MainDialog (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Dialog
      - ij.gui.GenericDialog
        
        bunwarpj.MainDialog

All Implemented Interfaces:

ActionListener, AdjustmentListener, FocusListener, ItemListener, KeyListener, TextListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible
```
public class MainDialog
extends GenericDialog
```
Class to create the dialog for bUnwarpJ. It extends GenericDialog to allow the user interacting with the other windows.

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class java.awt.Dialog
  Dialog.AccessibleAWTDialog, Dialog.ModalExclusionType, Dialog.ModalityType
- Nested classes/interfaces inherited from class java.awt.Window
  Window.AccessibleAWTWindow, Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ACCURATE_MODE` accurate mode constant
`static int`	`FAST_MODE` fast mode constant
`static int`	`MONO_MODE` unidirectional ("mono") mode constant
`static String[]`	`sMaxScaleDeformationChoices` final deformation options
`static String[]`	`sMinScaleDeformationChoices` initial deformation options

Fields inherited from class ij.gui.GenericDialog
checkbox, choice, defaultChoiceIndexes, defaultStrings, defaultText, defaultValues, numberField, radioButtonGroups, slider, stringField, textArea1, textArea2, theLabel

Fields inherited from class java.awt.Dialog
DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component
accessibleContext, 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

Constructor Summary

Constructors
Constructor and Description
`MainDialog(Frame parentWindow, ij.ImagePlus[] imageList, int mode, int maxImageSubsamplingFactor, int min_scale_deformation, int max_scale_deformation, double divWeight, double curlWeight, double landmarkWeight, double imageWeight, double consistencyWeight, double stopThreshold, boolean richOutput, boolean saveTransformation)` Create a new instance of MainDialog.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`actionPerformed(ActionEvent ae)` Actions to be taken during the dialog.
`void`	`applyRawTransformationToSource(double[][] transformation_x, double[][] transformation_y)` Apply a raw transformation to the source image.
`void`	`applyTransformationToSource(int intervals, double[][] cx, double[][] cy)` Apply the transformation defined by the spline coefficients to the source image.
`void`	`freeMemory()` Free the memory used in the program.
`String`	`getMacroArgs()` Get arguments from the macro call
`ij.process.ImageProcessor`	`getOriginalSourceIP()` Get original source image processor.
`ij.process.ImageProcessor`	`getOriginalTargetIP()` Get original target image processor.
`BSplineModel`	`getSource()` Get source image model.
`double[][]`	`getSourceAffineMatrix()` Get the source initial affine matrix.
`ij.ImagePlus`	`getSourceImp()` Get reference to source image
`Mask`	`getSourceMask()` Get source Mask.
`Mask`	`getSourceMsk()` Get source mask.
`PointHandler`	`getSourcePh()` Get source point handler.
`BSplineModel`	`getTarget()` Get target image model.
`double[][]`	`getTargetAffineMatrix()` Get the target initial affine matrix.
`ij.ImagePlus`	`getTargetImp()` Get reference to target image
`Mask`	`getTargetMask()` Get target Mask.
`Mask`	`getTargetMsk()` Get target mask.
`PointHandler`	`getTargetPh()` Get target point handler.
`void`	`grayImage(PointHandler ph)` Method to color the area of the mask.
`boolean`	`isClearMaskSet()` Get clearMask flag.
`boolean`	`isFinalActionLaunched()` Get finalActionLaunched flag.
`boolean`	`isMacroCall()` Get the macro flag
`boolean`	`isSaveTransformationSet()` Get saveTransformation flag.
`boolean`	`isStopRegistrationSet()` Get stopRegistration flag.
`void`	`itemStateChanged(ItemEvent e)` Action to be taken when choices change.
`void`	`joinThreads()` Join the threads for the source and target images.
`void`	`repaintToolbar()` Repaint toolbar.
`void`	`restoreAll()` Restore the initial conditions.
`void`	`setClearMask(boolean val)` Set the clearMask flag.
`void`	`setFinalActionLaunched(boolean b)` Set final action launched flag.
`void`	`setSaveTransformation(boolean b)` Set saveTransformation flag.
`void`	`setSourceAffineMatrix(double[][] affineMatrix)` Set source intial affine matrix.
`void`	`setSourceMask(String sFileName)` Set source Mask.
`void`	`setStopRegistration()` Set the stopRegistration flag to true.
`void`	`setToolbarAllUp()` Set toolbar tools all up.
`void`	`showDialog()` Show main bUnwarpJ dialog
`void`	`ungrayImage(PointAction pa)` Ungray image.
`void`	`windowClosing(WindowEvent e)` Actions to be taken when closing the dialog.

Methods inherited from class ij.gui.GenericDialog
addCheckbox, addCheckboxGroup, addCheckboxGroup, addChoice, addDialogListener, addDirectoryField, addDirectoryField, addFileField, addFileField, addHelp, addImage, addImageChoice, addMessage, addMessage, addMessage, addNumericField, addNumericField, addNumericField, addPanel, addPanel, addPreviewCheckbox, addPreviewCheckbox, addRadioButtonGroup, addSlider, addSlider, addStringField, addStringField, addTextAreas, addToSameRow, adjustmentValueChanged, centerDialog, dispose, enableYesNoCancel, enableYesNoCancel, focusGained, focusLost, getButtons, getCheckboxes, getChoices, getErrorMessage, getInsets, getInstance, getLabel, getMessage, getNextBoolean, getNextChoice, getNextChoiceIndex, getNextImage, getNextNumber, getNextRadioButton, getNextString, getNextText, getNumericFields, getPreviewCheckbox, getRadioButtonGroups, getSliders, getStringFields, getTextArea1, getTextArea2, getValue, hideCancelButton, invalidNumber, isMacro, isPreviewActive, keyPressed, keyReleased, keyTyped, paint, parseDouble, previewRunning, repaint, setCancelLabel, setDefaultString, setEchoChar, setFont, setHelpLabel, setInsets, setLocation, setOKLabel, setSmartRecording, setup, textValueChanged, wasCanceled, wasOKed, windowActivated, windowClosed, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.awt.Dialog
addNotify, getAccessibleContext, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, paramString, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, setVisible, show, toBack

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, 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, postEvent, processEvent, processWindowEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, update, 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, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, 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, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, 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
  - FAST_MODE
```
public static int FAST_MODE
```
    fast mode constant
  - ACCURATE_MODE
```
public static int ACCURATE_MODE
```
    accurate mode constant
  - MONO_MODE
```
public static int MONO_MODE
```
    unidirectional ("mono") mode constant
  - sMinScaleDeformationChoices
```
public static String[] sMinScaleDeformationChoices
```
    initial deformation options
  - sMaxScaleDeformationChoices
```
public static String[] sMaxScaleDeformationChoices
```
    final deformation options
- Constructor Detail
  - MainDialog
```
public MainDialog(Frame parentWindow,
                  ij.ImagePlus[] imageList,
                  int mode,
                  int maxImageSubsamplingFactor,
                  int min_scale_deformation,
                  int max_scale_deformation,
                  double divWeight,
                  double curlWeight,
                  double landmarkWeight,
                  double imageWeight,
                  double consistencyWeight,
                  double stopThreshold,
                  boolean richOutput,
                  boolean saveTransformation)
```
    Create a new instance of MainDialog.
    
    Parameters:
    
    parentWindow - pointer to the parent window
    
    imageList - list of images from ImageJ
    
    mode - default registration mode (0 = Fast, 1 = Accurate, 2 = Mono)
    
    maxImageSubsamplingFactor - subsampling factor at highest resolution level
    
    min_scale_deformation - default minimum scale deformation value
    
    max_scale_deformation - default maximum scale deformation value
    
    divWeight - default divergence weight
    
    curlWeight - default curl weight
    
    landmarkWeight - default landmarks weight
    
    imageWeight - default image similarity weight
    
    consistencyWeight - default consistency weight
    
    stopThreshold - default stopping threshold
    
    richOutput - default verbose flag
    
    saveTransformation - default save transformations flag
- Method Detail
  - setSourceMask
```
public void setSourceMask(String sFileName)
```
    Set source Mask.
    
    Parameters:
    
    sFileName - source mask file name
  - setSourceAffineMatrix
```
public void setSourceAffineMatrix(double[][] affineMatrix)
```
    Set source intial affine matrix.
    
    Parameters:
    
    affineMatrix - initial affine matrix
  - getSourceMask
```
public Mask getSourceMask()
```
    Get source Mask.
    
    Returns:
    
    source mask
  - getTargetMask
```
public Mask getTargetMask()
```
    Get target Mask.
    
    Returns:
    
    target mask
  - actionPerformed
```
public void actionPerformed(ActionEvent ae)
```
    Actions to be taken during the dialog.
    
    Specified by:
    
    actionPerformed in interface ActionListener
    
    Overrides:
    
    actionPerformed in class GenericDialog
  - windowClosing
```
public void windowClosing(WindowEvent e)
```
    Actions to be taken when closing the dialog.
    
    Specified by:
    
    windowClosing in interface WindowListener
    
    Overrides:
    
    windowClosing in class GenericDialog
  - showDialog
```
public void showDialog()
```
    Show main bUnwarpJ dialog
    
    Overrides:
    
    showDialog in class GenericDialog
  - itemStateChanged
```
public void itemStateChanged(ItemEvent e)
```
    Action to be taken when choices change.
    
    Specified by:
    
    itemStateChanged in interface ItemListener
    
    Overrides:
    
    itemStateChanged in class GenericDialog
    
    Parameters:
    
    e - item event
  - applyTransformationToSource
```
public void applyTransformationToSource(int intervals,
                                        double[][] cx,
                                        double[][] cy)
```
    Apply the transformation defined by the spline coefficients to the source image.
    
    Parameters:
    
    intervals - intervals in the deformation
    
    cx - b-spline X- coefficients
    
    cy - b-spline Y- coefficients
  - applyRawTransformationToSource
```
public void applyRawTransformationToSource(double[][] transformation_x,
                                           double[][] transformation_y)
```
    Apply a raw transformation to the source image.
    
    Parameters:
    
    transformation_x - X- mapping
    
    transformation_y - Y- mapping
  - freeMemory
```
public void freeMemory()
```
    Free the memory used in the program.
  - grayImage
```
public void grayImage(PointHandler ph)
```
    Method to color the area of the mask.
    
    Parameters:
    
    ph - image point handler
  - isFinalActionLaunched
```
public boolean isFinalActionLaunched()
```
    Get finalActionLaunched flag.
    
    Returns:
    
    true if the final action has started
  - isClearMaskSet
```
public boolean isClearMaskSet()
```
    Get clearMask flag.
    
    Returns:
    
    true to clear mask
  - isSaveTransformationSet
```
public boolean isSaveTransformationSet()
```
    Get saveTransformation flag.
    
    Returns:
    
    true if the transformations have to be saved
  - setSaveTransformation
```
public void setSaveTransformation(boolean b)
```
    Set saveTransformation flag.
    
    Parameters:
    
    b - set to true to save transformations into file
  - isStopRegistrationSet
```
public boolean isStopRegistrationSet()
```
    Get stopRegistration flag.
    
    Returns:
    
    true if the registration has been stopped
  - joinThreads
```
public void joinThreads()
```
    Join the threads for the source and target images.
  - restoreAll
```
public void restoreAll()
```
    Restore the initial conditions.
  - setClearMask
```
public void setClearMask(boolean val)
```
    Set the clearMask flag.
    
    Parameters:
    
    val - flag to clear mask
  - setStopRegistration
```
public void setStopRegistration()
```
    Set the stopRegistration flag to true.
  - getSourceAffineMatrix
```
public double[][] getSourceAffineMatrix()
```
    Get the source initial affine matrix.
    
    Returns:
    
    initial affine transform of source image
  - getTargetAffineMatrix
```
public double[][] getTargetAffineMatrix()
```
    Get the target initial affine matrix.
    
    Returns:
    
    initial affine transform of target image
  - ungrayImage
```
public void ungrayImage(PointAction pa)
```
    Ungray image. It restores the original version of the image (without mask).
    
    Parameters:
    
    pa - point action pointer
  - getSourcePh
```
public PointHandler getSourcePh()
```
    Get source point handler.
    
    Returns:
    
    source point handler
  - getTargetPh
```
public PointHandler getTargetPh()
```
    Get target point handler.
    
    Returns:
    
    target point handler
  - getSourceMsk
```
public Mask getSourceMsk()
```
    Get source mask.
    
    Returns:
    
    source mask
  - getTargetMsk
```
public Mask getTargetMsk()
```
    Get target mask.
    
    Returns:
    
    target mask
  - setFinalActionLaunched
```
public void setFinalActionLaunched(boolean b)
```
    Set final action launched flag.
    
    Parameters:
    
    b - set to true if the final action has started
  - setToolbarAllUp
```
public void setToolbarAllUp()
```
    Set toolbar tools all up.
  - repaintToolbar
```
public void repaintToolbar()
```
    Repaint toolbar.
  - getTarget
```
public BSplineModel getTarget()
```
    Get target image model.
    
    Returns:
    
    target image model
  - getOriginalSourceIP
```
public ij.process.ImageProcessor getOriginalSourceIP()
```
    Get original source image processor.
    
    Returns:
    
    original source image processor
  - getOriginalTargetIP
```
public ij.process.ImageProcessor getOriginalTargetIP()
```
    Get original target image processor.
    
    Returns:
    
    original target image processor
  - getSource
```
public BSplineModel getSource()
```
    Get source image model.
    
    Returns:
    
    source image model
  - isMacroCall
```
public boolean isMacroCall()
```
    Get the macro flag
    
    Returns:
    
    macro flag
  - getMacroArgs
```
public String getMacroArgs()
```
    Get arguments from the macro call
    
    Returns:
    
    macro call arguments
  - getSourceImp
```
public ij.ImagePlus getSourceImp()
```
    Get reference to source image
    
    Returns:
    
    source image
  - getTargetImp
```
public ij.ImagePlus getTargetImp()
```
    Get reference to target image
    
    Returns:
    
    target image

Class MainDialog

Nested Class Summary

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 ij.gui.GenericDialog

Fields inherited from class java.awt.Dialog

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class ij.gui.GenericDialog

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

FAST_MODE

ACCURATE_MODE

MONO_MODE

sMinScaleDeformationChoices

sMaxScaleDeformationChoices

Constructor Detail

MainDialog

Method Detail

setSourceMask

setSourceAffineMatrix

getSourceMask

getTargetMask

actionPerformed

windowClosing

showDialog

itemStateChanged

applyTransformationToSource

applyRawTransformationToSource

freeMemory

grayImage

isFinalActionLaunched

isClearMaskSet

isSaveTransformationSet

setSaveTransformation

isStopRegistrationSet

joinThreads

restoreAll

setClearMask

setStopRegistration

getSourceAffineMatrix

getTargetAffineMatrix

ungrayImage

getSourcePh

getTargetPh

getSourceMsk

getTargetMsk

setFinalActionLaunched

setToolbarAllUp

repaintToolbar

getTarget

getOriginalSourceIP

getOriginalTargetIP

getSource

isMacroCall

getMacroArgs

getSourceImp

getTargetImp