Package gov.nih.mipav.view.dialogs

Class JDialogDTIEstimateTensor

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

public class JDialogDTIEstimateTensor
extends JDialogBase
implements AlgorithmInterface, 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

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
private JTextField	bValueTextField	textfields *
private String	currDir	current directory *
private ModelImage	DTI	Diffusion Tensor image.
private JTextField	formatTextField	textfields *
private JTextField	gapTextField	textfields *
private GridBagConstraints	gbc	grid bag constraints *
private GridBagConstraints	gbc2	grid bag constraints *
private GridBagConstraints	gbc3	grid bag constraints *
private JTextField	hFOVTextField	textfields *
private JTextField	imagePlaneTextField	textfields *
private AlgorithmDWI2DTI	kAlgorithm	handle to algorithm *
private File	listFile	list file *
private JButton	loadMaskButton	button *
private 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 String	m_kParentDir	paren tdir *
private String	m_kRawFormat	raw image format read from the .list file:
private JPanel	mainPanel	main panel *
private ModelImage	maskImage	mask Image *
private JTextField	maskImageTextField	textfields *
private JTextField	numSlicesTextField	textfields *
private JTextField	numVolumesTextField	textfields *
private JTextField	outputDirTextField	textfields *
private JTextField	phaseEncodingTextField	textfields *
private final Vector<ArrayList<String>>	slicesVector	slices *
private JTextField	sliceThicknessTextField	textfields *
private ModelImage	srcImage	src image *
private JTable	srcImagesTable	table to display the src image names.
private DefaultTableModel	srcTableModel	table model for the srcimages.
private JTextField	vFOVTextField	textfields *
private JTextField	xdimTextField	textfields *
private 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

Modifier and Type	Method	Description
void	actionPerformed(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(File file)	Parses study directory
private boolean	populateFields()
private void	processDWI()	Calls AlgorithmDWI2DTI to create the diffusion tensor image.
private void	readBMatrixFile(String kFileName)	Loads the BMatrix file.
boolean	readBValGradientFile(String gradientFilePath)	reads the bval/gradient file...both dti studio format and fsl format are accepted
private void	readListFile()	read list file
void	readPathFile(String kFileName)	Loads the .path file.
private boolean	validateData()	validate data
void	windowClosing(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 Details

gbc

private GridBagConstraints gbc

grid bag constraints *

gbc2

private GridBagConstraints gbc2

grid bag constraints *

gbc3

private GridBagConstraints gbc3

grid bag constraints *

mainPanel

private JPanel mainPanel

main panel *

srcImagesTable

private JTable srcImagesTable

table to display the src image names.

srcTableModel

private DefaultTableModel srcTableModel

table model for the srcimages.

currDir

private String currDir

current directory *

srcImage

private ModelImage srcImage

src image *

slicesVector

private final Vector<ArrayList<String>> slicesVector

slices *

bValueTextField

private JTextField bValueTextField

textfields *

xdimTextField

private JTextField xdimTextField

textfields *

ydimTextField

private JTextField ydimTextField

textfields *

numSlicesTextField

private JTextField numSlicesTextField

textfields *

numVolumesTextField

private JTextField numVolumesTextField

textfields *

hFOVTextField

private JTextField hFOVTextField

textfields *

vFOVTextField

private JTextField vFOVTextField

textfields *

outputDirTextField

private JTextField outputDirTextField

textfields *

formatTextField

private JTextField formatTextField

textfields *

gapTextField

private JTextField gapTextField

textfields *

sliceThicknessTextField

private JTextField sliceThicknessTextField

textfields *

imagePlaneTextField

private JTextField imagePlaneTextField

textfields *

phaseEncodingTextField

private JTextField phaseEncodingTextField

textfields *

maskImageTextField

private JTextField maskImageTextField

textfields *

maskImage

private ModelImage maskImage

mask Image *

listFile

private File listFile

list file *

m_kParentDir

private 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 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 JButton loadMaskButton

button *

m_aakDWIList

private String[][] m_aakDWIList

List of file names for the Diffusion Weighted Images, from the .path *

Constructor Details

JDialogDTIEstimateTensor

public JDialogDTIEstimateTensor()

constructor

Method Details

init

public void init()

init

actionPerformed

public void actionPerformed(ActionEvent e)

action performed

Specified by:

actionPerformed in interface ActionListener

Overrides:

actionPerformed in class JDialogBase

parse

public boolean parse(File file)

Parses study directory

Parameters:

file -

Returns:

populateFields

private boolean populateFields()

readBValGradientFile

public boolean readBValGradientFile(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(String kFileName)

Loads the .path file.

Parameters:

kFileName - path file name.

kPathName - parent directory.

readBMatrixFile

private void readBMatrixFile(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(WindowEvent event)

window closing

Specified by:

windowClosing in interface WindowListener

Overrides:

windowClosing in class JDialogBase

Parameters:

event - WindowEvent