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

Class JDialogProstate2DSlicesAtlasPngConverter3DSurface

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.JDialogProstate2DSlicesAtlasPngConverter3DSurface

All Implemented Interfaces:

AlgorithmInterface, DialogDefaultsInterface, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants

public class JDialogProstate2DSlicesAtlasPngConverter3DSurface
extends JDialogBase
implements AlgorithmInterface

For ISBI 2017 paper: Data given: Dr. Choyke's group gave us the 3D prostate MRI data ( axial, sagittal, coronal images with corresponding 3D stl prostate surfaces. No, ground truth VOIs were given. This class reads the images and stl surfaces, converts 3D surface to VOI contours. And save axial, sagittal, coronal VOIs with corresponding image in .xml file format.

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

JDialog.AccessibleJDialog

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

Dialog.AccessibleAWTDialog, Dialog.ModalExclusionType, Dialog.ModalityType

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

Window.AccessibleAWTWindow, Window.Type

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field	Description
private JButton	buttonKeyImage
private JButton	buttonSaveImage
(package private) Hashtable<String,Integer>	dicomTable
(package private) Hashtable<String,Hashtable<String,ModelImage>>	imageHashtable
(package private) Hashtable<String,Hashtable<String,Vector<String>>>	imageNameHashtable
private JPanel	imageSelectionPanel
private JLabel	labelKeyImage	key image directory.
private JLabel	labelSaveImage	saved 2D slices atlas dir.
(package private) Hashtable<String,Hashtable<String,ModelImage>>	origImageTable
private JFileChooser	saveImageChooser
private String	saveImageDirectory
private static final long	serialVersionUID
(package private) Hashtable<String,Vector<ModelImage>>	srcImageTable
(package private) Hashtable<String,Vector<VOI>>	srcVOITable
private JTextField	textFieldKeyImage
private JTextField	textFieldSaveImage
private ViewUserInterface	UI	The main user interface.
(package private) Hashtable<String,Vector<VOI>>	voiHashtable
(package private) Hashtable<String,Hashtable<String,String>>	voiNameHashtable
(package private) Hashtable<String,Integer>	voiTable

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
JDialogProstate2DSlicesAtlasPngConverter3DSurface(Frame theParentFrame)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(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	crossValidationTrain()
void	disposeLocal()	dispose memory
void	init()	Initial panel
void	loadFiles()	load image files and voi files
private void	loadSTLBinaryMesh(File file, ModelImage kImage, int imageOrientation)
private void	loadSTLBinaryMesh(File file, ModelImage kImage, int imageOrientation, String hashID)
static void	pause()
void	readFile()
private void	readKeyImageDir()	Read 3D images atlas directory.
private void	readSTLBinary(FileInputStream data, ModelImage kImage, int imageOrientation)
private void	readSTLBinary(FileInputStream data, ModelImage kImage, int imageOrientation, String hashID)	This method read the STL surface file, convert the 3D surface into VOI contours.
private void	recordSaveImageDir()	Let user specify the saved 2D slices atlas, record the save directory.
void	saveGroundTruth()
void	saveImages(ModelImage image, int[] index, String folderName, String orientation)
void	saveImagesTest(String key, int[] index, String folderName)
private void	savePNGfile(String dirName, String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)
void	smoothVOI60(ModelImage maskImage, ModelImage resultImage)	Smooth VOIs to 60 points.
private void	traverse_firstLayer(File firstDir, String child)
private void	traverse_Layer(File dir)
private void	traverse_scanLayer(File secondLayer, String hashID)
private void	traverse_secondLayer(File firstLayer, String hashID)
private void	traverse_T2Layer(File T2Layer, String hashID, String orientationLabel)
private void	traverse_T2Layer_deeper(File T2Layer, String hashID, String orientationLabel)
private void	traverse_voiLayer(File secondLayer, 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 Details

serialVersionUID

private static final long serialVersionUID

See Also:

• Constant Field Values

UI

private ViewUserInterface UI

The main user interface.

labelKeyImage

private JLabel labelKeyImage

key image directory.

textFieldKeyImage

private JTextField textFieldKeyImage

buttonKeyImage

private JButton buttonKeyImage

imageSelectionPanel

private JPanel imageSelectionPanel

labelSaveImage

private JLabel labelSaveImage

saved 2D slices atlas dir.

textFieldSaveImage

private JTextField textFieldSaveImage

buttonSaveImage

private JButton buttonSaveImage

saveImageChooser

private JFileChooser saveImageChooser

saveImageDirectory

private String saveImageDirectory

imageNameHashtable

Hashtable<String,Hashtable<String,Vector<String>>> imageNameHashtable

voiNameHashtable

Hashtable<String,Hashtable<String,String>> voiNameHashtable

imageHashtable

Hashtable<String,Hashtable<String,ModelImage>> imageHashtable

voiHashtable

Hashtable<String,Vector<VOI>> voiHashtable

srcImageTable

Hashtable<String,Vector<ModelImage>> srcImageTable

srcVOITable

Hashtable<String,Vector<VOI>> srcVOITable

origImageTable

Hashtable<String,Hashtable<String,ModelImage>> origImageTable

dicomTable

Hashtable<String,Integer> dicomTable

voiTable

Hashtable<String,Integer> voiTable

Constructor Details

JDialogProstate2DSlicesAtlasPngConverter3DSurface

public JDialogProstate2DSlicesAtlasPngConverter3DSurface(Frame theParentFrame)

Constructor.

Parameters:

theParentFrame -

Method Details

disposeLocal

public void disposeLocal()

dispose memory

actionPerformed

public void actionPerformed(ActionEvent event)

Dialog local actionPerformed handler.

Specified by:

actionPerformed in interface 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(File dir)

traverse_firstLayer

private void traverse_firstLayer(File firstDir,
 String child)

traverse_secondLayer

private void traverse_secondLayer(File firstLayer,
 String hashID)

traverse_scanLayer

private void traverse_scanLayer(File secondLayer,
 String hashID)

traverse_T2Layer

private void traverse_T2Layer(File T2Layer,
 String hashID,
 String orientationLabel)

traverse_T2Layer_deeper

private void traverse_T2Layer_deeper(File T2Layer,
 String hashID,
 String orientationLabel)

traverse_voiLayer

private void traverse_voiLayer(File secondLayer,
 String hashID)

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.

saveGroundTruth

public void saveGroundTruth()

crossValidationTrain

public void crossValidationTrain()

saveImages

public void saveImages(ModelImage image,
 int[] index,
 String folderName,
 String orientation)

saveImagesTest

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

savePNGfile

private void savePNGfile(String dirName,
 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

readFile

public void readFile()

loadSTLBinaryMesh

private void loadSTLBinaryMesh(File file,
 ModelImage kImage,
 int imageOrientation)

loadSTLBinaryMesh

private void loadSTLBinaryMesh(File file,
 ModelImage kImage,
 int imageOrientation,
 String hashID)

readSTLBinary

private void readSTLBinary(FileInputStream data,
 ModelImage kImage,
 int imageOrientation)
                    throws IOException

Throws:

IOException

readSTLBinary

private void readSTLBinary(FileInputStream data,
 ModelImage kImage,
 int imageOrientation,
 String hashID)
                    throws IOException

This method read the STL surface file, convert the 3D surface into VOI contours.

Parameters:

data -

kImage -

imageOrientation -

hashID -

Throws:

IOException

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.