Package gov.nih.mipav.view.dialogs

Class JDialogDTIEstimateTensor

  • 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 JDialogDTIEstimateTensor
extends JDialogBase
implements AlgorithmInterface, java.awt.event.WindowListener
    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 e)
      action performed
      void algorithmPerformed​(AlgorithmBase algorithm)
      algorithm performed
      private void createBMatrixFile()
      create b-matrix file
      private void createListFile()
      create list file
      private void createPathFile()
      create path file
      void init()
      init
      boolean parse​(java.io.File file)
      Parses study directory
      private boolean populateFields()  
      private void processDWI()
      Calls AlgorithmDWI2DTI to create the diffusion tensor image.
      private void readBMatrixFile​(java.lang.String kFileName)
      Loads the BMatrix file.
      boolean readBValGradientFile​(java.lang.String gradientFilePath)
      reads the bval/gradient file...both dti studio format and fsl format are accepted
      private void readListFile()
      read list file
      void readPathFile​(java.lang.String kFileName)
      Loads the .path file.
      private boolean validateData()
      validate data
      void windowClosing​(java.awt.event.WindowEvent event)
      window closing

      • 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

      • Methods inherited from interface java.awt.event.WindowListener

        windowActivated, windowClosed, windowDeactivated, windowDeiconified, windowIconified, windowOpened

    • Field Detail

      • gbc

        private java.awt.GridBagConstraints gbc
        grid bag constraints *

      • gbc2

        private java.awt.GridBagConstraints gbc2
        grid bag constraints *

      • gbc3

        private java.awt.GridBagConstraints gbc3
        grid bag constraints *

      • mainPanel

        private javax.swing.JPanel mainPanel
        main panel *

      • srcImagesTable

        private javax.swing.JTable srcImagesTable
        table to display the src image names.

      • srcTableModel

        private javax.swing.table.DefaultTableModel srcTableModel
        table model for the srcimages.

      • currDir

        private java.lang.String currDir
        current directory *

      • srcImage

        private ModelImage srcImage
        src image *

      • slicesVector

        private final java.util.Vector<java.util.ArrayList<java.lang.String>> slicesVector
        slices *

      • bValueTextField

        private javax.swing.JTextField bValueTextField
        textfields *

      • xdimTextField

        private javax.swing.JTextField xdimTextField
        textfields *

      • ydimTextField

        private javax.swing.JTextField ydimTextField
        textfields *

      • numSlicesTextField

        private javax.swing.JTextField numSlicesTextField
        textfields *

      • numVolumesTextField

        private javax.swing.JTextField numVolumesTextField
        textfields *

      • hFOVTextField

        private javax.swing.JTextField hFOVTextField
        textfields *

      • vFOVTextField

        private javax.swing.JTextField vFOVTextField
        textfields *

      • outputDirTextField

        private javax.swing.JTextField outputDirTextField
        textfields *

      • formatTextField

        private javax.swing.JTextField formatTextField
        textfields *

      • gapTextField

        private javax.swing.JTextField gapTextField
        textfields *

      • sliceThicknessTextField

        private javax.swing.JTextField sliceThicknessTextField
        textfields *

      • imagePlaneTextField

        private javax.swing.JTextField imagePlaneTextField
        textfields *

      • phaseEncodingTextField

        private javax.swing.JTextField phaseEncodingTextField
        textfields *

      • maskImageTextField

        private javax.swing.JTextField maskImageTextField
        textfields *

      • maskImage

        private ModelImage maskImage
        mask Image *

      • listFile

        private java.io.File listFile
        list file *

      • m_kParentDir

        private java.lang.String m_kParentDir
        paren tdir *

      • m_iDimX

        private int m_iDimX
        X-dimensions for Diffusion Weighted Images.

      • m_iDimY

        private int m_iDimY
        Y-dimensions for Diffusion Weighted Images.

      • m_fMeanNoise

        private float m_fMeanNoise
        Mean noise vale read from the .list file

      • m_kRawFormat

        private java.lang.String m_kRawFormat
        raw image format read from the .list file:

      • m_iSlices

        private int m_iSlices
        Number of slices in the Diffusion Weighted Images series.

      • m_iWeights

        private int m_iWeights
        Number of weights in the Diffusion Weighted Images series.

      • m_fResX

        private float m_fResX
        Slice thickness read from .list file

      • m_fResY

        private float m_fResY
        Slice thickness read from .list file

      • m_fResZ

        private float m_fResZ
        Slice thickness read from .list file

      • m_kBMatrix

        private WildMagic.LibFoundation.Mathematics.GMatrixd m_kBMatrix
        General matrix storing BMatrix values.

      • m_aiMatrixEntries

        private int[] m_aiMatrixEntries
        keeps track of unique entries in the BMatrix

      • m_iBOrig

        private int m_iBOrig
        Number of different BMatrix rows:

      • DTI

        private ModelImage DTI
        Diffusion Tensor image.

      • loadMaskButton

        private javax.swing.JButton loadMaskButton
        button *

      • m_aakDWIList

        private java.lang.String[][] m_aakDWIList
        List of file names for the Diffusion Weighted Images, from the .path *

    • Constructor Detail

      • JDialogDTIEstimateTensor

        public JDialogDTIEstimateTensor()
        constructor

    • Method Detail

      • init

        public void init()
        init

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent e)
        action performed
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener
        Overrides:
        actionPerformed in class JDialogBase

      • parse

        public boolean parse​(java.io.File file)
        Parses study directory
        Parameters:
        file -
        Returns:

      • populateFields

        private boolean populateFields()

      • readBValGradientFile

        public boolean readBValGradientFile​(java.lang.String gradientFilePath)
        reads the bval/gradient file...both dti studio format and fsl format are accepted
        Parameters:
        gradientFilePath -
        Returns:

      • createListFile

        private void createListFile()
        create list file

      • createBMatrixFile

        private void createBMatrixFile()
        create b-matrix file

      • createPathFile

        private void createPathFile()
        create path file

      • readListFile

        private void readListFile()
        read list file

      • readPathFile

        public void readPathFile​(java.lang.String kFileName)
        Loads the .path file.
        Parameters:
        kFileName - path file name.
        kPathName - parent directory.

      • readBMatrixFile

        private void readBMatrixFile​(java.lang.String kFileName)
        Loads the BMatrix file.
        Parameters:
        kFileName - name of BMatrix file.

      • processDWI

        private void processDWI()
        Calls AlgorithmDWI2DTI to create the diffusion tensor image.

      • validateData

        private boolean validateData()
        validate data
        Returns:

      • windowClosing

        public void windowClosing​(java.awt.event.WindowEvent event)
        window closing
        Specified by:
        windowClosing in interface java.awt.event.WindowListener
        Overrides:
        windowClosing in class JDialogBase
        Parameters:
        event - WindowEvent