Class JDialogPromise12_2DVolumetrieHED
- 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.JDialogPromise12_2DVolumetrieHED
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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 JDialogPromise12_2DVolumetrieHED extends JDialogBase implements AlgorithmInterface
For Miccai promise 12 prostate data, we apply wp segmentation using HED deep learning model. Data: given promise 12 data, we apply N4 correction, cropping, and isotropic upsampling. Steps: 1. read promise 12 image data with corresponding masks after pre-processing. 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
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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 int
axial_index
private java.util.Vector<ModelImage>
axialList
private java.util.Vector<ModelImage>
axialMaskList
private javax.swing.JButton
buttonKeyImage
private javax.swing.JButton
buttonSaveImage
(package private) java.util.Hashtable<java.lang.Integer,ModelImage>
cedTableAxial
(package private) java.util.Hashtable<java.lang.Integer,ModelImage>
cedTableCoronal
(package private) java.util.Hashtable<java.lang.Integer,ModelImage>
cedTableSagittal
private int
coronal_index
private java.util.Vector<ModelImage>
coronalList
private java.util.Vector<ModelImage>
coronalMaskList
private javax.swing.JPanel
imageSelectionPanel
private java.util.Vector<ModelImage>
keyImages
image vector to hold the actual images.private java.util.Vector<ModelImage>
keyImagesMask
private java.util.Vector<ModelImage>
keyImagesN4Crop
private java.util.Vector<ModelImage>
keyImagesScaleIntensity
private java.util.Vector<java.lang.String>
keyImageVector1
private java.util.Vector<java.lang.String>
keyImageVector2
private javax.swing.JLabel
labelKeyImage
key image directory.private javax.swing.JLabel
labelSaveImage
saved 2D slices atlas dir.private int
sagittal_index
private java.util.Vector<ModelImage>
sagittalList
private java.util.Vector<ModelImage>
sagittalMaskList
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.-
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 JDialogPromise12_2DVolumetrieHED(java.awt.Frame theParentFrame)
Constructor.
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Method Summary
All 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)
void
callAlgorithm()
Driver function to read image and VOIs, and convert each 3D image to 2D slices.void
conversion()
void
disposeLocal()
dispose memoryvoid
init()
Initial panelvoid
loadFiles()
load image files and voi filesprivate void
processDir_folder_1(java.io.File dir)
private void
processDir_folder_2(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.void
runCED()
void
saveHED2DsliceCED()
void
saveHED2DsliceMRI()
void
saveImage(ModelImage image, ModelImage imageMask, java.lang.String orientation)
private void
savePNGfile(java.lang.String dirName, java.lang.String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)
void
saveTestedImages()
ModelImage
scaleIntensity(ModelImage image)
void
sortKeyImage_1()
void
sortKeyImage_2()
private void
traverse_folder_1(java.io.File dir)
private void
traverse_folder_2(java.io.File dir)
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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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keyImages
private java.util.Vector<ModelImage> keyImages
image vector to hold the actual images.
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keyImagesScaleIntensity
private java.util.Vector<ModelImage> keyImagesScaleIntensity
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keyImagesMask
private java.util.Vector<ModelImage> keyImagesMask
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keyImagesN4Crop
private java.util.Vector<ModelImage> keyImagesN4Crop
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keyImageVector1
private java.util.Vector<java.lang.String> keyImageVector1
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keyImageVector2
private java.util.Vector<java.lang.String> keyImageVector2
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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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axialList
private java.util.Vector<ModelImage> axialList
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axialMaskList
private java.util.Vector<ModelImage> axialMaskList
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sagittalList
private java.util.Vector<ModelImage> sagittalList
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sagittalMaskList
private java.util.Vector<ModelImage> sagittalMaskList
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coronalList
private java.util.Vector<ModelImage> coronalList
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coronalMaskList
private java.util.Vector<ModelImage> coronalMaskList
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axial_index
private int axial_index
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sagittal_index
private int sagittal_index
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coronal_index
private int coronal_index
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cedTableAxial
java.util.Hashtable<java.lang.Integer,ModelImage> cedTableAxial
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cedTableSagittal
java.util.Hashtable<java.lang.Integer,ModelImage> cedTableSagittal
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cedTableCoronal
java.util.Hashtable<java.lang.Integer,ModelImage> cedTableCoronal
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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_folder_1
private void traverse_folder_1(java.io.File dir)
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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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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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saveHED2DsliceMRI
public void saveHED2DsliceMRI()
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runCED
public void runCED()
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saveHED2DsliceCED
public void saveHED2DsliceCED()
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saveImage
public void saveImage(ModelImage image, ModelImage imageMask, java.lang.String orientation)
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calculateCoherenceEnhancingDiffusion
private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)
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conversion
public void conversion()
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scaleIntensity
public ModelImage scaleIntensity(ModelImage image)
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saveTestedImages
public void saveTestedImages()
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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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loadFiles
public void loadFiles()
load image files and voi files
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readFile
public void readFile()
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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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