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

All Methods Static Methods Instance Methods Concrete Methods
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)

Class JDialogPatellaTraceSectionsNIH

Nested Class Summary

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

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

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

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

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

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

Field Summary

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

Fields inherited from class javax.swing.JDialog

Fields inherited from class java.awt.Dialog

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface javax.swing.WindowConstants

Constructor Summary

Method Summary

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

Methods inherited from class javax.swing.JDialog

Methods inherited from class java.awt.Dialog

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

UI

model

labelModel

textFieldModel

buttonModel

labelImageFAT

textFieldImageFAT

buttonImageFAT

labelImageGRE

textFieldImageGRE

buttonImageGRE

imageSelectionPanel

buttonPanel

modelChooser

modelDirectory

fatImageChooser

fatImageName

fatImageDirectory

greImageChooser

greImageName

greImageDirectory

fatImage

greImage

boxYmin

boxYmax

boxXmin

boxXmax

xBounds

yBounds

zBounds

axisList

labelAxis

Axial

Saggital

Coronal

axis

statsToCalculate

checkList

MipavCoordinateSystem

mainPanel

startSlice

endSlice

endSliceImageNames

endSliceRangeNames

endSliceImages

endSliceRange

imageStackFuzzyC

gaussianMap

rowNumber

colNumber

startPt

midPt

endPt

voiVectorFinal