable

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

      • scaleIntensityTable

        java.util.Hashtable<java.lang.Integer,​ModelImage> scaleIntensityTable

      • scaleCedTable

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

      • scaleVoiTable

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

      • transformTable

        java.util.Hashtable<java.lang.Integer,​ModelImage> transformTable

      • cropTable

        java.util.Hashtable<java.lang.Integer,​ModelImage> cropTable

    • Constructor Detail

      • JDialogProstateSPIEcancerChallenge

        public JDialogProstateSPIEcancerChallenge​(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_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)

      • 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.

      • disposeMemory

        public void disposeMemory()

      • runCrop

        public void runCrop()

      • runCED

        public void runCED()

      • runMask

        public void runMask()

      • runTransform

        public void runTransform()

      • calculateTransform_dim_fixed

        public ModelImage calculateTransform_dim_fixed​(ModelImage image)

      • calculateTransform_resol_fix

        public ModelImage calculateTransform_resol_fix​(ModelImage image)

      • runScaleIntensity

        public void runScaleIntensity()

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

      • saveImagesTest

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

      • smoothVOI60

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

      • 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.