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

Class JPanelEPIDistortionCorrection

  • All Implemented Interfaces:
    java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible
    public class JPanelEPIDistortionCorrection
extends javax.swing.JPanel
implements java.awt.event.ActionListener
    See Also:
    Serialized Form

    • Nested Class Summary

      • Nested classes/interfaces inherited from class javax.swing.JPanel

        javax.swing.JPanel.AccessibleJPanel

      • Nested classes/interfaces inherited from class javax.swing.JComponent

        javax.swing.JComponent.AccessibleJComponent

      • 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)  
      private void applyDefField​(ModelImage vol4DIn, ModelImage vol4DOut, int vol, Jama.Matrix m, ModelImage defField, int[] extents, float[] resolutions)
      Creates a deformation field from the input matrix and deformation field and applies it to the input image.
      private ModelImage applyDeformationField​(int indexB0, TransMatrix b0toStructMatrix, TransMatrix[] arrayTransMatrix, ModelImage defField, ModelImage result35RegImage)
      Applies the input B0 to T2 matrix, list of within-volume matrices and input deformation field to the 4D volume series.
      javax.swing.JPanel buildLoadPanel​(java.awt.event.ActionListener listener, javax.swing.JPanel mainPanel, javax.swing.JLabel label, javax.swing.JTextField imageName, java.lang.String tooltip, java.lang.String actionCommand, javax.swing.JPanel panelName)  
      private void enableComputeEpiDistortion()
      Checks that all the parameters necessary to run the epi-distortion correction are set and enables the compute button and display check-box.
      private void enableComputeVabra()
      Checks that all the parameters necessary to run the VABRA registration are set and enables the compute button and display check-boxes.
      static ModelImage extractSubVolume​(ModelImage dwiImage, int index)  
      ModelImage getResult()
      Returns the distortion-corrected DWI 4D image series.
      private void init()
      User-interface intialization.
      private ModelImage loadFile​(javax.swing.JTextField textField)
      Loads a user-selected image file.
      private TransMatrix[] readMultiTransformMatrix​(javax.swing.JTextField textField)
      Reads the multiple-matrix file from disk.
      private TransMatrix readTransformMatrix​(javax.swing.JTextField textField)
      Reads a single matrix file from disk.
      private void runVabra()
      Run the VABRA registration.
      void setB0toT2Matrix​(TransMatrix matrix, java.lang.String fileName)
      Sets the B0 to T2 matrix.
      void setRegisteredDWIImage​(ModelImage registeredImage)
      Sets the with-in volume registered 4D DWI image.
      void setRegisteredMatrices​(TransMatrix[] matrix, java.lang.String fileName)
      Sets the within-volume array of matrices.
      void setResampledT2Image​(ModelImage resampledImage)
      Sets the resampled T2 structural image, from the DTIPipeline pre-processing panel, or by the user loading the file disk.

      • Methods inherited from class javax.swing.JPanel

        getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

      • Methods inherited from class javax.swing.JComponent

        addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

      • Methods inherited from class java.awt.Container

        add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, 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

      • pipeline

        private DTIPipeline pipeline
        reference to the DTI Pipeline

      • mainPanel

        private javax.swing.JPanel mainPanel
        main panel

      • refImageNumText

        private javax.swing.JTextField refImageNumText
        Text fields for entering the input images:

      • resampledT2Text

        private javax.swing.JTextField resampledT2Text

      • registeredDWIText

        private javax.swing.JTextField registeredDWIText

      • deformationB0T2Text

        private javax.swing.JTextField deformationB0T2Text

      • matricesFile

        private javax.swing.JTextField matricesFile

      • B0MatrixFile

        private javax.swing.JTextField B0MatrixFile

      • outputDir

        private javax.swing.JTextField outputDir

      • displayDeformationField

        private javax.swing.JCheckBox displayDeformationField
        output image display options:

      • displayRegisteredB0

        private javax.swing.JCheckBox displayRegisteredB0

      • displayEPIResult

        private javax.swing.JCheckBox displayEPIResult

      • loadT2Command

        private java.lang.String loadT2Command
        button commands

      • loadDWICommand

        private java.lang.String loadDWICommand

      • loadDeformationFieldCommand

        private java.lang.String loadDeformationFieldCommand

      • outputCommand

        private java.lang.String outputCommand

      • computeDefFieldCommand

        private java.lang.String computeDefFieldCommand

      • computeEpiCommand

        private java.lang.String computeEpiCommand

      • loadB0MatrixComand

        private java.lang.String loadB0MatrixComand

      • loadAllMatrixComand

        private java.lang.String loadAllMatrixComand

      • computeDeformationFieldButton

        private javax.swing.JButton computeDeformationFieldButton
        button for computing the deformation field:

      • computeEpiCorrectionButton

        private javax.swing.JButton computeEpiCorrectionButton
        button for applying the deformation field to the input 4D image

      • resampledT2

        private ModelImage resampledT2
        Structural T2 image, resampled to match the DWI image series.

      • registeredDWI

        private ModelImage registeredDWI
        DWI image series that has been registered within series to the B0 volume.

      • registeredB0

        private ModelImage registeredB0
        B0 volume extracted from the DWI series.

      • deformationB0T2

        private ModelImage deformationB0T2
        deformation field from registering the B0 volume to the resampled T2 volume with VABRA

      • deformedDWI

        private ModelImage deformedDWI
        DWI image series after applying the list of deformation fields

      • matB0T2

        private TransMatrix matB0T2
        Transformation matrix from registering B0 to T2.

      • matRegistered

        private TransMatrix[] matRegistered
        Array of transformation matrices after registering the DWI image series to the B0 reference volume.

      • T2loadPanel

        private javax.swing.JPanel T2loadPanel

      • RegisteredDWIPanel

        private javax.swing.JPanel RegisteredDWIPanel

      • DefLoadPanel

        private javax.swing.JPanel DefLoadPanel

      • B0toStructTransPanel

        private javax.swing.JPanel B0toStructTransPanel

      • DWITransPanel

        private javax.swing.JPanel DWITransPanel

      • OutputPanel

        private javax.swing.JPanel OutputPanel

    • Constructor Detail

      • JPanelEPIDistortionCorrection

        public JPanelEPIDistortionCorrection​(DTIPipeline pipeline)
        Creates the EPI-Distortion correction panel for the DTI Pipeline
        Parameters:
        pipeline -

    • Method Detail

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent event)
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener

      • getResult

        public ModelImage getResult()
        Returns the distortion-corrected DWI 4D image series.
        Returns:
        the distortion-corrected DWI 4D image series.

      • setB0toT2Matrix

        public void setB0toT2Matrix​(TransMatrix matrix,
                            java.lang.String fileName)
        Sets the B0 to T2 matrix. Set from the DTI Pipeline pre-processing panel, or by the user loading the .mtx file from disk.
        Parameters:
        matrix -
        fileName -

      • setRegisteredDWIImage

        public void setRegisteredDWIImage​(ModelImage registeredImage)
        Sets the with-in volume registered 4D DWI image. Can be set from the DTI Pipeline pre-processing panel or by the user loading the file from disk.
        Parameters:
        registeredImage -

      • setRegisteredMatrices

        public void setRegisteredMatrices​(TransMatrix[] matrix,
                                  java.lang.String fileName)
        Sets the within-volume array of matrices. Set from the DTI Pipeline pre-processing panel, or by the user loading the .mtx file from disk.
        Parameters:
        matrix -
        fileName -

      • setResampledT2Image

        public void setResampledT2Image​(ModelImage resampledImage)
        Sets the resampled T2 structural image, from the DTIPipeline pre-processing panel, or by the user loading the file disk.
        Parameters:
        resampledImage -

      • applyDefField

        private void applyDefField​(ModelImage vol4DIn,
                           ModelImage vol4DOut,
                           int vol,
                           Jama.Matrix m,
                           ModelImage defField,
                           int[] extents,
                           float[] resolutions)
        Creates a deformation field from the input matrix and deformation field and applies it to the input image. Returns the new image result.
        Parameters:
        m - input matrix
        image - input image
        defField - input deformation field
        resolutions - resolutions of the input image

      • applyDeformationField

        private ModelImage applyDeformationField​(int indexB0,
                                         TransMatrix b0toStructMatrix,
                                         TransMatrix[] arrayTransMatrix,
                                         ModelImage defField,
                                         ModelImage result35RegImage)
        Applies the input B0 to T2 matrix, list of within-volume matrices and input deformation field to the 4D volume series.
        Parameters:
        indexB0 - index of the B0 image in the 4D image
        b0toStructMatrix - B0 to T2 transformation matrix
        arrayTransMatrix - array of transformation matrices from the within-volume registration
        defField - B0 to T2 deformation field, computed from VABRA
        result35RegImage - input 4D image
        Returns:
        new image result

      • enableComputeEpiDistortion

        private void enableComputeEpiDistortion()
        Checks that all the parameters necessary to run the epi-distortion correction are set and enables the compute button and display check-box.

      • enableComputeVabra

        private void enableComputeVabra()
        Checks that all the parameters necessary to run the VABRA registration are set and enables the compute button and display check-boxes.

      • init

        private void init()
        User-interface intialization.

      • loadFile

        private ModelImage loadFile​(javax.swing.JTextField textField)
        Loads a user-selected image file. Sets the input text field to the file name.
        Parameters:
        textField -
        Returns:

      • readMultiTransformMatrix

        private TransMatrix[] readMultiTransformMatrix​(javax.swing.JTextField textField)
        Reads the multiple-matrix file from disk. Sets the input text field to list the file name.
        Parameters:
        textField -
        Returns:

      • readTransformMatrix

        private TransMatrix readTransformMatrix​(javax.swing.JTextField textField)
        Reads a single matrix file from disk. Sets the input text field to match the file name.
        Parameters:
        textField -
        Returns:

      • runVabra

        private void runVabra()
        Run the VABRA registration. Saves the deformation field and the registered B0 image to disk. Enables the epi-distortion correction.

      • buildLoadPanel

        public javax.swing.JPanel buildLoadPanel​(java.awt.event.ActionListener listener,
                                         javax.swing.JPanel mainPanel,
                                         javax.swing.JLabel label,
                                         javax.swing.JTextField imageName,
                                         java.lang.String tooltip,
                                         java.lang.String actionCommand,
                                         javax.swing.JPanel panelName)