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

Class JDialogProstateXReRunWholeProstate

  • 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 JDialogProstateXReRunWholeProstate
extends JDialogBase
implements AlgorithmInterface
    For NIH prostate data, we apply wp and cg segmentation using HED deep learning model. Data: given NIH prostate data, axial images with corresponing VOIs for Cg and Wp. Steps: 1. read image file and VOIs 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 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 keyImage)  
      void callAlgorithm()
      Driver function to read image and VOIs, and convert each 3D image to 2D slices.
      void conversion()  
      void crossValidationTrain()  
      void disposeLocal()
      dispose memory
      void disposeMemory()  
      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 runMask()  
      void runTransform()  
      void saveHED2DsliceCED()  
      void saveImage​(ModelImage image, ModelImage imageMask, java.lang.String orientation)  
      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)  
      void saveOrthogonalCEDImage()  
      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)  
      private void traverse_DicomLayer​(java.io.File lastLayer, java.lang.String hashID)  
      private void traverse_firstLayer_noCoil​(java.io.File firstDir, java.lang.String child)  
      private void traverse_Layer_noCoil​(java.io.File dir)  
      private void traverse_secondLayer_noCoil​(java.io.File firstLayer, 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

      • 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

      • 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

      • voiNameHashtableWp

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

      • voiNameHashtableCg

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

      • imageNameHashtable_ext

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

      • voiNameHashtableWp_ext

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

      • voiNameHashtableCg_ext

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

      • imageHashtableWp_ext

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

      • imageHashtableCg_ext

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

      • cedTable_ext

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

      • voiTable_ext

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

      • imageHashtableWp

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

      • imageHashtableCg

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

      • 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

      • scaleImageTable_ext

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

      • scaleIntensityTable_ext

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

      • scaleCedTable_ext

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

      • scaleVoiTable_ext

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

      • transformTable_ext

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

      • transformTable

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

      • voiHashtable

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

      • cropTable_ext

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

      • cropVoiTable_ext

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

      • scaleIntensityTable

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

      • axialList

        private java.util.Hashtable<java.lang.String,​ModelImage> axialList

      • axialMaskList

        private java.util.Hashtable<java.lang.String,​ModelImage> axialMaskList

      • sagittalList

        private java.util.Hashtable<java.lang.String,​ModelImage> sagittalList

      • sagittalMaskList

        private java.util.Hashtable<java.lang.String,​ModelImage> sagittalMaskList

      • coronalList

        private java.util.Hashtable<java.lang.String,​ModelImage> coronalList

      • coronalMaskList

        private java.util.Hashtable<java.lang.String,​ModelImage> coronalMaskList

      • cedTableAxial

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

      • cedTableSagittal

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

      • cedTableCoronal

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

      • axial_index

        private int axial_index

      • sagittal_index

        private int sagittal_index

      • coronal_index

        private int coronal_index

      • startIndex

        private int startIndex

      • endIndex

        private int endIndex

    • Constructor Detail

      • JDialogProstateXReRunWholeProstate

        public JDialogProstateXReRunWholeProstate​(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_noCoil

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

      • traverse_firstLayer_noCoil

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

      • traverse_secondLayer_noCoil

        private void traverse_secondLayer_noCoil​(java.io.File firstLayer,
                                         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.

      • saveOrthogonalCEDImage

        public void saveOrthogonalCEDImage()

      • saveHED2DsliceCED

        public void saveHED2DsliceCED()

      • saveImage

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

      • disposeMemory

        public void disposeMemory()

      • runMask

        public void runMask()

      • runTransform

        public void runTransform()

      • conversion

        public void conversion()

      • runCED

        public void runCED()

      • calculateCoherenceEnhancingDiffusion

        private ModelImage calculateCoherenceEnhancingDiffusion​(ModelImage inImage)

      • crossValidationTrain

        public void crossValidationTrain()

      • 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)

      • 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()

      • 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.