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.dialogs.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 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
`private javax.swing.JTextField`	`bValueTextField`	textfields *
`private java.lang.String`	`currDir`	current directory *
`private ModelImage`	`DTI`	Diffusion Tensor image.
`private javax.swing.JTextField`	`formatTextField`	textfields *
`private javax.swing.JTextField`	`gapTextField`	textfields *
`private java.awt.GridBagConstraints`	`gbc`	grid bag constraints *
`private java.awt.GridBagConstraints`	`gbc2`	grid bag constraints *
`private java.awt.GridBagConstraints`	`gbc3`	grid bag constraints *
`private javax.swing.JTextField`	`hFOVTextField`	textfields *
`private javax.swing.JTextField`	`imagePlaneTextField`	textfields *
`private AlgorithmDWI2DTI`	`kAlgorithm`	handle to algorithm *
`private java.io.File`	`listFile`	list file *
`private javax.swing.JButton`	`loadMaskButton`	button *
`private java.lang.String[][]`	`m_aakDWIList`	List of file names for the Diffusion Weighted Images, from the .path *
`private int[]`	`m_aiMatrixEntries`	keeps track of unique entries in the BMatrix
`private float`	`m_fMeanNoise`	Mean noise vale read from the .list file
`private float`	`m_fResX`	Slice thickness read from .list file
`private float`	`m_fResY`	Slice thickness read from .list file
`private float`	`m_fResZ`	Slice thickness read from .list file
`private int`	`m_iBOrig`	Number of different BMatrix rows:
`private int`	`m_iDimX`	X-dimensions for Diffusion Weighted Images.
`private int`	`m_iDimY`	Y-dimensions for Diffusion Weighted Images.
`private int`	`m_iSlices`	Number of slices in the Diffusion Weighted Images series.
`private int`	`m_iWeights`	Number of weights in the Diffusion Weighted Images series.
`private WildMagic.LibFoundation.Mathematics.GMatrixd`	`m_kBMatrix`	General matrix storing BMatrix values.
`private java.lang.String`	`m_kParentDir`	paren tdir *
`private java.lang.String`	`m_kRawFormat`	raw image format read from the .list file:
`private javax.swing.JPanel`	`mainPanel`	main panel *
`private ModelImage`	`maskImage`	mask Image *
`private javax.swing.JTextField`	`maskImageTextField`	textfields *
`private javax.swing.JTextField`	`numSlicesTextField`	textfields *
`private javax.swing.JTextField`	`numVolumesTextField`	textfields *
`private javax.swing.JTextField`	`outputDirTextField`	textfields *
`private javax.swing.JTextField`	`phaseEncodingTextField`	textfields *
`private java.util.Vector<java.util.ArrayList<java.lang.String>>`	`slicesVector`	slices *
`private javax.swing.JTextField`	`sliceThicknessTextField`	textfields *
`private ModelImage`	`srcImage`	src image *
`private javax.swing.JTable`	`srcImagesTable`	table to display the src image names.
`private javax.swing.table.DefaultTableModel`	`srcTableModel`	table model for the srcimages.
`private javax.swing.JTextField`	`vFOVTextField`	textfields *
`private javax.swing.JTextField`	`xdimTextField`	textfields *
`private javax.swing.JTextField`	`ydimTextField`	textfields *

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

JDialogDTIEstimateTensor()
constructor

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 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, 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

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:
  - kAlgorithm
```
private AlgorithmDWI2DTI kAlgorithm
```
    handle to algorithm *
  - 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.
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    algorithm performed
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - the algorithm which has just completed
  - 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

Class JDialogDTIEstimateTensor

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

Methods inherited from interface java.awt.event.WindowListener

Field Detail

gbc

gbc2

gbc3

mainPanel

srcImagesTable

srcTableModel

currDir

srcImage

slicesVector

bValueTextField

xdimTextField

ydimTextField

numSlicesTextField

numVolumesTextField

hFOVTextField

vFOVTextField

outputDirTextField

formatTextField

gapTextField

sliceThicknessTextField

imagePlaneTextField

phaseEncodingTextField

maskImageTextField

maskImage

listFile

m_kParentDir

m_iDimX

m_iDimY

m_fMeanNoise

m_kRawFormat

m_iSlices

m_iWeights

m_fResX

m_fResY

m_fResZ

m_kBMatrix

m_aiMatrixEntries

m_iBOrig

kAlgorithm

DTI

loadMaskButton

m_aakDWIList

Constructor Detail

JDialogDTIEstimateTensor

Method Detail

init

actionPerformed

parse

populateFields

readBValGradientFile

createListFile

createBMatrixFile

createPathFile

readListFile