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

Class JDialogProstate2DSlicesAtlasPngConverterCentralGland_miccai

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.JDialogProstate2DSlicesAtlasPngConverterCentralGland_miccai

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 JDialogProstate2DSlicesAtlasPngConverterCentralGland_miccai
extends JDialogBase
implements AlgorithmInterface

This is the trial-and-error test, which applying the NIH data for training, Prostate promise 12 data for testing. Failed test. ----------------------------------------------------------------------------------------- For backup purpose only. Will delete after SVN check-in. -----------------------------------------------------------------------------------------

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 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 java.util.Hashtable<java.lang.String,ModelImage>	cedHashtable
private AlgorithmAddMargins	cropAlgo	crop margin algorithm.
private java.util.Vector<ModelImage>	cropKeyImages	cropped key image vector.
private java.util.Hashtable<java.lang.String,ModelImage>	imageHashtable
private java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>>	imageNameHashtable
private javax.swing.JPanel	imageSelectionPanel
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>	keyImageVector5
private java.util.Vector<java.lang.String>	keyImageVOIVector1
private java.util.Vector<java.lang.String>	keyImageVOIVector5
private javax.swing.JLabel	labelKeyImage	key image directory.
private javax.swing.JLabel	labelSaveImage	saved 2D slices atlas dir.
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 java.util.Hashtable<java.lang.String,VOI>	voiHashtable
private java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>>	voiNameHashtable
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
JDialogProstate2DSlicesAtlasPngConverterCentralGland_miccai(java.awt.Frame theParentFrame)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(java.awt.event.ActionEvent event)	Dialog local actionPerformed handler.
void	addVOIsToCED()
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.
private ModelImage	calculateCoherenceEnhancingDiffusion(ModelImage inImage)
ModelImage	calculateTransform(ModelImage image, int scaledDimX, int scaledDimY)
void	callAlgorithm()	Driver function to read image and VOIs, and convert each 3D image to 2D slices.
void	crossValidationTest()
static boolean	deleteDir(java.io.File dir)	Debugger to test dir deletion.
void	disposeLocal()	dispose memory
void	init()	Initial panel
void	loadFiles()	load image files and voi files
static void	pause()
void	printImages()	Debugger for test the image and VOis reading.
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.
void	runCED()
void	saveImages(java.lang.String key, int[] index, java.lang.String folderName)
void	saveImagesCED(java.lang.String key, int[] index, java.lang.String folderName)
void	saveImagesTest(java.lang.String key, int[] index, java.lang.String folderName)
private void	savePNGfile(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)
void	saveTestedImages()
void	smoothVOI60(ModelImage maskImage, ModelImage resultImage)	Smooth VOIs to 60 points.
void	sortKeyImage_5()
void	train()
private void	traverse_DicomLayer(java.io.File lastLayer, java.lang.String hashID)
private void	traverse_firstLayer(java.io.File firstDir, java.lang.String child)
private void	traverse_Layer(java.io.File dir)
private void	traverse_scanLayer(java.io.File secondLayer, java.lang.String hashID)
private void	traverse_secondLayer(java.io.File firstLayer, java.lang.String hashID)
private void	traverse_T2Layer(java.io.File T2Layer, java.lang.String hashID)
private void	traverse_thirdLayer(java.io.File secondLayer, java.lang.String hashID)
private void	traverse_voiLayer(java.io.File secondLayer, java.lang.String hashID)

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.

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

keyImages

private java.util.Vector<ModelImage> keyImages

image vector to hold the actual images.

keyImageVector1

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

keyImageVOIVector1

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

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

imageNameHashtable

private java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> imageNameHashtable

voiNameHashtable

private java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> voiNameHashtable

imageHashtable

private java.util.Hashtable<java.lang.String,ModelImage> imageHashtable

voiHashtable

private java.util.Hashtable<java.lang.String,VOI> voiHashtable

cedHashtable

private java.util.Hashtable<java.lang.String,ModelImage> cedHashtable

Constructor Detail

JDialogProstate2DSlicesAtlasPngConverterCentralGland_miccai

public JDialogProstate2DSlicesAtlasPngConverterCentralGland_miccai(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_Layer

private void traverse_Layer(java.io.File dir)

traverse_firstLayer

private void traverse_firstLayer(java.io.File firstDir,
                                 java.lang.String child)

traverse_secondLayer

private void traverse_secondLayer(java.io.File firstLayer,
                                  java.lang.String hashID)

traverse_thirdLayer

private void traverse_thirdLayer(java.io.File secondLayer,
                                 java.lang.String hashID)

traverse_scanLayer

private void traverse_scanLayer(java.io.File secondLayer,
                                java.lang.String hashID)

traverse_T2Layer

private void traverse_T2Layer(java.io.File T2Layer,
                              java.lang.String hashID)

traverse_DicomLayer

private void traverse_DicomLayer(java.io.File lastLayer,
                                 java.lang.String hashID)

traverse_voiLayer

private void traverse_voiLayer(java.io.File secondLayer,
                               java.lang.String hashID)

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.

runCED

public void runCED()

calculateCoherenceEnhancingDiffusion

private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)

saveTestedImages

public void saveTestedImages()

crossValidationTest

public void crossValidationTest()

train

public void train()

saveImages

public void saveImages(java.lang.String key,
                       int[] index,
                       java.lang.String folderName)

saveImagesCED

public void saveImagesCED(java.lang.String key,
                          int[] index,
                          java.lang.String folderName)

calculateTransform

public ModelImage calculateTransform(ModelImage image,
                                     int scaledDimX,
                                     int scaledDimY)

saveImagesTest

public void saveImagesTest(java.lang.String key,
                           int[] index,
                           java.lang.String folderName)

savePNGfile

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

smoothVOI60

public void smoothVOI60(ModelImage maskImage,
                        ModelImage resultImage)

Smooth VOIs to 60 points.

Parameters:

maskImage -

resultImage -

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()

addVOIsToCED

public void addVOIsToCED()

pause

public static void pause()

init

public void init()

Initial panel

buildKeyImagePanel

public void buildKeyImagePanel()

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