Class JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_train
- java.lang.Object
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- java.awt.Component
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- java.awt.Container
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- java.awt.Window
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- java.awt.Dialog
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- javax.swing.JDialog
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- gov.nih.mipav.view.dialogs.JDialogBase
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- gov.nih.mipav.view.renderer.WildMagic.ProstateFramework.JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_train
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- 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_train extends JDialogBase implements AlgorithmInterface
This class is the trial-and-error approach for HED deep learning experiment. 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). Training case only. Basic steps: 1) generate binary mask 2) run CED against MRI images 3) isotropic transform NO intensity scale 4) extract png slices- Author:
- Ruida Cheng
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase
JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction
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Nested classes/interfaces inherited from class javax.swing.JDialog
javax.swing.JDialog.AccessibleJDialog
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Nested classes/interfaces inherited from class java.awt.Dialog
java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType
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Nested classes/interfaces inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type
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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,VOI>
voiHashtable
(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
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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
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Fields inherited from class javax.swing.JDialog
accessibleContext, rootPane, rootPaneCheckingEnabled
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Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Constructor Summary
Constructors Constructor Description JDialogProstate2DSlicesAtlasPngConverterCentralGland_CED_scale_train(java.awt.Frame theParentFrame)
Constructor.
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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 memoryvoid
init()
Initial panelvoid
loadFiles()
load image files and voi filesstatic 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()
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, boolean isMask)
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)
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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
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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
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Methods inherited from class java.awt.Dialog
addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack
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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
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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
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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
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Field Detail
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serialVersionUID
private static final long serialVersionUID
- See Also:
- Constant Field Values
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UI
private ViewUserInterface UI
The main user interface.
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labelKeyImage
private javax.swing.JLabel labelKeyImage
key image directory.
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textFieldKeyImage
private javax.swing.JTextField textFieldKeyImage
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buttonKeyImage
private javax.swing.JButton buttonKeyImage
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imageSelectionPanel
private javax.swing.JPanel imageSelectionPanel
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labelSaveImage
private javax.swing.JLabel labelSaveImage
saved 2D slices atlas dir.
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textFieldSaveImage
private javax.swing.JTextField textFieldSaveImage
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buttonSaveImage
private javax.swing.JButton buttonSaveImage
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saveImageChooser
private javax.swing.JFileChooser saveImageChooser
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saveImageDirectory
private java.lang.String saveImageDirectory
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imageNameHashtable
java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> imageNameHashtable
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voiNameHashtable
java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> voiNameHashtable
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imageHashtable
java.util.Hashtable<java.lang.String,ModelImage> imageHashtable
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cedTable
java.util.Hashtable<java.lang.String,ModelImage> cedTable
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voiTable
java.util.Hashtable<java.lang.String,ModelImage> voiTable
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scaleImageTable
java.util.Hashtable<java.lang.String,ModelImage> scaleImageTable
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scaleCedTable
java.util.Hashtable<java.lang.String,ModelImage> scaleCedTable
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scaleVoiTable
java.util.Hashtable<java.lang.String,ModelImage> scaleVoiTable
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voiHashtable
java.util.Hashtable<java.lang.String,VOI> voiHashtable
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algoTrans
private AlgorithmTransform algoTrans
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Method Detail
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disposeLocal
public void disposeLocal()
dispose memory
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actionPerformed
public void actionPerformed(java.awt.event.ActionEvent event)
Dialog local actionPerformed handler.- Specified by:
actionPerformed
in interfacejava.awt.event.ActionListener
- Overrides:
actionPerformed
in classJDialogBase
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recordSaveImageDir
private void recordSaveImageDir()
Let user specify the saved 2D slices atlas, record the save directory.
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readKeyImageDir
private void readKeyImageDir()
Read 3D images atlas directory.
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traverse_Layer
private void traverse_Layer(java.io.File dir)
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traverse_firstLayer
private void traverse_firstLayer(java.io.File firstDir, java.lang.String child)
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traverse_secondLayer
private void traverse_secondLayer(java.io.File firstLayer, java.lang.String hashID)
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traverse_thirdLayer
private void traverse_thirdLayer(java.io.File secondLayer, java.lang.String hashID)
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traverse_scanLayer
private void traverse_scanLayer(java.io.File secondLayer, java.lang.String hashID)
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traverse_T2Layer
private void traverse_T2Layer(java.io.File T2Layer, java.lang.String hashID)
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traverse_DicomLayer
private void traverse_DicomLayer(java.io.File lastLayer, java.lang.String hashID)
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traverse_voiLayer
private void traverse_voiLayer(java.io.File secondLayer, java.lang.String hashID)
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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 interfaceAlgorithmInterface
- Parameters:
algorithm
- Algorithm that caused the event.
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callAlgorithm
public void callAlgorithm()
Driver function to read image and VOIs, and convert each 3D image to 2D slices.
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runMask
public void runMask()
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runCED
public void runCED()
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runTransform
public void runTransform()
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calculateTransform
public ModelImage calculateTransform(ModelImage image)
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calculateCoherenceEnhancingDiffusion
private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)
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crossValidationTest
public void crossValidationTest()
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crossValidationTrain
public void crossValidationTrain()
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saveImages
public void saveImages()
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savePNGfile
private void savePNGfile(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)
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saveImages
public void saveImages(java.lang.String key, int[] index, java.lang.String folderName, java.util.Hashtable<java.lang.String,ModelImage> whichTable)
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saveImagesTest
public void saveImagesTest(java.lang.String key, int[] index, java.lang.String folderName)
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savePNGfile
private void savePNGfile(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, boolean isMask)
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loadFiles
public void loadFiles()
load image files and voi files
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readFile
public void readFile()
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pause
public static void pause()
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init
public void init()
Initial panel
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buildKeyImagePanel
public void buildKeyImagePanel()
Panel contains both the 3D image dir and saved 2D slices atlas dir.
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