Class JDialogCopyFiles
- 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.JDialogCopyFiles
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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 JDialogCopyFiles extends JDialogBase implements AlgorithmInterface
This class convert the 3D images to 2D slices based atlas. Users specify the 3D prostate images dir, and output 2D slices based dir, the algorithm auto convert each 3D image to 2D slices with corresponding VOIs. Each saved VOIs is 2-contour based VOI, which is used to build the Active Appearance Model (AAM).- 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 static int
Axial
private int
axis
private javax.swing.JComboBox
axisList
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 static int
Coronal
private AlgorithmAddMargins
cropAlgo
crop margin algorithm.private ModelImage
cropImage
result cropped image.private java.util.Vector<ModelImage>
cropKeyImages
cropped key image vector.(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.JFileChooser
keyImageChooser
key images variables.private java.lang.String
keyImageDirectory
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>
keyImageVector2
private java.util.Vector<java.lang.String>
keyImageVector3
private java.util.Vector<java.lang.String>
keyImageVector4
private java.util.Vector<java.lang.String>
keyImageVector5
private java.util.Vector<VOI[]>
keyImageVOIs
voi vector to hold the actual vois.private java.util.Vector<java.lang.String>
keyImageVOIVector1
private java.util.Vector<java.lang.String>
keyImageVOIVector2
private java.util.Vector<java.lang.String>
keyImageVOIVector3
private java.util.Vector<java.lang.String>
keyImageVOIVector4
private java.util.Vector<java.lang.String>
keyImageVOIVector5
private javax.swing.JLabel
labelAxis
private javax.swing.JLabel
labelKeyImage
key image directory.private javax.swing.JLabel
labelSaveImage
saved 2D slices atlas dir.private static int
Saggital
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.(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,java.util.Vector<java.lang.String>>
voiNameHashtableNathan
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
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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 JDialogCopyFiles(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.void
callAlgorithm()
Driver function to read image and VOIs, and convert each 3D image to 2D slices.private void
copyFiles()
void
cropKeyImages()
Crop key images.void
crossValidationTest()
void
crossValidationTrain()
static boolean
deleteDir(java.io.File dir)
Debugger to test dir deletion.void
disposeLocal()
dispose memoryprivate void
generateBoundaryContours(VOIBase srcContour, ModelImage targetImageSlice)
Convert VOI from one contour to two contoursvoid
init()
Initial panelvoid
loadFiles()
load image files and voi filesstatic void
pause()
void
printImages()
Debugger for test the image and VOis reading.private void
processDir_folder_1(java.io.File dir)
private void
processDir_folder_2(java.io.File dir)
private void
processDir_folder_3(java.io.File dir)
private void
processDir_folder_4(java.io.File dir)
private void
processDir_folder_5(java.io.File dir)
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.private void
rotateToStartingPoint_leftMost(float[] xPts, float[] yPts, int xDim, int yDim)
private void
rotateToStartingPoint_yMid(float[] xPts, float[] yPts, int xDim, int yDim)
Re-oriented the starting and ending VOIs.void
saveImages(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, boolean isMask)
void
saveTestedImages()
void
smoothVOI60(ModelImage maskImage, ModelImage resultImage)
Smooth VOIs to 60 points.void
sortKeyImage_1()
void
sortKeyImage_2()
void
sortKeyImage_3()
void
sortKeyImage_4()
void
sortKeyImage_5()
private void
traverse_firstLayer(java.io.File firstDir, java.lang.String child)
private void
traverse_firstLayer_ForNathan(java.io.File firstDir, java.lang.String child)
private void
traverse_folder_2(java.io.File dir)
private void
traverse_folder_3(java.io.File dir)
private void
traverse_folder_4(java.io.File dir)
private void
traverse_folder_5(java.io.File dir)
private void
traverse_Layer(java.io.File dir)
private void
traverse_Layer_ForNathan(java.io.File dir)
private void
traverse_secondLayer(java.io.File firstLayer, java.lang.String hashID)
private void
traverse_secondLayer_ForNathan(java.io.File firstLayer, java.lang.String hashID)
private void
traverse_thirdLayer(java.io.File secondLayer, java.lang.String hashID)
private void
traverse_thirdLayer_ForNathan(java.io.File secondLayer, java.lang.String hashID)
private void
traverse_voiLayer(java.io.File secondLayer, java.lang.String hashID)
private void
traverse_voiLayer_ForNathan(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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boxYmin
private int boxYmin
bounding box for crop the image. Currently set from 0 to 512, the orginal image slice size.
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boxYmax
private int boxYmax
bounding box for crop the image. Currently set from 0 to 512, the orginal image slice size.
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boxXmin
private int boxXmin
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boxXmax
private int boxXmax
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xBounds
private int[] xBounds
X cropped region bounds.
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yBounds
private int[] yBounds
Y cropped region bounds.
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zBounds
private int[] zBounds
Z cropped region bound.
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cropAlgo
private AlgorithmAddMargins cropAlgo
crop margin algorithm.
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cropImage
private ModelImage cropImage
result cropped image.
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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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keyImageChooser
private javax.swing.JFileChooser keyImageChooser
key images variables.
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keyImageDirectory
private java.lang.String keyImageDirectory
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axisList
private javax.swing.JComboBox axisList
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labelAxis
private javax.swing.JLabel labelAxis
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Axial
private static int Axial
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Saggital
private static int Saggital
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Coronal
private static int Coronal
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axis
private int axis
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keyImages
private java.util.Vector<ModelImage> keyImages
image vector to hold the actual images.
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keyImageVOIs
private java.util.Vector<VOI[]> keyImageVOIs
voi vector to hold the actual vois.
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keyImageVector1
private java.util.Vector<java.lang.String> keyImageVector1
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keyImageVOIVector1
private java.util.Vector<java.lang.String> keyImageVOIVector1
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keyImageVector2
private java.util.Vector<java.lang.String> keyImageVector2
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keyImageVOIVector2
private java.util.Vector<java.lang.String> keyImageVOIVector2
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keyImageVector3
private java.util.Vector<java.lang.String> keyImageVector3
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keyImageVOIVector3
private java.util.Vector<java.lang.String> keyImageVOIVector3
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keyImageVector4
private java.util.Vector<java.lang.String> keyImageVector4
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keyImageVOIVector4
private java.util.Vector<java.lang.String> keyImageVOIVector4
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keyImageVector5
private java.util.Vector<java.lang.String> keyImageVector5
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keyImageVOIVector5
private java.util.Vector<java.lang.String> keyImageVOIVector5
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cropKeyImages
private java.util.Vector<ModelImage> cropKeyImages
cropped key image vector.
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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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voiNameHashtableNathan
java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> voiNameHashtableNathan
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imageHashtable
java.util.Hashtable<java.lang.String,ModelImage> imageHashtable
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voiHashtable
java.util.Hashtable<java.lang.String,VOI> voiHashtable
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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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copyFiles
private void copyFiles()
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traverse_Layer_ForNathan
private void traverse_Layer_ForNathan(java.io.File dir)
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traverse_firstLayer_ForNathan
private void traverse_firstLayer_ForNathan(java.io.File firstDir, java.lang.String child)
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traverse_secondLayer_ForNathan
private void traverse_secondLayer_ForNathan(java.io.File firstLayer, java.lang.String hashID)
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traverse_thirdLayer_ForNathan
private void traverse_thirdLayer_ForNathan(java.io.File secondLayer, java.lang.String hashID)
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traverse_voiLayer_ForNathan
private void traverse_voiLayer_ForNathan(java.io.File secondLayer, java.lang.String hashID)
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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_voiLayer
private void traverse_voiLayer(java.io.File secondLayer, java.lang.String hashID)
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processDir_folder_1
private void processDir_folder_1(java.io.File dir)
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sortKeyImage_1
public void sortKeyImage_1()
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traverse_folder_2
private void traverse_folder_2(java.io.File dir)
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processDir_folder_2
private void processDir_folder_2(java.io.File dir)
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sortKeyImage_2
public void sortKeyImage_2()
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traverse_folder_3
private void traverse_folder_3(java.io.File dir)
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processDir_folder_3
private void processDir_folder_3(java.io.File dir)
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sortKeyImage_3
public void sortKeyImage_3()
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traverse_folder_4
private void traverse_folder_4(java.io.File dir)
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processDir_folder_4
private void processDir_folder_4(java.io.File dir)
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sortKeyImage_4
public void sortKeyImage_4()
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traverse_folder_5
private void traverse_folder_5(java.io.File dir)
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processDir_folder_5
private void processDir_folder_5(java.io.File dir)
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sortKeyImage_5
public void sortKeyImage_5()
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printImages
public void printImages()
Debugger for test the image and VOis reading.
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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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saveTestedImages
public void saveTestedImages()
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crossValidationTest
public void crossValidationTest()
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crossValidationTrain
public void crossValidationTrain()
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saveImages
public void saveImages(java.lang.String key, int[] index, java.lang.String folderName)
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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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rotateToStartingPoint_yMid
private void rotateToStartingPoint_yMid(float[] xPts, float[] yPts, int xDim, int yDim)
Re-oriented the starting and ending VOIs.- Parameters:
xPts
- voi x coordinateyPts
- voi y coordinatexDim
- image x dimensionyDim
- image y dimension
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rotateToStartingPoint_leftMost
private void rotateToStartingPoint_leftMost(float[] xPts, float[] yPts, int xDim, int yDim)
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smoothVOI60
public void smoothVOI60(ModelImage maskImage, ModelImage resultImage)
Smooth VOIs to 60 points.- Parameters:
maskImage
-resultImage
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generateBoundaryContours
private void generateBoundaryContours(VOIBase srcContour, ModelImage targetImageSlice)
Convert VOI from one contour to two contours- Parameters:
srcContour
- single VOI contourtargetImageSlice
- target 2D image slice
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cropKeyImages
public void cropKeyImages()
Crop key images.
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loadFiles
public void loadFiles()
load image files and voi files
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deleteDir
public static boolean deleteDir(java.io.File dir)
Debugger to test dir deletion.- Parameters:
dir
-- Returns:
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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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