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_CED_scale_boundary_test

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_CED_scale_boundary_test
extends JDialogBase
implements AlgorithmInterface
```
This class is the trial-and-error approach for HED deep learning experiment. This experiment applied to the boundary only, not the binary image masks. The first try is to use the MRI image and CED image together without intensity normalization. The data we used is the prostate NIH data (cg and wp). Test case only. I didn't get a chance to finish the experiment. Basic steps: 1) generate boundary mask 2) run CED against MRI images 3) isotropic transform NO intensity scale 4) extract png slices

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 AlgorithmTransform`	`algoTrans`
`private javax.swing.JButton`	`buttonKeyImage`
`private javax.swing.JButton`	`buttonSaveImage`
`(package private) java.util.Hashtable<java.lang.String,ModelImage>`	`cedTable`
`(package private) java.util.Hashtable<java.lang.String,ModelImage>`	`imageHashtable`
`(package private) java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>>`	`imageNameHashtable`
`private javax.swing.JPanel`	`imageSelectionPanel`
`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`
`(package private) java.util.Hashtable<java.lang.String,ModelImage>`	`scaleCedTable`
`(package private) java.util.Hashtable<java.lang.String,ModelImage>`	`scaleImageTable`
`(package private) java.util.Hashtable<java.lang.String,ModelImage>`	`scaleVoiTable`
`private static long`	`serialVersionUID`
`private javax.swing.JTextField`	`textFieldKeyImage`
`private javax.swing.JTextField`	`textFieldSaveImage`
`private ViewUserInterface`	`UI`	The main user interface.
`(package private) java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>>`	`voiNameHashtable`
`(package private) java.util.Hashtable<java.lang.String,ModelImage>`	`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

JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_boundary_test(java.awt.Frame theParentFrame)
Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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.
`private ModelImage`	`calculateCoherenceEnhancingDiffusion(ModelImage inImage)`
`ModelImage`	`calculateTransform(ModelImage image)`
`void`	`callAlgorithm()`	Driver function to read image and VOIs, and convert each 3D image to 2D slices.
`void`	`crossValidationTest()`
`void`	`crossValidationTrain()`
`void`	`disposeLocal()`	dispose memory
`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`	`saveImages(java.lang.String key, int[] index, java.lang.String folderName, java.util.Hashtable<java.lang.String,ModelImage> whichTable)`
`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)`
`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.

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

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

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

voiNameHashtable

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

imageHashtable

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

cedTable

java.util.Hashtable<java.lang.String,ModelImage> cedTable

voiTable

java.util.Hashtable<java.lang.String,ModelImage> voiTable

scaleImageTable

java.util.Hashtable<java.lang.String,ModelImage> scaleImageTable

scaleCedTable

java.util.Hashtable<java.lang.String,ModelImage> scaleCedTable

scaleVoiTable

java.util.Hashtable<java.lang.String,ModelImage> scaleVoiTable

algoTrans
```
private AlgorithmTransform algoTrans
```

Constructor Detail
- JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_boundary_test
```
public JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_boundary_test(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)

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.

runMask
```
public void runMask()
```

runCED
```
public void runCED()
```

runTransform
```
public void runTransform()
```

calculateTransform

public ModelImage calculateTransform(ModelImage image)

calculateCoherenceEnhancingDiffusion

private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)

crossValidationTest
```
public void crossValidationTest()
```

crossValidationTrain
```
public void crossValidationTrain()
```

savePNGfile

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

saveImages

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

saveImagesTest

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

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.

Class JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_boundary_test

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

serialVersionUID

UI

labelKeyImage

textFieldKeyImage

buttonKeyImage

imageSelectionPanel

labelSaveImage

textFieldSaveImage

buttonSaveImage

saveImageChooser

saveImageDirectory

imageNameHashtable

voiNameHashtable

imageHashtable

cedTable

voiTable

scaleImageTable

scaleCedTable

scaleVoiTable

algoTrans

Constructor Detail

JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_boundary_test

Method Detail

disposeLocal

actionPerformed

recordSaveImageDir

readKeyImageDir

traverse_Layer

traverse_firstLayer

traverse_secondLayer

traverse_thirdLayer

traverse_scanLayer

traverse_T2Layer

traverse_DicomLayer

traverse_voiLayer

algorithmPerformed

callAlgorithm

runMask

runCED

runTransform

calculateTransform

calculateCoherenceEnhancingDiffusion

crossValidationTest

crossValidationTrain

savePNGfile

saveImages

saveImagesTest

loadFiles

readFile

pause

init

buildKeyImagePanel