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

Class JDialogPatellaTraceSectionsNIH

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.Knees.JDialogPatellaTraceSectionsNIH

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 JDialogPatellaTraceSectionsNIH
extends JDialogBase
implements AlgorithmInterface

The class is the driver for the AAM classification. User specifies the AAM trained Atlas directory and target image. The algorithm performs NMI based similarity measure between each 2D slice in target image and the 2D slices atlas, find the closed image, then invoke the corresponding AAM model to do automatic segmentation on prostate MRI image.

Author:

Ruida Cheng

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	JDialogPatellaTraceSectionsNIH.Line
(package private) class	JDialogPatellaTraceSectionsNIH.ModelString
(package private) class	JDialogPatellaTraceSectionsNIH.PolygonShapeInfo	Polygon shape info class to do shape comparison after the AAM classification applied to do the segmentation.
(package private) class	JDialogPatellaTraceSectionsNIH.Range	Ending slice start and end indexes.
(package private) class	JDialogPatellaTraceSectionsNIH.ShapeFactor	shape descriptor class.
(package private) class	JDialogPatellaTraceSectionsNIH.TracingPoint

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 static int	Axial	axis orientation.
private int	axis
private javax.swing.JComboBox	axisList	axis region
private int	boxXmax
private int	boxXmin
private int	boxYmax	Cropped image region.
private int	boxYmin	Cropped image region.
private javax.swing.JButton	buttonImageFAT
private javax.swing.JButton	buttonImageGRE
private javax.swing.JButton	buttonModel
private javax.swing.JPanel	buttonPanel
private static boolean[]	checkList
private static int	Class1
private static int	Class1_corner
private static int	Class1_lowInten
private static int	Class1_weak
private static int	Class2
private static int	Class3
private static int[]	colNumber
private CornerEdgePattern	cornerEdgePattern
private static int	Coronal
private RegularEdgePattern	edgePattern
private int	endPt
private int	endSlice
private java.util.Vector<java.lang.String>	endSliceImageNames
private java.util.Vector<ModelImage>	endSliceImages
private java.util.Vector<JDialogPatellaTraceSectionsNIH.Range>	endSliceRange
private java.util.Vector<java.lang.String>	endSliceRangeNames
private ModelImage	fatImage
private javax.swing.JFileChooser	fatImageChooser	target image variables.
private java.lang.String	fatImageDirectory
private java.lang.String	fatImageName
(package private) boolean	firstAssigned
private static int	FuzzyC
private ModelImage	gaussianMap
private static int	GRE
private ModelImage	greImage
private javax.swing.JFileChooser	greImageChooser
private java.lang.String	greImageDirectory
private java.lang.String	greImageName
private HolesPattern	holesPattern
private javax.swing.JPanel	imageSelectionPanel
private java.util.Vector<java.util.Vector<ModelImage>>	imageStackFuzzyC
private javax.swing.JLabel	labelAxis
private javax.swing.JLabel	labelImageFAT	Target image directory.
private javax.swing.JLabel	labelImageGRE	GRE image directory.
private javax.swing.JLabel	labelModel	key image directory.
private javax.swing.JPanel	mainPanel
private int	midPt
private static java.lang.String	MipavCoordinateSystem
private C_AAMMODEL	model	AAM model reference.
private javax.swing.JFileChooser	modelChooser	key images variables.
private java.lang.String	modelDirectory
(package private) int	numSteps
private static int[]	rowNumber
private static int	Saggital
(package private) static float	section1_degree_end
(package private) static float	section1_degree_start
(package private) static float	section2_degree_end
(package private) static float	section2_degree_start
(package private) static float	section3_degree_end
(package private) static float	section3_degree_start
(package private) static float	section4_degree_end
(package private) static float	section4_degree_start
(package private) static float	section5_degree_lowerHalf_end
(package private) static float	section5_degree_lowerHalf_start
(package private) static float	section5_degree_upperHalf_end
(package private) static float	section5_degree_upperHalf_start
(package private) static float	section6_degree_end
(package private) static float	section6_degree_start
private static long	serialVersionUID
(package private) java.util.Hashtable<java.lang.Integer,java.util.Hashtable<java.lang.Integer,JDialogPatellaTraceSectionsNIH.Line>>	slicesPts
private int	startPt
private int	startSlice
private static java.lang.String[]	statsToCalculate
(package private) int	tenPercent
private javax.swing.JTextField	textFieldImageFAT
private javax.swing.JTextField	textFieldImageGRE
private javax.swing.JTextField	textFieldModel
(package private) int	twentyPercent
private ViewUserInterface	UI	The main user interface.
(package private) VOI	voiNewFinal
private VOIVector	voiVectorFinal
private WeakConnectedEdgePatternHorizontal	weakEdgePatternHorizontal
private WeakConnectedEdgePatternVertical	weakEdgePatternVertical
private int[]	xBounds	Cropped region bounding.
private int[]	yBounds
private int[]	zBounds

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
JDialogPatellaTraceSectionsNIH(java.awt.Frame theParentFrame, ModelImage srcImage)	Constructor. the parent frame

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(java.awt.event.ActionEvent event)	actionPerformed handler.
void	algorithmPerformed(AlgorithmBase algorithm)	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
private void	computeGradient(float xCoord, float yCoord, float zCoord, double[] result, double[] grad, double[] gradDir, ModelImage targetImageSlice)
private void	computeGradient(ModelImage image, float xCoord, float yCoord, float zCoord, double[] result, double[] grad, double[] gradDir)
private void	computeNormalLine(WildMagic.LibFoundation.Mathematics.Vector3f startPt, WildMagic.LibFoundation.Mathematics.Vector3f endPt, WildMagic.LibFoundation.Mathematics.Vector3f midPt, WildMagic.LibFoundation.Mathematics.Vector3f outNormPt, WildMagic.LibFoundation.Mathematics.Vector3f inNormPt, float stepPct, WildMagic.LibFoundation.Mathematics.Vector3f normStep, WildMagic.LibFoundation.Mathematics.Vector3f interpPt)
void	condenseVOI(ModelImage targetImageSlice, int voiNumber)
void	configVOIsNumbers(ModelImage image, int[] slices)
void	createOneContours(ModelImage targetImageSlice)
void	createTwoContours(ModelImage targetImageSlice)
(package private) void	DFS(int row, int col, ModelImage fuzzyCImage, int[][] visited, int[] xmin, int[] xmax, int[] ymin, int[] ymax)
private WildMagic.LibFoundation.Mathematics.Vector3f	displaySlices(ModelImage fuzzyCImage, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage greImageSlice, ModelImage gaussianImageSlice, int sliceNumber)
private void	displaySlicesRadical(ModelImage fuzzyCImage, ModelImage class1Image, ModelImage greImageSlice, ModelImage gaussianImageSlice, int sliceNumber, WildMagic.LibFoundation.Mathematics.Vector3f pos)
void	disposeLocal()
static double	distance(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2, float[] res)
void	doFuzzyCmean(ModelImage coherenceEnhancingDiffusionImage, java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC)
void	doSegmentation(boolean doCropImage)	First time the dialog called, this function is invoked to do segmentation.
private void	findBestGradientChange(WildMagic.LibFoundation.Mathematics.Vector3f interpPt, WildMagic.LibFoundation.Mathematics.Vector3f normStep, float sliceZ, float[] x, float[] y, ModelImage targetImageSlice)
private void	findBoundingContour(int sliceNumber, VOI resultVOIBoundary, VOI resultVOIInner, VOI resultVOIOuter, WildMagic.LibFoundation.Mathematics.Vector3f center, ModelImage fatImageSlice)
private boolean	findCornerEdgeOnImage(int x, int y, ModelImage imageSlice, int range, double intensity, int type)
private boolean	findEdgeOnImage(int x, int y, ModelImage imageSlice, int range, double intensity, int type)
private boolean	findHolesOnImage(int x, int y, ModelImage imageSlice, int range, double intensity, int type)
private void	findSections(VOI boundary, float[][] sections, WildMagic.LibFoundation.Mathematics.Vector3f center)
private boolean	findWeakConnectedEdgeOnImageHorizontal(int x, int y, ModelImage imageSlice, int range, int type, boolean searchOnRight, int[] xResult)
private boolean	findWeakConnectedEdgeOnImageVertical(int x, int y, ModelImage imageSlice, int range, int type, boolean searchOnRight, int[] xResult)
private void	generateBoundaryContours(VOIBase srcContour, ModelImage targetImageSlice)
ModelImage	generateGaussianMap()
private void	generateInnerContour(VOIBase srcContour, ModelImage targetImageSlice)
void	generateInOutContours(VOIBase startVOI, float[] innerDist, float[] outerDist, WildMagic.LibFoundation.Mathematics.Vector3f[] pt_inner, WildMagic.LibFoundation.Mathematics.Vector3f[] pt_outer, WildMagic.LibFoundation.Mathematics.Vector3f[] pt_voi, float[] center)
(package private) void	generateMap(int x, int y, ModelImage imageSlice, int[][] visited, int[][] map, int Xmin, int Xmax, int Ymin, int Ymax, int type)
private float[]	getCentroids(ModelImage srcImage, AlgorithmFuzzyCMeans fcmAlgo, float[] centroids)
void	init()	Init() function to create the GUI dialog.
(package private) boolean	isSafe(int row, int col, int[][] visited, ModelImage fuzzyCImage, int[] xmin, int[] xmax, int[] ymin, int[] ymax)
(package private) boolean	isSafe(int x, int y, int[][] visited, ModelImage fatImageSlice, int Xmin, int Xmax, int Ymin, int Ymax, int xDim, int yDim)
static void	pause()	Pauses the display until the user hits enter.
(package private) void	printVector(java.util.Vector<JDialogPatellaTraceSectionsNIH.TracingPoint> v)
private void	processingEndSliceData(java.lang.String endSliceModelDir)	Process the ending slice atlas directory.
private void	readEndingSlicesDir()	Read the ending slice index to guide the segmentation towards apex and base.
private void	readFATImage()	File chooser to select target image directory.
void	readFATImagesAndVOIs()	read target image.
ModelImage	runCED(ModelImage targetImage)
private void	runLevelSet(ModelImage fuzzyCImage)
void	segmentationAuto()	Driver to do the auto segmentation with AAM model.
void	smoothVOI120Single(ModelImage maskImage, ModelImage resultImage)
void	smoothVOI150Single(ModelImage maskImage, ModelImage resultImage)
void	smoothVOI60(ModelImage maskImage, ModelImage resultImage)
void	smoothVOI60DualContour(ModelImage maskImage, ModelImage resultImage)
void	smoothVOI60Single(ModelImage maskImage, ModelImage resultImage)
void	smoothVOI60Special(ModelImage maskImage, ModelImage resultImage)
void	smoothVOISingle(ModelImage maskImage, ModelImage resultImage, int nPts)
private void	strain()
private void	strain1()
private WildMagic.LibFoundation.Mathematics.Vector2f	traceSection1(float posX, float posY, float stepX, float stepY, WildMagic.LibFoundation.Mathematics.Vector3f center, float degree, int sliceNumber, int currentStep, float distCurrent, float distOuter, ModelImage greImageSlice, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage fuzzyCImage)
private WildMagic.LibFoundation.Mathematics.Vector2f	traceSection2(float posX, float posY, float stepX, float stepY, WildMagic.LibFoundation.Mathematics.Vector3f center, float degree, int sliceNumber, int currentStep, float distCurrent, float distOuter, ModelImage greImageSlice, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage fuzzyCImage)
private WildMagic.LibFoundation.Mathematics.Vector2f	traceSection3(float posX, float posY, float stepX, float stepY, WildMagic.LibFoundation.Mathematics.Vector3f center, float degree, int sliceNumber, int currentStep, float distCurrent, float distOuter, ModelImage greImageSlice, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage fuzzyCImage)
private WildMagic.LibFoundation.Mathematics.Vector2f	traceSection4(float posX, float posY, float stepX, float stepY, WildMagic.LibFoundation.Mathematics.Vector3f center, float degree, int sliceNumber, int currentStep, float distCurrent, float distOuter, ModelImage greImageSlice, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage fuzzyCImage)
private WildMagic.LibFoundation.Mathematics.Vector2f	traceSection5(float posX, float posY, float stepX, float stepY, WildMagic.LibFoundation.Mathematics.Vector3f center, float degree, int sliceNumber, int currentStep, float distCurrent, float distOuter, ModelImage greImageSlice, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage fuzzyCImage)
private WildMagic.LibFoundation.Mathematics.Vector2f	traceSection6(float posX, float posY, float stepX, float stepY, WildMagic.LibFoundation.Mathematics.Vector3f center, float degree, int sliceNumber, int currentStep, float distCurrent, float distOuter, ModelImage greImageSlice, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage fuzzyCImage)
private void	tracingDFS(ModelImage fatImageSlice, ModelImage fuzzyCImage, ModelImage class1Image, ModelImage class2Image, ModelImage class3Image, ModelImage greImageSlice, ModelImage gaussianImageSlice, int sliceNumber, VOI resultVOIBoundary, VOI resultVOIInner, VOI resultVOIOuter)
private void	tracingDFS_mid(ModelImage greImageSlice, ModelImage fatImageSliceMid, VOI boundary, VOI inner, VOI outer, boolean first)
void	transformVOI()	BSpline smooth the final auto segmentation VOI contours.
void	updateTargetImage(int sliceNumber, ModelImage targetImageSlice)	After auto segmentation, update the target image with corresponding segmented VOIs.

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

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

UI

private ViewUserInterface UI

The main user interface.

model

private C_AAMMODEL model

AAM model reference.

labelModel

private javax.swing.JLabel labelModel

key image directory.

textFieldModel

private javax.swing.JTextField textFieldModel

buttonModel

private javax.swing.JButton buttonModel

labelImageFAT

private javax.swing.JLabel labelImageFAT

Target image directory.

textFieldImageFAT

private javax.swing.JTextField textFieldImageFAT

buttonImageFAT

private javax.swing.JButton buttonImageFAT

labelImageGRE

private javax.swing.JLabel labelImageGRE

GRE image directory.

textFieldImageGRE

private javax.swing.JTextField textFieldImageGRE

buttonImageGRE

private javax.swing.JButton buttonImageGRE

imageSelectionPanel

private javax.swing.JPanel imageSelectionPanel

buttonPanel

private javax.swing.JPanel buttonPanel

modelChooser

private javax.swing.JFileChooser modelChooser

key images variables.

modelDirectory

private java.lang.String modelDirectory

fatImageChooser

private javax.swing.JFileChooser fatImageChooser

target image variables.

fatImageName

private java.lang.String fatImageName

fatImageDirectory

private java.lang.String fatImageDirectory

greImageChooser

private javax.swing.JFileChooser greImageChooser

greImageName

private java.lang.String greImageName

greImageDirectory

private java.lang.String greImageDirectory

fatImage

private ModelImage fatImage

greImage

private ModelImage greImage

boxYmin

private int boxYmin

Cropped image region.

boxYmax

private int boxYmax

Cropped image region.

boxXmin

private int boxXmin

boxXmax

private int boxXmax

xBounds

private int[] xBounds

Cropped region bounding.

yBounds

private int[] yBounds

zBounds

private int[] zBounds

axisList

private javax.swing.JComboBox axisList

axis region

labelAxis

private javax.swing.JLabel labelAxis

Axial

private static int Axial

axis orientation. Will be used later.

Saggital

private static int Saggital

Coronal

private static int Coronal

axis

private int axis

statsToCalculate

private static final java.lang.String[] statsToCalculate

checkList

private static final boolean[] checkList

MipavCoordinateSystem

private static final java.lang.String MipavCoordinateSystem

mainPanel

private javax.swing.JPanel mainPanel

startSlice

private int startSlice

endSlice

private int endSlice

endSliceImageNames

private java.util.Vector<java.lang.String> endSliceImageNames

endSliceRangeNames

private java.util.Vector<java.lang.String> endSliceRangeNames

endSliceImages

private java.util.Vector<ModelImage> endSliceImages

endSliceRange

private java.util.Vector<JDialogPatellaTraceSectionsNIH.Range> endSliceRange

imageStackFuzzyC

private java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC

gaussianMap

private ModelImage gaussianMap

rowNumber

private static int[] rowNumber

colNumber

private static int[] colNumber

startPt

private int startPt

midPt

private int midPt

endPt

private int endPt

voiVectorFinal

private VOIVector voiVectorFinal

voiNewFinal

VOI voiNewFinal

FuzzyC

private static int FuzzyC

Class1

private static int Class1

Class2

private static int Class2

Class3

private static int Class3

GRE

private static int GRE

Class1_weak

private static int Class1_weak

Class1_lowInten

private static int Class1_lowInten

Class1_corner

private static int Class1_corner

section1_degree_start

static float section1_degree_start

section1_degree_end

static float section1_degree_end

section2_degree_start

static float section2_degree_start

section2_degree_end

static float section2_degree_end

section3_degree_start

static float section3_degree_start

section3_degree_end

static float section3_degree_end

section4_degree_start

static float section4_degree_start

section4_degree_end

static float section4_degree_end

section5_degree_upperHalf_start

static float section5_degree_upperHalf_start

section5_degree_upperHalf_end

static float section5_degree_upperHalf_end

section5_degree_lowerHalf_start

static float section5_degree_lowerHalf_start

section5_degree_lowerHalf_end

static float section5_degree_lowerHalf_end

section6_degree_start

static float section6_degree_start

section6_degree_end

static float section6_degree_end

firstAssigned

boolean firstAssigned

numSteps

int numSteps

tenPercent

int tenPercent

twentyPercent

int twentyPercent

edgePattern

private RegularEdgePattern edgePattern

holesPattern

private HolesPattern holesPattern

weakEdgePatternHorizontal

private WeakConnectedEdgePatternHorizontal weakEdgePatternHorizontal

cornerEdgePattern

private CornerEdgePattern cornerEdgePattern

weakEdgePatternVertical

private WeakConnectedEdgePatternVertical weakEdgePatternVertical

slicesPts

java.util.Hashtable<java.lang.Integer,java.util.Hashtable<java.lang.Integer,JDialogPatellaTraceSectionsNIH.Line>> slicesPts

Constructor Detail

JDialogPatellaTraceSectionsNIH

public JDialogPatellaTraceSectionsNIH(java.awt.Frame theParentFrame,
                                      ModelImage srcImage)

Constructor. the parent frame

Parameters:

theParentFrame -

Method Detail

configVOIsNumbers

public void configVOIsNumbers(ModelImage image,
                              int[] slices)

algorithmPerformed

public void algorithmPerformed(AlgorithmBase algorithm)

Description copied from interface: AlgorithmInterface

Called after an algorithm this listener is registered to exits (maybe successfully, maybe not). If the algorithm is run in a separate thread, this call will be made within that thread. If not, this call will be made from that same, shared thread.

Specified by:

algorithmPerformed in interface AlgorithmInterface

Parameters:

algorithm - the algorithm which has just completed

actionPerformed

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

actionPerformed handler.

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class JDialogBase

init

public void init()

Init() function to create the GUI dialog.

doSegmentation

public void doSegmentation(boolean doCropImage)

First time the dialog called, this function is invoked to do segmentation.

generateGaussianMap

public ModelImage generateGaussianMap()

doFuzzyCmean

public void doFuzzyCmean(ModelImage coherenceEnhancingDiffusionImage,
                         java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC)

getCentroids

private float[] getCentroids(ModelImage srcImage,
                             AlgorithmFuzzyCMeans fcmAlgo,
                             float[] centroids)

transformVOI

public void transformVOI()

BSpline smooth the final auto segmentation VOI contours.

generateInOutContours

public void generateInOutContours(VOIBase startVOI,
                                  float[] innerDist,
                                  float[] outerDist,
                                  WildMagic.LibFoundation.Mathematics.Vector3f[] pt_inner,
                                  WildMagic.LibFoundation.Mathematics.Vector3f[] pt_outer,
                                  WildMagic.LibFoundation.Mathematics.Vector3f[] pt_voi,
                                  float[] center)

segmentationAuto

public void segmentationAuto()

Driver to do the auto segmentation with AAM model.

strain1

private void strain1()

strain

private void strain()

runLevelSet

private void runLevelSet(ModelImage fuzzyCImage)

createOneContours

public void createOneContours(ModelImage targetImageSlice)

generateInnerContour

private void generateInnerContour(VOIBase srcContour,
                                  ModelImage targetImageSlice)

runCED

public ModelImage runCED(ModelImage targetImage)

createTwoContours

public void createTwoContours(ModelImage targetImageSlice)

generateBoundaryContours

private void generateBoundaryContours(VOIBase srcContour,
                                      ModelImage targetImageSlice)

condenseVOI

public void condenseVOI(ModelImage targetImageSlice,
                        int voiNumber)

findBestGradientChange

private void findBestGradientChange(WildMagic.LibFoundation.Mathematics.Vector3f interpPt,
                                    WildMagic.LibFoundation.Mathematics.Vector3f normStep,
                                    float sliceZ,
                                    float[] x,
                                    float[] y,
                                    ModelImage targetImageSlice)

computeGradient

private void computeGradient(float xCoord,
                             float yCoord,
                             float zCoord,
                             double[] result,
                             double[] grad,
                             double[] gradDir,
                             ModelImage targetImageSlice)

computeNormalLine

private void computeNormalLine(WildMagic.LibFoundation.Mathematics.Vector3f startPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f endPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f midPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f outNormPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f inNormPt,
                               float stepPct,
                               WildMagic.LibFoundation.Mathematics.Vector3f normStep,
                               WildMagic.LibFoundation.Mathematics.Vector3f interpPt)

smoothVOI60

public void smoothVOI60(ModelImage maskImage,
                        ModelImage resultImage)

smoothVOI60Single

public void smoothVOI60Single(ModelImage maskImage,
                              ModelImage resultImage)

smoothVOI150Single

public void smoothVOI150Single(ModelImage maskImage,
                               ModelImage resultImage)

smoothVOI120Single

public void smoothVOI120Single(ModelImage maskImage,
                               ModelImage resultImage)

smoothVOI60DualContour

public void smoothVOI60DualContour(ModelImage maskImage,
                                   ModelImage resultImage)

smoothVOI60Special

public void smoothVOI60Special(ModelImage maskImage,
                               ModelImage resultImage)

updateTargetImage

public void updateTargetImage(int sliceNumber,
                              ModelImage targetImageSlice)

After auto segmentation, update the target image with corresponding segmented VOIs.

Parameters:

sliceNumber - slice number.

targetImageSlice - 2D target image slice.

pause

public static void pause()

Pauses the display until the user hits enter.

readFATImagesAndVOIs

public void readFATImagesAndVOIs()

read target image.

readFATImage

private void readFATImage()

File chooser to select target image directory.

readEndingSlicesDir

private void readEndingSlicesDir()

Read the ending slice index to guide the segmentation towards apex and base.

processingEndSliceData

private void processingEndSliceData(java.lang.String endSliceModelDir)

Process the ending slice atlas directory.

Parameters:

endSliceModelDir - atlas directory.

disposeLocal

public void disposeLocal()

computeGradient

private void computeGradient(ModelImage image,
                             float xCoord,
                             float yCoord,
                             float zCoord,
                             double[] result,
                             double[] grad,
                             double[] gradDir)

displaySlicesRadical

private void displaySlicesRadical(ModelImage fuzzyCImage,
                                  ModelImage class1Image,
                                  ModelImage greImageSlice,
                                  ModelImage gaussianImageSlice,
                                  int sliceNumber,
                                  WildMagic.LibFoundation.Mathematics.Vector3f pos)

displaySlices

private WildMagic.LibFoundation.Mathematics.Vector3f displaySlices(ModelImage fuzzyCImage,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage gaussianImageSlice,
                                                                   int sliceNumber)

traceSection6

private WildMagic.LibFoundation.Mathematics.Vector2f traceSection6(float posX,
                                                                   float posY,
                                                                   float stepX,
                                                                   float stepY,
                                                                   WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                   float degree,
                                                                   int sliceNumber,
                                                                   int currentStep,
                                                                   float distCurrent,
                                                                   float distOuter,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage fuzzyCImage)

traceSection1

private WildMagic.LibFoundation.Mathematics.Vector2f traceSection1(float posX,
                                                                   float posY,
                                                                   float stepX,
                                                                   float stepY,
                                                                   WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                   float degree,
                                                                   int sliceNumber,
                                                                   int currentStep,
                                                                   float distCurrent,
                                                                   float distOuter,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage fuzzyCImage)

traceSection2

private WildMagic.LibFoundation.Mathematics.Vector2f traceSection2(float posX,
                                                                   float posY,
                                                                   float stepX,
                                                                   float stepY,
                                                                   WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                   float degree,
                                                                   int sliceNumber,
                                                                   int currentStep,
                                                                   float distCurrent,
                                                                   float distOuter,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage fuzzyCImage)

traceSection3

private WildMagic.LibFoundation.Mathematics.Vector2f traceSection3(float posX,
                                                                   float posY,
                                                                   float stepX,
                                                                   float stepY,
                                                                   WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                   float degree,
                                                                   int sliceNumber,
                                                                   int currentStep,
                                                                   float distCurrent,
                                                                   float distOuter,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage fuzzyCImage)

traceSection4

private WildMagic.LibFoundation.Mathematics.Vector2f traceSection4(float posX,
                                                                   float posY,
                                                                   float stepX,
                                                                   float stepY,
                                                                   WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                   float degree,
                                                                   int sliceNumber,
                                                                   int currentStep,
                                                                   float distCurrent,
                                                                   float distOuter,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage fuzzyCImage)

traceSection5

private WildMagic.LibFoundation.Mathematics.Vector2f traceSection5(float posX,
                                                                   float posY,
                                                                   float stepX,
                                                                   float stepY,
                                                                   WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                   float degree,
                                                                   int sliceNumber,
                                                                   int currentStep,
                                                                   float distCurrent,
                                                                   float distOuter,
                                                                   ModelImage greImageSlice,
                                                                   ModelImage class1Image,
                                                                   ModelImage class2Image,
                                                                   ModelImage class3Image,
                                                                   ModelImage fuzzyCImage)

tracingDFS

private void tracingDFS(ModelImage fatImageSlice,
                        ModelImage fuzzyCImage,
                        ModelImage class1Image,
                        ModelImage class2Image,
                        ModelImage class3Image,
                        ModelImage greImageSlice,
                        ModelImage gaussianImageSlice,
                        int sliceNumber,
                        VOI resultVOIBoundary,
                        VOI resultVOIInner,
                        VOI resultVOIOuter)

smoothVOISingle

public void smoothVOISingle(ModelImage maskImage,
                            ModelImage resultImage,
                            int nPts)

distance

public static final double distance(WildMagic.LibFoundation.Mathematics.Vector3f pt1,
                                    WildMagic.LibFoundation.Mathematics.Vector3f pt2,
                                    float[] res)

findBoundingContour

private void findBoundingContour(int sliceNumber,
                                 VOI resultVOIBoundary,
                                 VOI resultVOIInner,
                                 VOI resultVOIOuter,
                                 WildMagic.LibFoundation.Mathematics.Vector3f center,
                                 ModelImage fatImageSlice)

findSections

private void findSections(VOI boundary,
                          float[][] sections,
                          WildMagic.LibFoundation.Mathematics.Vector3f center)

tracingDFS_mid

private void tracingDFS_mid(ModelImage greImageSlice,
                            ModelImage fatImageSliceMid,
                            VOI boundary,
                            VOI inner,
                            VOI outer,
                            boolean first)

findCornerEdgeOnImage

private boolean findCornerEdgeOnImage(int x,
                                      int y,
                                      ModelImage imageSlice,
                                      int range,
                                      double intensity,
                                      int type)

findWeakConnectedEdgeOnImageHorizontal

private boolean findWeakConnectedEdgeOnImageHorizontal(int x,
                                                       int y,
                                                       ModelImage imageSlice,
                                                       int range,
                                                       int type,
                                                       boolean searchOnRight,
                                                       int[] xResult)

findWeakConnectedEdgeOnImageVertical

private boolean findWeakConnectedEdgeOnImageVertical(int x,
                                                     int y,
                                                     ModelImage imageSlice,
                                                     int range,
                                                     int type,
                                                     boolean searchOnRight,
                                                     int[] xResult)

findHolesOnImage

private boolean findHolesOnImage(int x,
                                 int y,
                                 ModelImage imageSlice,
                                 int range,
                                 double intensity,
                                 int type)

findEdgeOnImage

private boolean findEdgeOnImage(int x,
                                int y,
                                ModelImage imageSlice,
                                int range,
                                double intensity,
                                int type)

generateMap

void generateMap(int x,
                 int y,
                 ModelImage imageSlice,
                 int[][] visited,
                 int[][] map,
                 int Xmin,
                 int Xmax,
                 int Ymin,
                 int Ymax,
                 int type)

isSafe

boolean isSafe(int x,
               int y,
               int[][] visited,
               ModelImage fatImageSlice,
               int Xmin,
               int Xmax,
               int Ymin,
               int Ymax,
               int xDim,
               int yDim)

DFS

void DFS(int row,
         int col,
         ModelImage fuzzyCImage,
         int[][] visited,
         int[] xmin,
         int[] xmax,
         int[] ymin,
         int[] ymax)

isSafe

boolean isSafe(int row,
               int col,
               int[][] visited,
               ModelImage fuzzyCImage,
               int[] xmin,
               int[] xmax,
               int[] ymin,
               int[] ymax)

printVector

void printVector(java.util.Vector<JDialogPatellaTraceSectionsNIH.TracingPoint> v)