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

Class DTIPipeline

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

gov.nih.mipav.view.dialogs.JDialogBase

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

All Implemented Interfaces:

DialogDefaultsInterface, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, ChangeListener, RootPaneContainer, WindowConstants

public class DTIPipeline
extends JDialogBase
implements ActionListener, ChangeListener

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase

JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction

Nested classes/interfaces inherited from class javax.swing.JDialog

JDialog.AccessibleJDialog

Nested classes/interfaces inherited from class java.awt.Dialog

Dialog.AccessibleAWTDialog, Dialog.ModalExclusionType, Dialog.ModalityType

Nested classes/interfaces inherited from class java.awt.Window

Window.AccessibleAWTWindow, Window.Type

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field	Description
TransMatrix[]	arrayTransMatrix
TransMatrix	b0toStructMatrix
double[][]	bmatValues
double[]	bvalues
ModelImage	currentImage	The current DWI image in the pipeline
private static final int	DEFAULT
private DTIParameters	dtiparams
private JPanelDTIPreprocessing	DTIPreprocessing
String	DWIDir
ViewJFrameImage	DWIframe
ModelImage	DWIImage	Diffusion weighted image read from file or from active image.
ModelImage	DWINewB0Image	Registered images, results from pre-processing tab:
private static final int	EPI_DISTORTION
private JPanelEPIDistortionCorrection	EPIpanel
private JPanelDTIEstimateTensor	estTensorPanel
private static final int	FIBER_TRACKING
private JPanelDTIFiberTracking	fiberTrack
private JButton	goBackButton	DOCUMENT ME!
double[][]	gradients
private static final int	IMPORT
private JPanelDTIImportData	importData
ModelImage	inputTensorImage	Input image for tensor estimation
static final int	LINEAR
private static final int	LLMSE
JPanel	mainPanel	main panel *
protected JButton	nextButton	DOCUMENT ME!
static final int	NON_LINEAR
private static final int	PRE_PROCESS
int	refImageNum
static final int	RESTORE
DefaultTableModel	srcBvalGradTable
ViewJFrameImage	T2frame
ModelImage	T2Image	Structural image as reference space (T2 image):
protected JTabbedPane	tabbedPane	DOCUMENT ME!
private static final int	TENSOR_ESTIMATION
ModelImage	tensorImage	Diffusion tensor image:
private JPanelDTIVisualization	visualization
private static final int	VISUALIZATION
static final int	WEIGHTED_LINEAR

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase

applyButton, bar, cancelButton, cancelFlag, closeButton, HELP, helpButton, mainDialogPanel, NEW, OKButton, parentFrame, progressBar, REPLACE, runInSeparateThread, runningScriptFlag, runQuiet, serif12, serif12B, voiManager

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Constructor Summary

Constructors

Constructor	Description
DTIPipeline()

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent event)	action performed
private JPanel	buildEPIPanel()
private JPanelDTIFiberTracking	buildFiberTrackingPanel()
private TitledBorder	buildGrayTitledBorder(String title)
private JScrollPane	buildImportDataPanel()
private JPanel	buildPreprocessingPanel()
private JPanel	buildTensorPanel()
private JPanel	buildVisuzalizationPanel()
void	finishEPIPanel()
void	finishPreProcessingPanel(ModelImage registeredDWI, ModelImage resampledT2, TransMatrix matB0toT2, String matB0FileName, TransMatrix[] matRegistered, String matRegisteredFileName)
void	finishTensorPanel(ModelImage resultImage)
void	init()	init
void	stateChanged(ChangeEvent e)

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase

buildApplyButton, buildButtons, buildCancelButton, buildCancelButton, buildCloseButton, buildHelpButton, buildImageComboBox, buildOKButton, buildOKButton, buildOKCancelButtons, buildTitledBorder, buildTitledBorder, createLabel, createProgressBar, createProgressBar, createTextField, focusGained, focusLost, getDialogName, isCancelled, isQuietRunning, isRunInSeparateThread, isScriptRunning, itemStateChanged, loadDefaults, loadDefaults, makeImageName, makeString, openNewFrame, saveDefaults, saveDefaults, setLeftHandSystem, setQuietRunning, setScriptRunning, setSeparateThread, setVisible, setVisible, setVisibleMenuBar, setVisibleStandard, setVOIManager, setWCSystem, testParameter, testParameterMin, updateFFTFileInfo, updateFileInfo, updateFileInfoOtherModality, updateFileInfoStatic, updateFileInfoStatic, updateFileTypeInfo, updateFileTypeInfo, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

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 Details

IMPORT

private static final int IMPORT

See Also:

• Constant Field Values

PRE_PROCESS

private static final int PRE_PROCESS

See Also:

• Constant Field Values

EPI_DISTORTION

private static final int EPI_DISTORTION

See Also:

• Constant Field Values

TENSOR_ESTIMATION

private static final int TENSOR_ESTIMATION

See Also:

• Constant Field Values

FIBER_TRACKING

private static final int FIBER_TRACKING

See Also:

• Constant Field Values

VISUALIZATION

private static final int VISUALIZATION

See Also:

• Constant Field Values

mainPanel

public JPanel mainPanel

main panel *

nextButton

protected JButton nextButton

DOCUMENT ME!

currentImage

public ModelImage currentImage

The current DWI image in the pipeline

DWIImage

public ModelImage DWIImage

Diffusion weighted image read from file or from active image.

inputTensorImage

public ModelImage inputTensorImage

Input image for tensor estimation

DWIDir

public String DWIDir

T2Image

public ModelImage T2Image

Structural image as reference space (T2 image):

DWINewB0Image

public ModelImage DWINewB0Image

Registered images, results from pre-processing tab:

tensorImage

public ModelImage tensorImage

Diffusion tensor image:

goBackButton

private JButton goBackButton

DOCUMENT ME!

importData

private JPanelDTIImportData importData

fiberTrack

private JPanelDTIFiberTracking fiberTrack

dtiparams

private DTIParameters dtiparams

visualization

private JPanelDTIVisualization visualization

DTIPreprocessing

private JPanelDTIPreprocessing DTIPreprocessing

estTensorPanel

private JPanelDTIEstimateTensor estTensorPanel

EPIpanel

private JPanelEPIDistortionCorrection EPIpanel

tabbedPane

protected JTabbedPane tabbedPane

DOCUMENT ME!

DWIframe

public ViewJFrameImage DWIframe

T2frame

public ViewJFrameImage T2frame

arrayTransMatrix

public TransMatrix[] arrayTransMatrix

b0toStructMatrix

public TransMatrix b0toStructMatrix

gradients

public double[][] gradients

bmatValues

public double[][] bmatValues

bvalues

public double[] bvalues

refImageNum

public int refImageNum

srcBvalGradTable

public DefaultTableModel srcBvalGradTable

DEFAULT

private static final int DEFAULT

See Also:

• Constant Field Values

LLMSE

private static final int LLMSE

See Also:

• Constant Field Values

LINEAR

public static final int LINEAR

See Also:

• Constant Field Values

NON_LINEAR

public static final int NON_LINEAR

See Also:

• Constant Field Values

RESTORE

public static final int RESTORE

See Also:

• Constant Field Values

WEIGHTED_LINEAR

public static final int WEIGHTED_LINEAR

See Also:

• Constant Field Values

Constructor Details

DTIPipeline

public DTIPipeline()

Method Details

init

public void init()

init

actionPerformed

public void actionPerformed(ActionEvent event)

action performed

Specified by:

actionPerformed in interface ActionListener

Overrides:

actionPerformed in class JDialogBase

buildGrayTitledBorder

private TitledBorder buildGrayTitledBorder(String title)

buildImportDataPanel

private JScrollPane buildImportDataPanel()

buildPreprocessingPanel

private JPanel buildPreprocessingPanel()

buildEPIPanel

private JPanel buildEPIPanel()

buildTensorPanel

private JPanel buildTensorPanel()

buildFiberTrackingPanel

private JPanelDTIFiberTracking buildFiberTrackingPanel()

buildVisuzalizationPanel

private JPanel buildVisuzalizationPanel()

finishPreProcessingPanel

public void finishPreProcessingPanel(ModelImage registeredDWI,
 ModelImage resampledT2,
 TransMatrix matB0toT2,
 String matB0FileName,
 TransMatrix[] matRegistered,
 String matRegisteredFileName)

finishEPIPanel

public void finishEPIPanel()

finishTensorPanel

public void finishTensorPanel(ModelImage resultImage)

stateChanged

public void stateChanged(ChangeEvent e)

Specified by:

stateChanged in interface ChangeListener