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

Class JDialogProstateXReRunWholeProstate

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.JDialogProstateXReRunWholeProstate

All Implemented Interfaces:

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

public class JDialogProstateXReRunWholeProstate
extends JDialogBase
implements AlgorithmInterface

For NIH prostate data, we apply wp and cg segmentation using HED deep learning model. Data: given NIH prostate data, axial images with corresponing VOIs for Cg and Wp. Steps: 1. read image file and VOIs 2. From VOIs, generate the binary mask images. 3. Transform into isotropic image (upsampling) with resolution: 0.35m x 0.35m x 0.35m. 4. Conversion: converts axial image to axial an coronal using JDialogReoriented. 5. Generate the CED images from MR images in three orientation: axial, sagittal, coronal. 6. Each orientation, save 3D MR images, CED images with corresponding binary mask images. This is the 2D-volumetric segmentation approach.

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 AlgorithmTransform	algoTrans
private int	axial_index
private Hashtable<String,ModelImage>	axialList
private Hashtable<String,ModelImage>	axialMaskList
private JButton	buttonKeyImage
private JButton	buttonSaveImage
(package private) Hashtable<String,ModelImage>	cedTable
(package private) Hashtable<String,ModelImage>	cedTable_ext
(package private) Hashtable<String,ModelImage>	cedTableAxial
(package private) Hashtable<String,ModelImage>	cedTableCoronal
(package private) Hashtable<String,ModelImage>	cedTableSagittal
private int	coronal_index
private Hashtable<String,ModelImage>	coronalList
private Hashtable<String,ModelImage>	coronalMaskList
(package private) Hashtable<String,ModelImage>	cropTable_ext
(package private) Hashtable<String,ModelImage>	cropVoiTable_ext
private int	endIndex
(package private) Hashtable<String,ModelImage>	imageHashtableCg
(package private) Hashtable<String,ModelImage>	imageHashtableCg_ext
(package private) Hashtable<String,ModelImage>	imageHashtableWp
(package private) Hashtable<String,ModelImage>	imageHashtableWp_ext
(package private) Hashtable<String,Vector<String>>	imageNameHashtable
(package private) Hashtable<String,Vector<String>>	imageNameHashtable_ext
private JPanel	imageSelectionPanel
private JLabel	labelKeyImage	key image directory.
private JLabel	labelSaveImage	saved 2D slices atlas dir.
private int	sagittal_index
private Hashtable<String,ModelImage>	sagittalList
private Hashtable<String,ModelImage>	sagittalMaskList
private JFileChooser	saveImageChooser
private String	saveImageDirectory
(package private) Hashtable<String,ModelImage>	scaleCedTable
(package private) Hashtable<String,ModelImage>	scaleCedTable_ext
(package private) Hashtable<String,ModelImage>	scaleImageTable
(package private) Hashtable<String,ModelImage>	scaleImageTable_ext
(package private) Hashtable<String,ModelImage>	scaleIntensityTable
(package private) Hashtable<String,ModelImage>	scaleIntensityTable_ext
(package private) Hashtable<String,ModelImage>	scaleVoiTable
(package private) Hashtable<String,ModelImage>	scaleVoiTable_ext
private static final long	serialVersionUID
private int	startIndex
private JTextField	textFieldKeyImage
private JTextField	textFieldSaveImage
(package private) Hashtable<String,ModelImage>	transformTable
(package private) Hashtable<String,ModelImage>	transformTable_ext
private ViewUserInterface	UI	The main user interface.
(package private) Hashtable<String,VOI>	voiHashtable
(package private) Hashtable<String,Vector<String>>	voiNameHashtableCg
(package private) Hashtable<String,Vector<String>>	voiNameHashtableCg_ext
(package private) Hashtable<String,Vector<String>>	voiNameHashtableWp
(package private) Hashtable<String,Vector<String>>	voiNameHashtableWp_ext
(package private) Hashtable<String,ModelImage>	voiTable
(package private) Hashtable<String,ModelImage>	voiTable_ext

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
JDialogProstateXReRunWholeProstate(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.
private ModelImage	calculateCoherenceEnhancingDiffusion(ModelImage inImage)
ModelImage	calculateTransform(ModelImage keyImage)
void	callAlgorithm()	Driver function to read image and VOIs, and convert each 3D image to 2D slices.
void	conversion()
void	crossValidationTrain()
void	disposeLocal()	dispose memory
void	disposeMemory()
void	init()	Initial panel
void	loadFiles()	load image files and voi files
static void	pause()
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	runMask()
void	runTransform()
void	saveHED2DsliceCED()
void	saveImage(ModelImage image, ModelImage imageMask, String orientation)
void	saveImages(String key, int[] index, String folderName, Hashtable<String,ModelImage> whichTable)
void	saveImagesTest(String key, int[] index, String folderName)
void	saveOrthogonalCEDImage()
private void	savePNGfile(String dirName, String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, boolean isMask)
private void	savePNGfile(String dirName, String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)
private void	traverse_DicomLayer(File lastLayer, String hashID)
private void	traverse_firstLayer_noCoil(File firstDir, String child)
private void	traverse_Layer_noCoil(File dir)
private void	traverse_secondLayer_noCoil(File firstLayer, 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,Vector<String>> imageNameHashtable

voiNameHashtableWp

Hashtable<String,Vector<String>> voiNameHashtableWp

voiNameHashtableCg

Hashtable<String,Vector<String>> voiNameHashtableCg

imageNameHashtable_ext

Hashtable<String,Vector<String>> imageNameHashtable_ext

voiNameHashtableWp_ext

Hashtable<String,Vector<String>> voiNameHashtableWp_ext

voiNameHashtableCg_ext

Hashtable<String,Vector<String>> voiNameHashtableCg_ext

imageHashtableWp_ext

Hashtable<String,ModelImage> imageHashtableWp_ext

imageHashtableCg_ext

Hashtable<String,ModelImage> imageHashtableCg_ext

cedTable_ext

Hashtable<String,ModelImage> cedTable_ext

voiTable_ext

Hashtable<String,ModelImage> voiTable_ext

imageHashtableWp

Hashtable<String,ModelImage> imageHashtableWp

imageHashtableCg

Hashtable<String,ModelImage> imageHashtableCg

cedTable

Hashtable<String,ModelImage> cedTable

voiTable

Hashtable<String,ModelImage> voiTable

scaleImageTable

Hashtable<String,ModelImage> scaleImageTable

scaleCedTable

Hashtable<String,ModelImage> scaleCedTable

scaleVoiTable

Hashtable<String,ModelImage> scaleVoiTable

scaleImageTable_ext

Hashtable<String,ModelImage> scaleImageTable_ext

scaleIntensityTable_ext

Hashtable<String,ModelImage> scaleIntensityTable_ext

scaleCedTable_ext

Hashtable<String,ModelImage> scaleCedTable_ext

scaleVoiTable_ext

Hashtable<String,ModelImage> scaleVoiTable_ext

transformTable_ext

Hashtable<String,ModelImage> transformTable_ext

transformTable

Hashtable<String,ModelImage> transformTable

voiHashtable

Hashtable<String,VOI> voiHashtable

cropTable_ext

Hashtable<String,ModelImage> cropTable_ext

cropVoiTable_ext

Hashtable<String,ModelImage> cropVoiTable_ext

algoTrans

private AlgorithmTransform algoTrans

scaleIntensityTable

Hashtable<String,ModelImage> scaleIntensityTable

axialList

private Hashtable<String,ModelImage> axialList

axialMaskList

private Hashtable<String,ModelImage> axialMaskList

sagittalList

private Hashtable<String,ModelImage> sagittalList

sagittalMaskList

private Hashtable<String,ModelImage> sagittalMaskList

coronalList

private Hashtable<String,ModelImage> coronalList

coronalMaskList

private Hashtable<String,ModelImage> coronalMaskList

cedTableAxial

Hashtable<String,ModelImage> cedTableAxial

cedTableSagittal

Hashtable<String,ModelImage> cedTableSagittal

cedTableCoronal

Hashtable<String,ModelImage> cedTableCoronal

axial_index

private int axial_index

sagittal_index

private int sagittal_index

coronal_index

private int coronal_index

startIndex

private int startIndex

endIndex

private int endIndex

Constructor Details

JDialogProstateXReRunWholeProstate

public JDialogProstateXReRunWholeProstate(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_noCoil

private void traverse_Layer_noCoil(File dir)

traverse_firstLayer_noCoil

private void traverse_firstLayer_noCoil(File firstDir,
 String child)

traverse_secondLayer_noCoil

private void traverse_secondLayer_noCoil(File firstLayer,
 String hashID)

traverse_DicomLayer

private void traverse_DicomLayer(File lastLayer,
 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.

saveOrthogonalCEDImage

public void saveOrthogonalCEDImage()

saveHED2DsliceCED

public void saveHED2DsliceCED()

saveImage

public void saveImage(ModelImage image,
 ModelImage imageMask,
 String orientation)

disposeMemory

public void disposeMemory()

runMask

public void runMask()

runTransform

public void runTransform()

conversion

public void conversion()

runCED

public void runCED()

calculateCoherenceEnhancingDiffusion

private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)

crossValidationTrain

public void crossValidationTrain()

saveImages

public void saveImages(String key,
 int[] index,
 String folderName,
 Hashtable<String,ModelImage> whichTable)

saveImagesTest

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

savePNGfile

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

savePNGfile

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

loadFiles

public void loadFiles()

load image files and voi files

readFile

public void readFile()

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.

calculateTransform

public ModelImage calculateTransform(ModelImage keyImage)