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

Class JDialogProstate2DSlicesAtlasPngConverter

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.JDialogProstate2DSlicesAtlasPngConverter

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 JDialogProstate2DSlicesAtlasPngConverter
extends JDialogBase
implements AlgorithmInterface

This class convert the 3D images to 2D slices based atlas. Users specify the 3D prostate images dir, and output 2D slices based dir, the algorithm auto convert each 3D image to 2D slices with corresponding VOIs. Each saved VOIs is 2-contour based VOI, which is used to build the Active Appearance Model (AAM).

Author:

Ruida Cheng

See Also:

Serialized Form

Nested Class Summary

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

JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction

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

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
private int	axis
private javax.swing.JComboBox	axisList
private int	boxXmax
private int	boxXmin
private int	boxYmax	bounding box for crop the image.
private int	boxYmin	bounding box for crop the image.
private javax.swing.JButton	buttonKeyImage
private javax.swing.JButton	buttonSaveImage
private static int	Coronal
private AlgorithmAddMargins	cropAlgo	crop margin algorithm.
private ModelImage	cropImage	result cropped image.
private java.util.Vector<ModelImage>	cropKeyImages	cropped key image vector.
private javax.swing.JPanel	imageSelectionPanel
private javax.swing.JFileChooser	keyImageChooser	key images variables.
private java.lang.String	keyImageDirectory
private java.util.Vector<ModelImage>	keyImages	image vector to hold the actual images.
private java.util.Vector<java.lang.String>	keyImageVector1
private java.util.Vector<java.lang.String>	keyImageVector2
private java.util.Vector<java.lang.String>	keyImageVector3
private java.util.Vector<java.lang.String>	keyImageVector4
private java.util.Vector<java.lang.String>	keyImageVector5
private java.util.Vector<VOI[]>	keyImageVOIs	voi vector to hold the actual vois.
private java.util.Vector<java.lang.String>	keyImageVOIVector1
private java.util.Vector<java.lang.String>	keyImageVOIVector2
private java.util.Vector<java.lang.String>	keyImageVOIVector3
private java.util.Vector<java.lang.String>	keyImageVOIVector4
private java.util.Vector<java.lang.String>	keyImageVOIVector5
private javax.swing.JLabel	labelAxis
private javax.swing.JLabel	labelKeyImage	key image directory.
private javax.swing.JLabel	labelSaveImage	saved 2D slices atlas dir.
private static int	Saggital
private javax.swing.JFileChooser	saveImageChooser
private java.lang.String	saveImageDirectory
private static long	serialVersionUID
private javax.swing.JTextField	textFieldKeyImage
private javax.swing.JTextField	textFieldSaveImage
private ViewUserInterface	UI	The main user interface.
private int[]	xBounds	X cropped region bounds.
private int[]	yBounds	Y cropped region bounds.
private int[]	zBounds	Z cropped region bound.

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
JDialogProstate2DSlicesAtlasPngConverter(java.awt.Frame theParentFrame)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(java.awt.event.ActionEvent event)	Dialog local actionPerformed handler.
void	algorithmPerformed(AlgorithmBase algorithm)	This method is required if the AlgorithmPerformed interface is implemented.
void	buildKeyImagePanel()	Panel contains both the 3D image dir and saved 2D slices atlas dir.
void	callAlgorithm()	Driver function to read image and VOIs, and convert each 3D image to 2D slices.
void	cropKeyImages()	Crop key images.
static boolean	deleteDir(java.io.File dir)	Debugger to test dir deletion.
void	disposeLocal()	dispose memory
private void	generateBoundaryContours(VOIBase srcContour, ModelImage targetImageSlice)	Convert VOI from one contour to two contours
void	init()	Initial panel
void	loadFiles()	load image files and voi files
void	printImages()	Debugger for test the image and VOis reading.
private void	processDir_folder_1(java.io.File dir)
private void	processDir_folder_2(java.io.File dir)
private void	processDir_folder_3(java.io.File dir)
private void	processDir_folder_4(java.io.File dir)
private void	processDir_folder_5(java.io.File dir)
void	readFile()
private void	readKeyImageDir()	Read 3D images atlas directory.
private void	recordSaveImageDir()	Let user specify the saved 2D slices atlas, record the save directory.
private void	rotateToStartingPoint_leftMost(float[] xPts, float[] yPts, int xDim, int yDim)
private void	rotateToStartingPoint_yMid(float[] xPts, float[] yPts, int xDim, int yDim)	Re-oriented the starting and ending VOIs.
void	saveImages()	Save the 2D slices and VOIs to user specified dir.
private void	savePNGfile(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, boolean isMask)
void	saveTestedImages()
void	smoothVOI60(ModelImage maskImage, ModelImage resultImage)	Smooth VOIs to 60 points.
void	sortKeyImage_1()
void	sortKeyImage_2()
void	sortKeyImage_3()
void	sortKeyImage_4()
void	sortKeyImage_5()
private void	traverse_folder_1(java.io.File dir)
private void	traverse_folder_2(java.io.File dir)
private void	traverse_folder_3(java.io.File dir)
private void	traverse_folder_4(java.io.File dir)
private void	traverse_folder_5(java.io.File dir)

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.

boxYmin

private int boxYmin

bounding box for crop the image. Currently set from 0 to 512, the orginal image slice size.

boxYmax

private int boxYmax

bounding box for crop the image. Currently set from 0 to 512, the orginal image slice size.

boxXmin

private int boxXmin

boxXmax

private int boxXmax

xBounds

private int[] xBounds

X cropped region bounds.

yBounds

private int[] yBounds

Y cropped region bounds.

zBounds

private int[] zBounds

Z cropped region bound.

cropAlgo

private AlgorithmAddMargins cropAlgo

crop margin algorithm.

cropImage

private ModelImage cropImage

result cropped image.

labelKeyImage

private javax.swing.JLabel labelKeyImage

key image directory.

textFieldKeyImage

private javax.swing.JTextField textFieldKeyImage

buttonKeyImage

private javax.swing.JButton buttonKeyImage

imageSelectionPanel

private javax.swing.JPanel imageSelectionPanel

keyImageChooser

private javax.swing.JFileChooser keyImageChooser

key images variables.

keyImageDirectory

private java.lang.String keyImageDirectory

axisList

private javax.swing.JComboBox axisList

labelAxis

private javax.swing.JLabel labelAxis

Axial

private static int Axial

Saggital

private static int Saggital

Coronal

private static int Coronal

axis

private int axis

keyImages

private java.util.Vector<ModelImage> keyImages

image vector to hold the actual images.

keyImageVOIs

private java.util.Vector<VOI[]> keyImageVOIs

voi vector to hold the actual vois.

keyImageVector1

private java.util.Vector<java.lang.String> keyImageVector1

keyImageVOIVector1

private java.util.Vector<java.lang.String> keyImageVOIVector1

keyImageVector2

private java.util.Vector<java.lang.String> keyImageVector2

keyImageVOIVector2

private java.util.Vector<java.lang.String> keyImageVOIVector2

keyImageVector3

private java.util.Vector<java.lang.String> keyImageVector3

keyImageVOIVector3

private java.util.Vector<java.lang.String> keyImageVOIVector3

keyImageVector4

private java.util.Vector<java.lang.String> keyImageVector4

keyImageVOIVector4

private java.util.Vector<java.lang.String> keyImageVOIVector4

keyImageVector5

private java.util.Vector<java.lang.String> keyImageVector5

keyImageVOIVector5

private java.util.Vector<java.lang.String> keyImageVOIVector5

cropKeyImages

private java.util.Vector<ModelImage> cropKeyImages

cropped key image vector.

labelSaveImage

private javax.swing.JLabel labelSaveImage

saved 2D slices atlas dir.

textFieldSaveImage

private javax.swing.JTextField textFieldSaveImage

buttonSaveImage

private javax.swing.JButton buttonSaveImage

saveImageChooser

private javax.swing.JFileChooser saveImageChooser

saveImageDirectory

private java.lang.String saveImageDirectory

Constructor Detail

JDialogProstate2DSlicesAtlasPngConverter

public JDialogProstate2DSlicesAtlasPngConverter(java.awt.Frame theParentFrame)

Constructor.

Parameters:

theParentFrame -

Method Detail

disposeLocal

public void disposeLocal()

dispose memory

actionPerformed

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

Dialog local actionPerformed handler.

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class JDialogBase

recordSaveImageDir

private void recordSaveImageDir()

Let user specify the saved 2D slices atlas, record the save directory.

readKeyImageDir

private void readKeyImageDir()

Read 3D images atlas directory.

traverse_folder_1

private void traverse_folder_1(java.io.File dir)

processDir_folder_1

private void processDir_folder_1(java.io.File dir)

sortKeyImage_1

public void sortKeyImage_1()

traverse_folder_2

private void traverse_folder_2(java.io.File dir)

processDir_folder_2

private void processDir_folder_2(java.io.File dir)

sortKeyImage_2

public void sortKeyImage_2()

traverse_folder_3

private void traverse_folder_3(java.io.File dir)

processDir_folder_3

private void processDir_folder_3(java.io.File dir)

sortKeyImage_3

public void sortKeyImage_3()

traverse_folder_4

private void traverse_folder_4(java.io.File dir)

processDir_folder_4

private void processDir_folder_4(java.io.File dir)

sortKeyImage_4

public void sortKeyImage_4()

traverse_folder_5

private void traverse_folder_5(java.io.File dir)

processDir_folder_5

private void processDir_folder_5(java.io.File dir)

sortKeyImage_5

public void sortKeyImage_5()

printImages

public void printImages()

Debugger for test the image and VOis reading.

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.

callAlgorithm

public void callAlgorithm()

Driver function to read image and VOIs, and convert each 3D image to 2D slices.

saveTestedImages

public void saveTestedImages()

saveImages

public void saveImages()

Save the 2D slices and VOIs to user specified dir.

savePNGfile

private void savePNGfile(java.lang.String dirName,
                         java.lang.String fileName,
                         ModelImage srcImage,
                         float minIntensity,
                         float maxIntensity,
                         boolean isMask)

rotateToStartingPoint_yMid

private void rotateToStartingPoint_yMid(float[] xPts,
                                        float[] yPts,
                                        int xDim,
                                        int yDim)

Re-oriented the starting and ending VOIs.

Parameters:

xPts - voi x coordinate

yPts - voi y coordinate

xDim - image x dimension

yDim - image y dimension

rotateToStartingPoint_leftMost

private void rotateToStartingPoint_leftMost(float[] xPts,
                                            float[] yPts,
                                            int xDim,
                                            int yDim)

smoothVOI60

public void smoothVOI60(ModelImage maskImage,
                        ModelImage resultImage)

Smooth VOIs to 60 points.

Parameters:

maskImage -

resultImage -

generateBoundaryContours

private void generateBoundaryContours(VOIBase srcContour,
                                      ModelImage targetImageSlice)

Convert VOI from one contour to two contours

Parameters:

srcContour - single VOI contour

targetImageSlice - target 2D image slice

cropKeyImages

public void cropKeyImages()

Crop key images.

loadFiles

public void loadFiles()

load image files and voi files

deleteDir

public static boolean deleteDir(java.io.File dir)

Debugger to test dir deletion.

Parameters:

dir -

Returns:

readFile

public void readFile()

init

public void init()

Initial panel

buildKeyImagePanel

public void buildKeyImagePanel()

Panel contains both the 3D image dir and saved 2D slices atlas dir.