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, 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.event.ChangeListener, javax.swing.RootPaneContainer, javax.swing.WindowConstants
```
public class DTIPipeline
extends JDialogBase
implements java.awt.event.ActionListener, javax.swing.event.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
  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

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 int`	`DEFAULT`
`private DTIParameters`	`dtiparams`
`private JPanelDTIPreprocessing`	`DTIPreprocessing`
`java.lang.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 int`	`EPI_DISTORTION`
`private JPanelEPIDistortionCorrection`	`EPIpanel`
`private JPanelDTIEstimateTensor`	`estTensorPanel`
`private static int`	`FIBER_TRACKING`
`private JPanelDTIFiberTracking`	`fiberTrack`
`private javax.swing.JButton`	`goBackButton`	DOCUMENT ME!
`double[][]`	`gradients`
`private static int`	`IMPORT`
`private JPanelDTIImportData`	`importData`
`ModelImage`	`inputTensorImage`	Input image for tensor estimation
`static int`	`LINEAR`
`private static int`	`LLMSE`
`javax.swing.JPanel`	`mainPanel`	main panel *
`protected javax.swing.JButton`	`nextButton`	DOCUMENT ME!
`static int`	`NON_LINEAR`
`private static int`	`PRE_PROCESS`
`int`	`refImageNum`
`static int`	`RESTORE`
`javax.swing.table.DefaultTableModel`	`srcBvalGradTable`
`ViewJFrameImage`	`T2frame`
`ModelImage`	`T2Image`	Structural image as reference space (T2 image):
`protected javax.swing.JTabbedPane`	`tabbedPane`	DOCUMENT ME!
`private static int`	`TENSOR_ESTIMATION`
`ModelImage`	`tensorImage`	Diffusion tensor image:
`private JPanelDTIVisualization`	`visualization`
`private static int`	`VISUALIZATION`
`static 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	action performed
`private javax.swing.JPanel`	`buildEPIPanel()`
`private JPanelDTIFiberTracking`	`buildFiberTrackingPanel()`
`private javax.swing.border.TitledBorder`	`buildGrayTitledBorder(java.lang.String title)`
`private javax.swing.JScrollPane`	`buildImportDataPanel()`
`private javax.swing.JPanel`	`buildPreprocessingPanel()`
`private javax.swing.JPanel`	`buildTensorPanel()`
`private javax.swing.JPanel`	`buildVisuzalizationPanel()`
`void`	`finishEPIPanel()`
`void`	`finishPreProcessingPanel(ModelImage registeredDWI, ModelImage resampledT2, TransMatrix matB0toT2, java.lang.String matB0FileName, TransMatrix[] matRegistered, java.lang.String matRegisteredFileName)`
`void`	`finishTensorPanel(ModelImage resultImage)`
`void`	`init()`	init
`void`	`stateChanged(javax.swing.event.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 Detail

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 javax.swing.JPanel mainPanel
```
main panel *

nextButton

protected javax.swing.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 java.lang.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 javax.swing.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 javax.swing.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 javax.swing.table.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 Detail
- DTIPipeline
```
public DTIPipeline()
```

Method Detail

init
```
public void init()
```
init

actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
action performed

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class JDialogBase

buildGrayTitledBorder

private javax.swing.border.TitledBorder buildGrayTitledBorder(java.lang.String title)

buildImportDataPanel

private javax.swing.JScrollPane buildImportDataPanel()

buildPreprocessingPanel

private javax.swing.JPanel buildPreprocessingPanel()

buildEPIPanel

private javax.swing.JPanel buildEPIPanel()

buildTensorPanel

private javax.swing.JPanel buildTensorPanel()

buildFiberTrackingPanel

private JPanelDTIFiberTracking buildFiberTrackingPanel()

buildVisuzalizationPanel

private javax.swing.JPanel buildVisuzalizationPanel()

finishPreProcessingPanel

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

finishEPIPanel
```
public void finishEPIPanel()
```

finishTensorPanel

public void finishTensorPanel(ModelImage resultImage)

stateChanged
```
public void stateChanged(javax.swing.event.ChangeEvent e)
```
Specified by:

stateChanged in interface javax.swing.event.ChangeListener

Class DTIPipeline

Nested Class Summary

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

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

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

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

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

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

Field Summary

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

Fields inherited from class javax.swing.JDialog

Fields inherited from class java.awt.Dialog

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface javax.swing.WindowConstants

Constructor Summary

Method Summary

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

Methods inherited from class javax.swing.JDialog

Methods inherited from class java.awt.Dialog

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

IMPORT

PRE_PROCESS

EPI_DISTORTION

TENSOR_ESTIMATION

FIBER_TRACKING

VISUALIZATION

mainPanel

nextButton

currentImage

DWIImage

inputTensorImage

DWIDir

T2Image

DWINewB0Image

tensorImage

goBackButton

importData

fiberTrack

dtiparams

visualization

DTIPreprocessing

estTensorPanel

EPIpanel

tabbedPane

DWIframe

T2frame

arrayTransMatrix

b0toStructMatrix

gradients

bmatValues

bvalues

refImageNum

srcBvalGradTable

DEFAULT

LLMSE

LINEAR

NON_LINEAR

RESTORE

WEIGHTED_LINEAR

Constructor Detail

DTIPipeline

Method Detail

init

actionPerformed

buildGrayTitledBorder

buildImportDataPanel

buildPreprocessingPanel

buildEPIPanel

buildTensorPanel

buildFiberTrackingPanel

buildVisuzalizationPanel

finishPreProcessingPanel

finishEPIPanel

finishTensorPanel

stateChanged