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.ProstateFramework.JDialogProstateSegmentationRegBSpline3D

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 JDialogProstateSegmentationRegBSpline3D
extends JDialogBase
implements AlgorithmInterface
```
Semi-automatic MR Prostate segmentation - Registration and Fuzzy-C guided segmentation model. The algorithm uses B-Spline registration and Fuzzy-C to guide the MR prostate segmentation. Basic steps: 1) User open the axial, sagittal, coronal images in the MIPAV frame. 2) User manually outline the three contours on separate slices for each axial, sagittal, and coronal images to define the middle, the apex and the base of the prostate. 3) User click the OK button to let a fully automatic registration guided algorithm to segment the prostate of all the three images.

Author:

Ruida Cheng

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`(package private) class`	`JDialogProstateSegmentationRegBSpline3D.Edge`
`(package private) class`	`JDialogProstateSegmentationRegBSpline3D.PolarPoint`

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`	Axial image type
`private static int`	`Coronal`	Coronal image type
`(package private) int`	`endVOIAxial`
`private int`	`endVOICoronal`
`(package private) int`	`endVOISagittal`
`private ModelImage`	`imageAxial`
`private ModelImage`	`imageCoronal`
`private ModelImage`	`imageSagittal`
`private javax.swing.JLabel`	`labelAxis`
`private javax.swing.JLabel`	`labelCoronal`
`private javax.swing.JLabel`	`labelEndVOIAxial`
`private javax.swing.JLabel`	`labelEndVOICoronal`
`private javax.swing.JLabel`	`labelEndVOISagittal`
`private javax.swing.JLabel`	`labelMidVOIAxial`
`private javax.swing.JLabel`	`labelMidVOICoronal`
`private javax.swing.JLabel`	`labelMidVOISagittal`
`private javax.swing.JLabel`	`labelSagittal`
`private javax.swing.JLabel`	`labelStartVOIAxial`
`private javax.swing.JLabel`	`labelStartVOICoronal`
`private javax.swing.JLabel`	`labelStartVOISagittal`
`(package private) int`	`midVOIAxial`
`private int`	`midVOICoronal`
`(package private) int`	`midVOISagittal`
`private javax.swing.JRadioButton`	`radioBSpline`
`private javax.swing.JRadioButton`	`radioOAR`
`private static int`	`Sagittal`	Sagittal image type
`(package private) int`	`startVOIAxial`
`private int`	`startVOICoronal`
`(package private) int`	`startVOISagittal`
`private javax.swing.JTextField`	`textFieldEndVOIAxial`
`private javax.swing.JTextField`	`textFieldEndVOICoronal`
`private javax.swing.JTextField`	`textFieldEndVOISagittal`
`private javax.swing.JTextField`	`textFieldMidVOIAxial`
`private javax.swing.JTextField`	`textFieldMidVOICoronal`
`private javax.swing.JTextField`	`textFieldMidVOISagittal`
`private javax.swing.JTextField`	`textFieldStartVOIAxial`
`private javax.swing.JTextField`	`textFieldStartVOICoronal`
`private javax.swing.JTextField`	`textFieldStartVOISagittal`
`private int`	`tracingSliceNumber`	number of slices to trace, start from the apex and base VOIs
`private ViewUserInterface`	`UI`	global user interface to get the three active images.
`private boolean`	`useBSpline`	Flag to indicate to use B-Spline registration or OAR registration

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

JDialogProstateSegmentationRegBSpline3D(java.awt.Frame theParentFrame)
GUI interface for semi-automatic MR prostate segmentation.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Just handle GUI button clicks event.
`void`	`adjustVOIs(ModelImage image)`	When user draws the 3 VOIs out of order, adjust the VOIs in ascending order
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	This method is required if the AlgorithmPerformed interface is implemented.
`void`	`autoConfigVOIsNumbers()`	After user manually draw the three VOIs on each axial, sagittal, coronal image, the drawn VOIs slices number is auto configured to appear in the dialog GUI interface.
`private ModelImage`	`calculateCoherenceEnhancingDiffusion(ModelImage cropImage)`	Apply the coherence enhancing diffusion filter to the croppred MR image.
`void`	`calculateVOIsVolume()`	Compute the VOIs binary mask based volumes.
`void`	`callAlgorithm(ModelImage image, int midVOI, int startVOI, int endVOI, int axis)`	Single thread based segmentation, which takes up to 40 minutes.
`void`	`configVOIsNumbers(ModelImage image, int[] slices)`	Configure the mid, apex and base VOIs, sort them in order.
`void`	`convertVOIToDicomSpace(VOIVector src, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> target, ModelImage image, int startSlice, int endSlice)`	Conver the VOIs from image space to Dicom space
`void`	`createImagePointTable(JDialogProstateSegmentationRegBSpline3D.Edge imageTable, ModelImage resultImage)`	Convert each image pixel to polar coordinate system, saved them in a table.
`private java.lang.Runnable`	`createTask(ModelImage image, int midVOI, int startVOI, int endVOI, int axis)`	Parallel processing the automatic segmentation algorithm to all the three images concurrently.
`private void`	`createVOIPointTable(JDialogProstateSegmentationRegBSpline3D.Edge voiTable, ModelImage resultImage)`	Create the VOI table in polar coodinate system.
`ModelImage`	`cropROI(ModelImage image, int[] xBounds, int[] yBounds, int[] zBounds, int[] boundingBox, int midVOI)`	Crop MR image with specified X, Y, Z bounds Use the mid slice as the initial guidance to find the bounds.
`void`	`doFuzzyCmean(ModelImage coherenceEnhancingDiffusionImage, java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC)`	Generate the Fuzzy-C means classes from the CED image
`void`	`doRegistrationEnd(ModelImage image, ModelImage coherenceEnhancingDiffusionImage, java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC, int endVOI, int[] boundingBox, int axis)`	Near the base, base contour starts as the initial estimate, and repeat the same process toward the end slices.
`void`	`doRegistrationMid(ModelImage image, ModelImage coherenceEnhancingDiffusionImage, java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC, int midVOI, int startVOI, int endVOI, int[] boundingBox, int axis)`	The proposed model uses 2D registration to register 2D slices from the middle slice to the adjacent slice.
`void`	`doRegistrationStart(ModelImage image, ModelImage coherenceEnhancingDiffusionImage, java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC, int startVOI, int[] boundingBox, int axis)`	Near the apex, apex contour starts as the initial estimate, and repeat the same process toward the end slices.
`void`	`drawNarrowBand(JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable, ModelImage resultImage)`	Draw the narrow band region.
`void`	`fillholes(ModelImage maskImage)`	Fill holes inside the binary mask image.
`void`	`findNarrowBand(JDialogProstateSegmentationRegBSpline3D.Edge voiTable, JDialogProstateSegmentationRegBSpline3D.Edge imageTable, JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable)`	Find the narrow band regions around VOI contours.
`void`	`findRegion(JDialogProstateSegmentationRegBSpline3D.Edge imageTable, float theta1, float theta2, java.util.Vector<JDialogProstateSegmentationRegBSpline3D.PolarPoint> voiPointsInRange, JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable)`	Looking for the narrow band region.
`void`	`findVOIpointsInRange(JDialogProstateSegmentationRegBSpline3D.Edge imageTable, java.util.Vector<JDialogProstateSegmentationRegBSpline3D.PolarPoint> voiPointsInRange, int min, int max, JDialogProstateSegmentationRegBSpline3D.Edge voiTable)`	Tracing generated VOI tables, convert it from image coordinate to Polar coordinate.
`private float[]`	`getCentroids(ModelImage srcImage, AlgorithmFuzzyCMeans fcmAlgo, float[] centroids)`	Gets the minimum and maximum of each image and initializes the centroids dialog appropriately.
`void`	`IDobjects(ModelImage maskImage)`	Eliminate the small binary mask components.
`void`	`init()`	Create the dialog interface.
`boolean`	`inRange(JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable, int x, int y)`	Check whether the given x, y pixel fall withing the narrow band region.
`boolean`	`isInsideVOI(int pos, ModelImage img)`	check if given pixl location is inside VOI or not.
`private boolean`	`isVOIsCloseEnough(int currentSlice, ModelImage resultImage, ModelImage refImage)`	Check the registration accuracy.
`void`	`maskToVOI(ModelImage maskImage, ModelImage testImage)`	Convert mask image to VOI
`void`	`maskVOIFill(ModelImage maskImage)`	Fill pixels inside VOI.
`void`	`morphologyPostProcessing(ModelImage maskImage, ModelImage resultImage, ModelImage testImage)`	Apply the morphology filter the generate binary mask image from Fuzz-C segmentation.
`void`	`particleSystem(ModelImage maskImage)`	Particle system analysis.
`static void`	`pause()`	Pauses the display until the user hits enter.
`void`	`printVolume(ModelImage srcImage, VOIVector voiVector, int viewOrientation)`	Print out the three VOIs volume in system console out.
`void`	`removeContourFromOtherOrientation()`	User central gland contours projection to remove the extra interpolated VOIs contours at the apex and base.
`void`	`removeVOIsInDicomSpace(int zSlice, float zDicom, ModelImage image, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> firstVOI, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> secondVOI, int viewOrientation)`	Remove the extra VOIs contours in Dicom space.
`void`	`segmentFromFuzzyC(java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC, int currentSlice, ModelImage resultImage, ModelImage refImage, ModelImage testImage, int axis)`	Apply the Fuzzy-C means segmentation to CED image stack.
`void`	`smoothVOI120(ModelImage maskImage, ModelImage resultImage)`	Convert the mask image to VOI with 120 points.
`void`	`smoothVOI50(ModelImage maskImage, ModelImage resultImage)`	Convert the mask image to VOI with 50 points
`void`	`sortCEDImageVOIs(ModelImage coherenceEnhancingDiffusionImage, int midVOI, int startVOI, int endVOI)`	Sort the CED image VOIs
`void`	`sortImageVOIs(ModelImage image)`	Sorting image VOI
`void`	`sortImageVOIsInit(ModelImage image, int midVOI, int startVOI, int endVOI)`	Sort the original MR image's specified VOIs
`void`	`threshold(ModelImage maskImage)`	Convert the mask image specified theshold values.
`void`	`transformVOI(ModelImage image, ModelImage resultImage, int[] boundingBox, int currentSlice)`	Transform the the resulting VOI from cropped image to oringal MR image.
`java.lang.Runnable`	`trimVOIsInSingleImage(ModelImage image, int startVOI, int endVOI, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> firstVOI, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> secondVOI, int viewOrientation)`	In Dicom space, central contours projections to eliminate the extra contours at the apex and base.

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
  - UI
```
private ViewUserInterface UI
```
    global user interface to get the three active images.
  - tracingSliceNumber
```
private int tracingSliceNumber
```
    number of slices to trace, start from the apex and base VOIs
  - Axial
```
private static int Axial
```
    Axial image type
  - Sagittal
```
private static int Sagittal
```
    Sagittal image type
  - Coronal
```
private static int Coronal
```
    Coronal image type
  - labelAxis
```
private javax.swing.JLabel labelAxis
```
  - labelStartVOIAxial
```
private javax.swing.JLabel labelStartVOIAxial
```
  - textFieldStartVOIAxial
```
private javax.swing.JTextField textFieldStartVOIAxial
```
  - labelEndVOIAxial
```
private javax.swing.JLabel labelEndVOIAxial
```
  - textFieldEndVOIAxial
```
private javax.swing.JTextField textFieldEndVOIAxial
```
  - labelMidVOIAxial
```
private javax.swing.JLabel labelMidVOIAxial
```
  - textFieldMidVOIAxial
```
private javax.swing.JTextField textFieldMidVOIAxial
```
  - startVOIAxial
```
int startVOIAxial
```
  - endVOIAxial
```
int endVOIAxial
```
  - midVOIAxial
```
int midVOIAxial
```
  - labelSagittal
```
private javax.swing.JLabel labelSagittal
```
  - labelStartVOISagittal
```
private javax.swing.JLabel labelStartVOISagittal
```
  - textFieldStartVOISagittal
```
private javax.swing.JTextField textFieldStartVOISagittal
```
  - labelEndVOISagittal
```
private javax.swing.JLabel labelEndVOISagittal
```
  - textFieldEndVOISagittal
```
private javax.swing.JTextField textFieldEndVOISagittal
```
  - labelMidVOISagittal
```
private javax.swing.JLabel labelMidVOISagittal
```
  - textFieldMidVOISagittal
```
private javax.swing.JTextField textFieldMidVOISagittal
```
  - startVOISagittal
```
int startVOISagittal
```
  - endVOISagittal
```
int endVOISagittal
```
  - midVOISagittal
```
int midVOISagittal
```
  - labelCoronal
```
private javax.swing.JLabel labelCoronal
```
  - labelStartVOICoronal
```
private javax.swing.JLabel labelStartVOICoronal
```
  - textFieldStartVOICoronal
```
private javax.swing.JTextField textFieldStartVOICoronal
```
  - labelEndVOICoronal
```
private javax.swing.JLabel labelEndVOICoronal
```
  - textFieldEndVOICoronal
```
private javax.swing.JTextField textFieldEndVOICoronal
```
  - labelMidVOICoronal
```
private javax.swing.JLabel labelMidVOICoronal
```
  - textFieldMidVOICoronal
```
private javax.swing.JTextField textFieldMidVOICoronal
```
  - radioBSpline
```
private javax.swing.JRadioButton radioBSpline
```
  - radioOAR
```
private javax.swing.JRadioButton radioOAR
```
  - startVOICoronal
```
private int startVOICoronal
```
  - endVOICoronal
```
private int endVOICoronal
```
  - midVOICoronal
```
private int midVOICoronal
```
  - imageAxial
```
private ModelImage imageAxial
```
  - imageSagittal
```
private ModelImage imageSagittal
```
  - imageCoronal
```
private ModelImage imageCoronal
```
  - useBSpline
```
private boolean useBSpline
```
    Flag to indicate to use B-Spline registration or OAR registration
- Constructor Detail
  - JDialogProstateSegmentationRegBSpline3D
```
public JDialogProstateSegmentationRegBSpline3D(java.awt.Frame theParentFrame)
```
    GUI interface for semi-automatic MR prostate segmentation.
    
    Parameters:
    
    theParentFrame - the MIPAV main frame.
- Method Detail
  - autoConfigVOIsNumbers
```
public void autoConfigVOIsNumbers()
```
    After user manually draw the three VOIs on each axial, sagittal, coronal image, the drawn VOIs slices number is auto configured to appear in the dialog GUI interface.
  - configVOIsNumbers
```
public void configVOIsNumbers(ModelImage image,
                              int[] slices)
```
    Configure the mid, apex and base VOIs, sort them in order.
    
    Parameters:
    
    image - oringial MRI image
    
    slices - Slice array to store the mid, apex and base VOIs slice number.
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Just handle GUI button clicks event.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Overrides:
    
    actionPerformed in class JDialogBase
  - calculateVOIsVolume
```
public void calculateVOIsVolume()
```
    Compute the VOIs binary mask based volumes.
  - printVolume
```
public void printVolume(ModelImage srcImage,
                        VOIVector voiVector,
                        int viewOrientation)
```
    Print out the three VOIs volume in system console out.
    
    Parameters:
    
    srcImage - original MRI image
    
    voiVector - segmented resulting VOIs contours
    
    viewOrientation - view axis orientation: axial, or sagittal or coronal.
  - removeContourFromOtherOrientation
```
public void removeContourFromOtherOrientation()
```
    User central gland contours projection to remove the extra interpolated VOIs contours at the apex and base. Parallel processing the algorithm with axial, sagittal and coronal images concurrently.
  - trimVOIsInSingleImage
```
public java.lang.Runnable trimVOIsInSingleImage(ModelImage image,
                                                int startVOI,
                                                int endVOI,
                                                java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> firstVOI,
                                                java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> secondVOI,
                                                int viewOrientation)
```
    In Dicom space, central contours projections to eliminate the extra contours at the apex and base. For example, axial image, project the sagittal, coronal VOIs onto the axial image Dicom space. The central gland part sagittal, coronal VOIs contours is projected on the axial image slices as points based contours. If there is no points on the corresponding axial image slice, however it has contour, the contour is eliminated.
    
    Parameters:
    
    image - original MRI image. i.e. axial image
    
    startVOI - apex VOI slice number
    
    endVOI - base VOI slice number
    
    firstVOI - sagittal image VOIs in Dicom space
    
    secondVOI - coronal image VOIs in Dicom space.
    
    viewOrientation - image axis orientation
    
    Returns:
  - removeVOIsInDicomSpace
```
public void removeVOIsInDicomSpace(int zSlice,
                                   float zDicom,
                                   ModelImage image,
                                   java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> firstVOI,
                                   java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> secondVOI,
                                   int viewOrientation)
```
    Remove the extra VOIs contours in Dicom space.
    
    Parameters:
    
    zSlice - axial z slice number
    
    zDicom - z slice number corresponding Dicom value
    
    image - original MRI image
    
    firstVOI - sagittal VOI
    
    secondVOI - coronal VOI
    
    viewOrientation - view axis
  - convertVOIToDicomSpace
```
public void convertVOIToDicomSpace(VOIVector src,
                                   java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> target,
                                   ModelImage image,
                                   int startSlice,
                                   int endSlice)
```
    Conver the VOIs from image space to Dicom space
    
    Parameters:
    
    src - source VOIs
    
    target - converted target VOIs
    
    image - original MRI image
    
    startSlice - starting slice
    
    endSlice - ending slice
  - createTask
```
private java.lang.Runnable createTask(ModelImage image,
                                      int midVOI,
                                      int startVOI,
                                      int endVOI,
                                      int axis)
```
    Parallel processing the automatic segmentation algorithm to all the three images concurrently.
    
    Parameters:
    
    image - original MRI image
    
    midVOI - mid slice VOI
    
    startVOI - apex slice VOI
    
    endVOI - base slice VOI
    
    axis - view axis
    
    Returns:
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    This method is required if the AlgorithmPerformed interface is implemented. It is called by the algorithms when it has completed or failed to to complete, so that the dialog can be display the result image and/or clean up.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - Algorithm that caused the event.
  - pause
```
public static void pause()
```
    Pauses the display until the user hits enter.
  - calculateCoherenceEnhancingDiffusion
```
private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage cropImage)
```
    Apply the coherence enhancing diffusion filter to the croppred MR image.
    
    Parameters:
    
    cropImage - cropped image
    
    Returns:
    
    the coherence enhancing diffusion image.
  - isVOIsCloseEnough
```
private boolean isVOIsCloseEnough(int currentSlice,
                                  ModelImage resultImage,
                                  ModelImage refImage)
```
    Check the registration accuracy. Check to see if the registration runs into errors. Check criterion include VOI area, VOI center, etc. If area and center difference exceed specified threshold, registration runs into error.
    
    Parameters:
    
    currentSlice - current image slice
    
    resultImage - result image after registration
    
    refImage - registration reference slice
    
    Returns:
    
    true registration wrong, false, registration wrong.
  - segmentFromFuzzyC
```
public void segmentFromFuzzyC(java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC,
                              int currentSlice,
                              ModelImage resultImage,
                              ModelImage refImage,
                              ModelImage testImage,
                              int axis)
```
    Apply the Fuzzy-C means segmentation to CED image stack.
    
    Parameters:
    
    imageStackFuzzyC - Fuzzy-C segmentation result stack packed from each image slice. It contains 5 fuzzy-C member function classes.
    
    currentSlice - current slice number
    
    resultImage - result image
    
    refImage - reference image
    
    testImage - test image
    
    axis - axis orientation.
  - createVOIPointTable
```
private void createVOIPointTable(JDialogProstateSegmentationRegBSpline3D.Edge voiTable,
                                 ModelImage resultImage)
```
    Create the VOI table in polar coodinate system. It will be used in the narrow band finding.
    
    Parameters:
    
    voiTable - result VOI points table.
    
    resultImage - result image after registration.
  - createImagePointTable
```
public void createImagePointTable(JDialogProstateSegmentationRegBSpline3D.Edge imageTable,
                                  ModelImage resultImage)
```
    Convert each image pixel to polar coordinate system, saved them in a table.
    
    Parameters:
    
    imageTable - image table.
    
    resultImage - result image after registration.
  - findNarrowBand
```
public void findNarrowBand(JDialogProstateSegmentationRegBSpline3D.Edge voiTable,
                           JDialogProstateSegmentationRegBSpline3D.Edge imageTable,
                           JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable)
```
    Find the narrow band regions around VOI contours.
    
    Parameters:
    
    voiTable - VOI table
    
    imageTable - image table
    
    narrowBandTable - narrow band region table.
  - drawNarrowBand
```
public void drawNarrowBand(JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable,
                           ModelImage resultImage)
```
    Draw the narrow band region. It is used for testing purpose.
    
    Parameters:
    
    narrowBandTable - narrow band region table.
    
    resultImage - result image after registration.
  - findRegion
```
public void findRegion(JDialogProstateSegmentationRegBSpline3D.Edge imageTable,
                       float theta1,
                       float theta2,
                       java.util.Vector<JDialogProstateSegmentationRegBSpline3D.PolarPoint> voiPointsInRange,
                       JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable)
```
    Looking for the narrow band region.
    
    Parameters:
    
    imageTable - image table
    
    theta1 - upper limit
    
    theta2 - lower limit
    
    voiPointsInRange - Vois point table
    
    narrowBandTable - narrow band table.
  - inRange
```
public boolean inRange(JDialogProstateSegmentationRegBSpline3D.Edge narrowBandTable,
                       int x,
                       int y)
```
    Check whether the given x, y pixel fall withing the narrow band region.
    
    Parameters:
    
    narrowBandTable - narrow band table
    
    x - pixel x coordinate
    
    y - pixel y coordinate
    
    Returns:
    
    in the range or not.
  - findVOIpointsInRange
```
public void findVOIpointsInRange(JDialogProstateSegmentationRegBSpline3D.Edge imageTable,
                                 java.util.Vector<JDialogProstateSegmentationRegBSpline3D.PolarPoint> voiPointsInRange,
                                 int min,
                                 int max,
                                 JDialogProstateSegmentationRegBSpline3D.Edge voiTable)
```
    Tracing generated VOI tables, convert it from image coordinate to Polar coordinate.
    
    Parameters:
    
    imageTable - image table
    
    voiPointsInRange - VOI table in polar coordinate
    
    min - narrow band lower limit
    
    max - narrow band upper limit
    
    voiTable - voi table in image coordinate
  - morphologyPostProcessing
```
public void morphologyPostProcessing(ModelImage maskImage,
                                     ModelImage resultImage,
                                     ModelImage testImage)
```
    Apply the morphology filter the generate binary mask image from Fuzz-C segmentation.
    
    Parameters:
    
    maskImage - generated binary mask image
    
    resultImage - resulting image
    
    testImage - intermediate image.
  - maskVOIFill
```
public void maskVOIFill(ModelImage maskImage)
```
    Fill pixels inside VOI. Currently not being used. For testing purpose.
    
    Parameters:
    
    maskImage -
  - smoothVOI50
```
public void smoothVOI50(ModelImage maskImage,
                        ModelImage resultImage)
```
    Convert the mask image to VOI with 50 points
    
    Parameters:
    
    maskImage - binary mask image
    
    resultImage - result image
  - smoothVOI120
```
public void smoothVOI120(ModelImage maskImage,
                         ModelImage resultImage)
```
    Convert the mask image to VOI with 120 points.
    
    Parameters:
    
    maskImage - binary mask image
    
    resultImage - result image
  - maskToVOI
```
public void maskToVOI(ModelImage maskImage,
                      ModelImage testImage)
```
    Convert mask image to VOI
    
    Parameters:
    
    maskImage - binary mask image
    
    testImage - intermediate image.
  - IDobjects
```
public void IDobjects(ModelImage maskImage)
```
    Eliminate the small binary mask components. Pixel numbers threshold based elimination.
    
    Parameters:
    
    maskImage -
  - particleSystem
```
public void particleSystem(ModelImage maskImage)
```
    Particle system analysis.
    
    Parameters:
    
    maskImage - binary mask image
  - fillholes
```
public void fillholes(ModelImage maskImage)
```
    Fill holes inside the binary mask image.
    
    Parameters:
    
    maskImage - binary mask image.
  - threshold
```
public void threshold(ModelImage maskImage)
```
    Convert the mask image specified theshold values.
    
    Parameters:
    
    maskImage - binary mask image
  - isInsideVOI
```
public boolean isInsideVOI(int pos,
                           ModelImage img)
```
    check if given pixl location is inside VOI or not.
    
    Parameters:
    
    pos - pixl location
    
    img - given image
    
    Returns:
  - transformVOI
```
public void transformVOI(ModelImage image,
                         ModelImage resultImage,
                         int[] boundingBox,
                         int currentSlice)
```
    Transform the the resulting VOI from cropped image to oringal MR image.
    
    Parameters:
    
    image - original MR image
    
    resultImage - resulting image after segmentation
    
    boundingBox - cropped image bounding box
    
    currentSlice - current image slice
  - callAlgorithm
```
public void callAlgorithm(ModelImage image,
                          int midVOI,
                          int startVOI,
                          int endVOI,
                          int axis)
```
    Single thread based segmentation, which takes up to 40 minutes. The currrent concurrent based segmentaion takes from 7 minutes to 10 minutes. The function is not called.
    
    Parameters:
    
    image -
    
    midVOI -
    
    startVOI -
    
    endVOI -
    
    axis -
  - sortImageVOIs
```
public void sortImageVOIs(ModelImage image)
```
    Sorting image VOI
    
    Parameters:
    
    image - original MR image
  - sortImageVOIsInit
```
public void sortImageVOIsInit(ModelImage image,
                              int midVOI,
                              int startVOI,
                              int endVOI)
```
    Sort the original MR image's specified VOIs
    
    Parameters:
    
    image - original MR image
    
    midVOI - mid slice VOI
    
    startVOI - apex slice VOI
    
    endVOI - base slice VOI
  - sortCEDImageVOIs
```
public void sortCEDImageVOIs(ModelImage coherenceEnhancingDiffusionImage,
                             int midVOI,
                             int startVOI,
                             int endVOI)
```
    Sort the CED image VOIs
    
    Parameters:
    
    coherenceEnhancingDiffusionImage - CED image
    
    midVOI - mid slice VOI
    
    startVOI - apex slice VOI
    
    endVOI - base slice VOI
  - doFuzzyCmean
```
public void doFuzzyCmean(ModelImage coherenceEnhancingDiffusionImage,
                         java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC)
```
    Generate the Fuzzy-C means classes from the CED image
    
    Parameters:
    
    coherenceEnhancingDiffusionImage - CED image
    
    imageStackFuzzyC - Fuzzy-C means classes image stack.
  - getCentroids
```
private float[] getCentroids(ModelImage srcImage,
                             AlgorithmFuzzyCMeans fcmAlgo,
                             float[] centroids)
```
    Gets the minimum and maximum of each image and initializes the centroids dialog appropriately.
    
    Returns:
    
    Flag indicating a successful get.
  - doRegistrationMid
```
public void doRegistrationMid(ModelImage image,
                              ModelImage coherenceEnhancingDiffusionImage,
                              java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC,
                              int midVOI,
                              int startVOI,
                              int endVOI,
                              int[] boundingBox,
                              int axis)
```
    The proposed model uses 2D registration to register 2D slices from the middle slice to the adjacent slice. It then generates a new VOI, and takes the VOI as the new initial estimate for the next slice in the series. This process is then iteratively propagated in both forward and backward directions.
    
    Parameters:
    
    image - original MR image
    
    coherenceEnhancingDiffusionImage - coherence enhance diffusion filter
    
    imageStackFuzzyC - Fuzzy-C segmentation stack
    
    midVOI - mid slice VOI
    
    startVOI - apex slice VOI
    
    endVOI - base slice VOI
    
    boundingBox - Cropped image bounding box
    
    axis - axis orientation
  - doRegistrationStart
```
public void doRegistrationStart(ModelImage image,
                                ModelImage coherenceEnhancingDiffusionImage,
                                java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC,
                                int startVOI,
                                int[] boundingBox,
                                int axis)
```
    Near the apex, apex contour starts as the initial estimate, and repeat the same process toward the end slices.
    
    Parameters:
    
    image - original MR image
    
    coherenceEnhancingDiffusionImage - coherence enhance diffusion filter
    
    imageStackFuzzyC - Fuzzy-C segmentation stack
    
    startVOI - apex starting slice VOI number
    
    boundingBox - Cropped image bounding box
    
    axis - axis orientation
  - doRegistrationEnd
```
public void doRegistrationEnd(ModelImage image,
                              ModelImage coherenceEnhancingDiffusionImage,
                              java.util.Vector<java.util.Vector<ModelImage>> imageStackFuzzyC,
                              int endVOI,
                              int[] boundingBox,
                              int axis)
```
    Near the base, base contour starts as the initial estimate, and repeat the same process toward the end slices.
    
    Parameters:
    
    image - original MR image
    
    coherenceEnhancingDiffusionImage - coherence enhance diffusion filter
    
    imageStackFuzzyC - Fuzzy-C segmentation stack
    
    startVOI - apex starting slice VOI number
    
    boundingBox - Cropped image bounding box
    
    axis - axis orientation
  - adjustVOIs
```
public void adjustVOIs(ModelImage image)
```
    When user draws the 3 VOIs out of order, adjust the VOIs in ascending order
    
    Parameters:
    
    image - source image, axial, sagittal or coronal
  - cropROI
```
public ModelImage cropROI(ModelImage image,
                          int[] xBounds,
                          int[] yBounds,
                          int[] zBounds,
                          int[] boundingBox,
                          int midVOI)
```
    Crop MR image with specified X, Y, Z bounds Use the mid slice as the initial guidance to find the bounds.
    
    Parameters:
    
    image - Original MR image
    
    xBounds - X bounds
    
    yBounds - Y bounds
    
    zBounds - Z bounds
    
    boundingBox - Cropped region rounding box
    
    midVOI - mid slice VOI
    
    Returns:
  - init
```
public void init()
```
    Create the dialog interface.

Class JDialogProstateSegmentationRegBSpline3D

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

UI

tracingSliceNumber

Axial

Sagittal

Coronal

labelAxis

labelStartVOIAxial

textFieldStartVOIAxial

labelEndVOIAxial

textFieldEndVOIAxial

labelMidVOIAxial

textFieldMidVOIAxial

startVOIAxial

endVOIAxial

midVOIAxial

labelSagittal

labelStartVOISagittal

textFieldStartVOISagittal

labelEndVOISagittal

textFieldEndVOISagittal

labelMidVOISagittal

textFieldMidVOISagittal

startVOISagittal

endVOISagittal

midVOISagittal

labelCoronal

labelStartVOICoronal

textFieldStartVOICoronal

labelEndVOICoronal

textFieldEndVOICoronal

labelMidVOICoronal

textFieldMidVOICoronal

radioBSpline

radioOAR

startVOICoronal

endVOICoronal

midVOICoronal

imageAxial

imageSagittal

imageCoronal

useBSpline

Constructor Detail

JDialogProstateSegmentationRegBSpline3D

Method Detail

autoConfigVOIsNumbers

configVOIsNumbers

actionPerformed

calculateVOIsVolume

printVolume

removeContourFromOtherOrientation

trimVOIsInSingleImage

removeVOIsInDicomSpace

convertVOIToDicomSpace

createTask

algorithmPerformed