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

Class JDialogPromise12_2DVolumetrieHED

  • 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 JDialogPromise12_2DVolumetrieHED
extends JDialogBase
implements AlgorithmInterface
    For Miccai promise 12 prostate data, we apply wp segmentation using HED deep learning model. Data: given promise 12 data, we apply N4 correction, cropping, and isotropic upsampling. Steps: 1. read promise 12 image data with corresponding masks after pre-processing. 2. From VOIs, generate the binary mask images. 3. Transform into isotropic image (upsampling) with resolution: 0.35m x 0.35m x 0.35m. 4. Conversion: converts axial image to axial an coronal using JDialogReoriented. 5. Generate the CED images from MR images in three orientation: axial, sagittal, coronal. 6. Each orientation, save 3D MR images, CED images with corresponding binary mask images. This is the 2D-volumetric segmentation approach.
    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)
      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)  
      void callAlgorithm()
      Driver function to read image and VOIs, and convert each 3D image to 2D slices.
      void conversion()  
      void disposeLocal()
      dispose memory
      void init()
      Initial panel
      void loadFiles()
      load image files and voi files
      private void processDir_folder_1​(java.io.File dir)  
      private void processDir_folder_2​(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.
      void runCED()  
      void saveHED2DsliceCED()  
      void saveHED2DsliceMRI()  
      void saveImage​(ModelImage image, ModelImage imageMask, java.lang.String orientation)  
      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 sortKeyImage_1()  
      void sortKeyImage_2()  
      private void traverse_folder_1​(java.io.File dir)  
      private void traverse_folder_2​(java.io.File dir)  

      • 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

      • 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

      • keyImages

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

      • keyImagesScaleIntensity

        private java.util.Vector<ModelImage> keyImagesScaleIntensity

      • keyImagesMask

        private java.util.Vector<ModelImage> keyImagesMask

      • keyImagesN4Crop

        private java.util.Vector<ModelImage> keyImagesN4Crop

      • keyImageVector1

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

      • keyImageVector2

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

      • 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

      • axialList

        private java.util.Vector<ModelImage> axialList

      • axialMaskList

        private java.util.Vector<ModelImage> axialMaskList

      • sagittalList

        private java.util.Vector<ModelImage> sagittalList

      • sagittalMaskList

        private java.util.Vector<ModelImage> sagittalMaskList

      • coronalList

        private java.util.Vector<ModelImage> coronalList

      • coronalMaskList

        private java.util.Vector<ModelImage> coronalMaskList

      • axial_index

        private int axial_index

      • sagittal_index

        private int sagittal_index

      • coronal_index

        private int coronal_index

      • cedTableAxial

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

      • cedTableSagittal

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

      • cedTableCoronal

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

    • Constructor Detail

      • JDialogPromise12_2DVolumetrieHED

        public JDialogPromise12_2DVolumetrieHED​(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_folder_1

        private void traverse_folder_1​(java.io.File dir)

      • 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()

      • 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.

      • saveHED2DsliceMRI

        public void saveHED2DsliceMRI()

      • runCED

        public void runCED()

      • saveHED2DsliceCED

        public void saveHED2DsliceCED()

      • saveImage

        public void saveImage​(ModelImage image,
                      ModelImage imageMask,
                      java.lang.String orientation)

      • calculateCoherenceEnhancingDiffusion

        private ModelImage calculateCoherenceEnhancingDiffusion​(ModelImage inImage)

      • conversion

        public void conversion()

      • saveTestedImages

        public void saveTestedImages()

      • savePNGfile

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

      • loadFiles

        public void loadFiles()
        load image files and voi files

      • readFile

        public void readFile()

      • init

        public void init()
        Initial panel

      • buildKeyImagePanel

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