bunwarpj
Class IODialog

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Dialog
                  bunwarpj.IODialog

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

public class IODialog
extends java.awt.Dialog
implements java.awt.event.ActionListener

Class to create the Input/Output dialog to deal with the files to keep the information of bUnwarpJ.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Dialog

java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

private MainDialog	dialog Dialog for bUnwarpJ interface
private ij.ImagePlus	sourceImp Pointer to the source image representation
private PointHandler	sourcePh Point handler for the source image
private ij.ImagePlus	targetImp Pointer to the target image representation
private PointHandler	targetPh Point handler for the target image

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

IODialog(java.awt.Frame parentWindow, ij.ImagePlus sourceImp, ij.ImagePlus targetImp, PointHandler sourcePh, PointHandler targetPh, MainDialog dialog)
Create a new instance of IODialog.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ae) Actions to be taking during the dialog.
private void	adaptCoefficients() Adapt the transformation coefficients to a new image size.
private void	compareElasticWithRaw() Compare an elastic B-spline transformation with a random deformation (in raw format) by the warping index.
private void	compareOppositeElasticTransformations() Compare two opposite transformations (direct and inverse) represented by B-splines through the warping index.
private void	compareRawTransformations() Compare two random (raw) deformations by the warping index.
private void	composeElasticTransformations() Compose two transformations represented by elastic B-splines into a raw mapping table (saved as usual).
private void	composeRawElasticTransformations() Compose a raw transformation with an elastic transformation represented by elastic B-splines into a raw mapping table (saved as usual).
private void	composeRawTransformations() Compose two random (raw) deformations.
private void	evaluateSimilarity() Calculate the similarity error between the source and target images.
java.awt.Insets	getInsets() Get the insets.
private void	invertRawTransformation() Invert a raw transformation
private void	loadPoints() Load the points from the point handlers.
private void	loadRawTransformation() Load a raw transformation and apply it to the source image.
private void	loadSourceInitialAffineMatrix() Load a source initial affine matrix.
private void	loadSourceMask() Load a source mask image from a file.
private void	loadTransformation() Load a transformation and apply it to the source image.
private void	savePoints() Save the landmark points into a file.
private void	saveTransformationInElastic() Save a raw transformation in elastic (B-spline) format
private void	saveTransformationInRaw() Save an elastic transformation in raw format
private void	showPoints() Display the points over the images.

Methods inherited from class java.awt.Dialog

addNotify, getAccessibleContext, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, paramString, setModal, setModalityType, setResizable, setTitle, setUndecorated, setVisible, show, toBack

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOwnedWindows, getOwner, getOwnerlessWindows, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, 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, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, 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, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, 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, isOpaque, 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, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

sourceImp

private ij.ImagePlus sourceImp

Pointer to the source image representation

targetImp

private ij.ImagePlus targetImp

Pointer to the target image representation

sourcePh

private PointHandler sourcePh

Point handler for the source image

targetPh

private PointHandler targetPh

Point handler for the target image

dialog

private MainDialog dialog

Dialog for bUnwarpJ interface

Constructor Detail

IODialog

public IODialog(java.awt.Frame parentWindow,
                ij.ImagePlus sourceImp,
                ij.ImagePlus targetImp,
                PointHandler sourcePh,
                PointHandler targetPh,
                MainDialog dialog)

Create a new instance of IODialog.

Parameters:

parentWindow - pointer to the parent window

sourceImp - pointer to the source image representation

targetImp - pointer to the target image representation

sourcePh - point handler for the source image

targetPh - point handler for the source image

dialog - dialog for bUnwarpJ interface

Method Detail

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ae)

Actions to be taking during the dialog.

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getInsets

public java.awt.Insets getInsets()

Get the insets.

Overrides:

getInsets in class java.awt.Container

Returns:

new insets

loadPoints

private void loadPoints()

Load the points from the point handlers.

loadTransformation

private void loadTransformation()

Load a transformation and apply it to the source image.

loadSourceMask

private void loadSourceMask()

Load a source mask image from a file.

loadSourceInitialAffineMatrix

private void loadSourceInitialAffineMatrix()

Load a source initial affine matrix.

loadRawTransformation

private void loadRawTransformation()

Load a raw transformation and apply it to the source image.

adaptCoefficients

private void adaptCoefficients()

Adapt the transformation coefficients to a new image size. It asks the user to introduce the image factor between the previous and the new image size. This factor can be a double to represent image size reductions. Powers of two (positive or negative) expected.

saveTransformationInRaw

private void saveTransformationInRaw()

Save an elastic transformation in raw format

saveTransformationInElastic

private void saveTransformationInElastic()

Save a raw transformation in elastic (B-spline) format

invertRawTransformation

private void invertRawTransformation()

Invert a raw transformation

compareOppositeElasticTransformations

private void compareOppositeElasticTransformations()

Compare two opposite transformations (direct and inverse) represented by B-splines through the warping index.

composeElasticTransformations

private void composeElasticTransformations()

Compose two transformations represented by elastic B-splines into a raw mapping table (saved as usual).

composeRawElasticTransformations

private void composeRawElasticTransformations()

Compose a raw transformation with an elastic transformation represented by elastic B-splines into a raw mapping table (saved as usual).

composeRawTransformations

private void composeRawTransformations()

Compose two random (raw) deformations.

compareElasticWithRaw

private void compareElasticWithRaw()

Compare an elastic B-spline transformation with a random deformation (in raw format) by the warping index.

compareRawTransformations

private void compareRawTransformations()

Compare two random (raw) deformations by the warping index.

evaluateSimilarity

private void evaluateSimilarity()

Calculate the similarity error between the source and target images. The error is calculated pixel by pixel without representing the images by B-splines coefficients. Mask are taken into account.

savePoints

private void savePoints()

Save the landmark points into a file.

showPoints

private void showPoints()

Display the points over the images.