Package gov.nih.mipav.view.dialogs

Class JDialogTLRC

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.JDialogTLRC

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.RootPaneContainer, javax.swing.WindowConstants

public class JDialogTLRC
extends JDialogBase

Dialog to enter points for creating an Talaraich image.

Author:

William Gandler, Pierre-Louis Bazin

See Also:

TalairachTransformInfo, AlgorithmTalairachTransform, JDialogTalairachTransform, JDialogACPC, 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 ModelImage	acpcImage
private javax.swing.JRadioButton	anteriorPt
private WildMagic.LibFoundation.Mathematics.Vector3f	anteriorPt3Df
private javax.swing.JButton	applyTalairachButton
private static float	ATLAS_AC_TO_LAT
private static float	ATLAS_AC_TO_TOP
private static float	ATLAS_BOT_TO_AC
private static float	ATLAS_FRONT_TO_AC
private static float	ATLAS_PC_TO_BACK
private javax.swing.JButton	cancelTalairachButton
private javax.swing.JButton	clearTalairachButton
private ViewJFrameTriImage	frame
private boolean	haveAnteriorPt
private boolean	haveInferiorPt
private boolean	haveLeftPt
private boolean	havePosteriorPt
private boolean	haveRightPt
private boolean	haveSuperiorPt
private javax.swing.JRadioButton	inferiorPt
private WildMagic.LibFoundation.Mathematics.Vector3f	inferiorPt3Df
private int	interpolation
private javax.swing.JRadioButton	leftPt
private WildMagic.LibFoundation.Mathematics.Vector3f	leftPt3Df
private static float	MAX_ALLOWED_DEVIATION
private static float	MIN_ALLOWED_DEVIATION
private ModelImage	originalImage
private javax.swing.JRadioButton	posteriorPt
private WildMagic.LibFoundation.Mathematics.Vector3f	posteriorPt3Df
private javax.swing.JRadioButton	rightPt
private WildMagic.LibFoundation.Mathematics.Vector3f	rightPt3Df
private javax.swing.JButton	setTalairachButton
private javax.swing.JRadioButton	superiorPt
private WildMagic.LibFoundation.Mathematics.Vector3f	superiorPt3Df
private ModelImage	talairachImage
private TalairachTransformInfo	transform

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
JDialogTLRC(ViewJFrameTriImage theParentFrame, ModelImage orig, ModelImage acpc, ModelImage tlrc, TalairachTransformInfo trans, int interp)	This method creates a dialog for selecting markers used for generating a Talairach view image from an AC-PC aligned view image

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(java.awt.event.ActionEvent event)	If user clicks "Set", sets point here and in component image.
private void	computeTrilinearImage(float[] img, float xi, float yi, float zi, int nix, int niy, int niz, float[] result, int xr, int yr, int zr, int nrx, int nry, int nrz)	Transforms and resamples volume using trilinear interpolation
private void	convertToTalairach()	Creates Talairach image based on points that were set in component images.
private void	init()	Initializes GUI components of dialog.
private void	setAnteriorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)	Sets anterior label based on the point.
private void	setInferiorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)	Sets inferior label based on the point.
private void	setLeftPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)	Sets left label based on the point.
private void	setPosteriorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)	Sets posterior label based on the point.
private void	setRightPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)	Sets right label based on the point.
private void	setSuperiorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)	Sets superior label based on the point.
void	setTalairachHeader(ModelImage img)	add the Talairach Transform to the image header
private WildMagic.LibFoundation.Mathematics.Vector3f	toOriginal(WildMagic.LibFoundation.Mathematics.Vector3f in)	to convert frame coordinates into the original image ones
private void	transformTalairachTrilinear(float[] imgBuffer, double[][] xfrm, float ires, int iXdim, int iYdim, int iZdim, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim, int oXlow, int oYlow, int oZlow, int oXhigh, int oYhigh, int oZhigh, ViewJProgressBar progressBar, ModelImage image)	Transforms and resamples volume using trilinear interpolation

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

MAX_ALLOWED_DEVIATION

private static final float MAX_ALLOWED_DEVIATION

See Also:

Constant Field Values

MIN_ALLOWED_DEVIATION

private static final float MIN_ALLOWED_DEVIATION

See Also:

Constant Field Values

ATLAS_FRONT_TO_AC

private static final float ATLAS_FRONT_TO_AC

See Also:

Constant Field Values

ATLAS_PC_TO_BACK

private static final float ATLAS_PC_TO_BACK

See Also:

Constant Field Values

ATLAS_BOT_TO_AC

private static final float ATLAS_BOT_TO_AC

See Also:

Constant Field Values

ATLAS_AC_TO_TOP

private static final float ATLAS_AC_TO_TOP

See Also:

Constant Field Values

ATLAS_AC_TO_LAT

private static final float ATLAS_AC_TO_LAT

See Also:

Constant Field Values

frame

private ViewJFrameTriImage frame

originalImage

private ModelImage originalImage

acpcImage

private ModelImage acpcImage

talairachImage

private ModelImage talairachImage

transform

private TalairachTransformInfo transform

applyTalairachButton

private javax.swing.JButton applyTalairachButton

cancelTalairachButton

private javax.swing.JButton cancelTalairachButton

anteriorPt

private javax.swing.JRadioButton anteriorPt

posteriorPt

private javax.swing.JRadioButton posteriorPt

superiorPt

private javax.swing.JRadioButton superiorPt

inferiorPt

private javax.swing.JRadioButton inferiorPt

leftPt

private javax.swing.JRadioButton leftPt

rightPt

private javax.swing.JRadioButton rightPt

setTalairachButton

private javax.swing.JButton setTalairachButton

clearTalairachButton

private javax.swing.JButton clearTalairachButton

anteriorPt3Df

private WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt3Df

posteriorPt3Df

private WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt3Df

superiorPt3Df

private WildMagic.LibFoundation.Mathematics.Vector3f superiorPt3Df

inferiorPt3Df

private WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt3Df

leftPt3Df

private WildMagic.LibFoundation.Mathematics.Vector3f leftPt3Df

rightPt3Df

private WildMagic.LibFoundation.Mathematics.Vector3f rightPt3Df

haveAnteriorPt

private boolean haveAnteriorPt

havePosteriorPt

private boolean havePosteriorPt

haveSuperiorPt

private boolean haveSuperiorPt

haveInferiorPt

private boolean haveInferiorPt

haveLeftPt

private boolean haveLeftPt

haveRightPt

private boolean haveRightPt

interpolation

private int interpolation

Constructor Detail

JDialogTLRC

public JDialogTLRC(ViewJFrameTriImage theParentFrame,
                   ModelImage orig,
                   ModelImage acpc,
                   ModelImage tlrc,
                   TalairachTransformInfo trans,
                   int interp)

This method creates a dialog for selecting markers used for generating a Talairach view image from an AC-PC aligned view image

Parameters:

theParentFrame - The tri planar view frame that called this dialog.

orig - Image to generate a Talairach view from.

acpc - ACPC-aligned image

tlrc - Talairach-aligned image

Method Detail

init

private void init()

Initializes GUI components of dialog.

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent event)

If user clicks "Set", sets point here and in component image. If user clicks "Clear", clears point here and in component image. If user clicks "Apply", creates new Talairach image based on points. If user clicks "Cancel", disposes this dialog.

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class JDialogBase

Parameters:

event - Event that triggered this method.

setAnteriorPt

private void setAnteriorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)

Sets anterior label based on the point. Enables "Apply" if all points have been set.

Parameters:

pt - Point that was set.

setPosteriorPt

private void setPosteriorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)

Sets posterior label based on the point. Enables "Apply" if all points have been set.

Parameters:

pt - Point that was set.

setSuperiorPt

private void setSuperiorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)

Sets superior label based on the point. Enables "Apply" if all points have been set.

Parameters:

pt - Point that was set.

setInferiorPt

private void setInferiorPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)

Sets inferior label based on the point. Enables "Apply" if all points have been set.

Parameters:

pt - Point that was set.

setLeftPt

private void setLeftPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)

Sets left label based on the point. Enables "Apply" if all points have been set.

Parameters:

pt - Point that was set.

setRightPt

private void setRightPt(WildMagic.LibFoundation.Mathematics.Vector3f pt)

Sets right label based on the point. Enables "Apply" if all points have been set.

Parameters:

pt - Point that was set.

convertToTalairach

private void convertToTalairach()

Creates Talairach image based on points that were set in component images.

setTalairachHeader

public void setTalairachHeader(ModelImage img)

add the Talairach Transform to the image header

toOriginal

private WildMagic.LibFoundation.Mathematics.Vector3f toOriginal(WildMagic.LibFoundation.Mathematics.Vector3f in)

to convert frame coordinates into the original image ones

transformTalairachTrilinear

private void transformTalairachTrilinear(float[] imgBuffer,
                                         double[][] xfrm,
                                         float ires,
                                         int iXdim,
                                         int iYdim,
                                         int iZdim,
                                         float oXres,
                                         float oYres,
                                         float oZres,
                                         int oXdim,
                                         int oYdim,
                                         int oZdim,
                                         int oXlow,
                                         int oYlow,
                                         int oZlow,
                                         int oXhigh,
                                         int oYhigh,
                                         int oZhigh,
                                         ViewJProgressBar progressBar,
                                         ModelImage image)

Transforms and resamples volume using trilinear interpolation

Parameters:

imgBuffer - Image array.

xfrm - Transformation matrix to be applied.

ires - In resolution (same in all dimensions).

iXdim - In X dimension.

iYdim - In Y dimension.

iZdim - In Z dimension.

oXres - Out X resolution.

oYres - Out Y resolution.

oZres - Out Z resolution.

oXdim - Out X dimension.

oYdim - Out Y dimension.

oZdim - Out Z dimension.

oXlow - Out X low.

oYlow - Out Y low.

oZlow - Out Z low.

oXhigh - Out X high.

oYhigh - Out Y high.

oZhigh - Out Z high.

progressBar - Progress bar.

image - Image.

computeTrilinearImage

private void computeTrilinearImage(float[] img,
                                   float xi,
                                   float yi,
                                   float zi,
                                   int nix,
                                   int niy,
                                   int niz,
                                   float[] result,
                                   int xr,
                                   int yr,
                                   int zr,
                                   int nrx,
                                   int nry,
                                   int nrz)

Transforms and resamples volume using trilinear interpolation