Package gov.nih.mipav.view.dialogs

Class JDialogRegistrationOAR2D

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

gov.nih.mipav.view.dialogs.JDialogBase

gov.nih.mipav.view.dialogs.JDialogScriptableBase

gov.nih.mipav.view.dialogs.JDialogRegistrationOAR2D

All Implemented Interfaces:

AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, ActionDiscovery, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants

public class JDialogRegistrationOAR2D
extends JDialogScriptableBase
implements AlgorithmInterface, ActionDiscovery, ScriptableActionInterface

Dialog to get user input, then call AlgorithmRegOAR2D.

Author:

Neva Cherniavsky

See Also:

• AlgorithmCostFunctions
• AlgorithmRegOAR2D
• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase

JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction

Nested classes/interfaces inherited from class javax.swing.JDialog

JDialog.AccessibleJDialog

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	Description
private JDialog	advancedDialog	Variables for Advanced Settings dialog.
private JCheckBox	bruteForceCheckBox	CheckBox to turn brute-force registration on or off:.
private JDialog	bruteForceDialog	Dialog to set the brute-force registration parameters:.
private JButton	buttonWeightInput	DOCUMENT ME!
private JButton	buttonWeightRef	DOCUMENT ME!
private float	coarseRate	DOCUMENT ME!
private JTextField	coarseRateText	DOCUMENT ME!
private JComboBox	comboBoxCostFunct	DOCUMENT ME!
private JComboBox	comboBoxDOF	DOCUMENT ME!
private JComboBox	comboBoxImage	DOCUMENT ME!
private JComboBox	comboBoxInterp	DOCUMENT ME!
private JComboBox	comboBoxInterp2	DOCUMENT ME!
private JComboBox	comboBoxSearchAlgo
private int	cost	DOCUMENT ME!
private int	dataType
private String	directoryWInput	DOCUMENT ME!
private String	directoryWRef	DOCUMENT ME!
private boolean	displayTransform	DOCUMENT ME!
private boolean	doColor	DOCUMENT ME!
private JCheckBox	doColorCheckBox	CheckBox to turn color registration on or off:.
private int	DOF	DOCUMENT ME!
private boolean	doJTEM
private boolean	doMultiThread
private boolean	doSubsample	DOCUMENT ME!
private final int	ELSUNC
private String	fileNameWInput	DOCUMENT ME!
private String	fileNameWRef	DOCUMENT ME!
private float	fillValue
private float	fineRate	DOCUMENT ME!
private JTextField	fineRateText	DOCUMENT ME!
private double	imageMax
private double	imageMin
private ModelImage	inputWeightImage	DOCUMENT ME!
private int	interp	DOCUMENT ME!
private int	interp2	DOCUMENT ME!
private JCheckBox	jtemCheckBox	DOCUMENT ME!
private JLabel	labelCoarse	DOCUMENT ME!
private JLabel	labelCoarseDegrees	DOCUMENT ME!
private JLabel	labelFine	DOCUMENT ME!
private JLabel	labelFineDegrees	DOCUMENT ME!
private JLabel	labelInterp2	DOCUMENT ME!
private JLabel	labelRotateDegrees	DOCUMENT ME!
private JLabel	labelRotateRange	DOCUMENT ME!
private JLabel	labelRotateRangeTo	DOCUMENT ME!
private final int	LEVENBERG_MARQUARDT
private boolean	m_bSubsetDialog	If true the dialog for this instance of JDialogRegistrationOAR2D will not activate the AlgorithmRegOAR2D:.
private ModelImage	matchImage	DOCUMENT ME!
private JComboBox	matrixComboBox
private String	matrixDirectory
private JLabel	matrixLabel
private int	maxIterations	DOCUMENT ME!
private int	maxIterations_def	DOCUMENT ME!
private JTextField	maxIterationsText	DOCUMENT ME!
private JCheckBox	multiThreadCheckBox
private final int	NL2SOL
private JRadioButton	noneRadio	DOCUMENT ME!
private int	numMinima	DOCUMENT ME!
private int	numMinima_def	DOCUMENT ME!
private JTextField	numMinText	DOCUMENT ME!
private JComboBox	outOfBoundsComboBox
private int	outOfBoundsIndex	Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum
private JLabel	outOfBoundsLabel
private final int	POWELL
private ModelImage	refImage	DOCUMENT ME!
private ModelImage	refWeightImage	DOCUMENT ME!
private AlgorithmRegOAR2D	reg2	DOCUMENT ME!
private AlgorithmRegELSUNCOAR2D	reg2E
private ModelImage	resultImage	DOCUMENT ME!
private float	rotateBegin	DOCUMENT ME!
private JTextField	rotateBeginText	DOCUMENT ME!
private float	rotateEnd	DOCUMENT ME!
private JTextField	rotateEndText	DOCUMENT ME!
private float	rotationBF	DOCUMENT ME!
private JTextField	rotationText	Brute-force registration parameters:.
private JCheckBox	sampleCheckBox	DOCUMENT ME!
private int	scaleStepsBF	DOCUMENT ME!
private JTextField	scaleStepsText	Brute-force registration parameters:.
private int	searchAlgorithm
private static final long	serialVersionUID	Use serialVersionUID for interoperability.
private JTextField	textInput	DOCUMENT ME!
private JTextField	textRef	DOCUMENT ME!
private JCheckBox	transformCheckbox	DOCUMENT ME!
private int	translationBF	DOCUMENT ME!
private JTextField	translationText	Brute-force registration parameters:.
private ViewUserInterface	UI	DOCUMENT ME!
private JLabel	userDirectoryLabel
private JTextField	userDirectoryText
private JLabel	valueLabel
private JTextField	valueText
private JRadioButton	voiRadio	DOCUMENT ME!
private boolean	voisOnly	DOCUMENT ME!
private boolean	weighted	DOCUMENT ME!
private JRadioButton	weightRadio	DOCUMENT ME!
private float	xscaleBF	DOCUMENT ME!
private JTextField	xscaleText	Brute-force registration parameters:.
private float	yscaleBF	DOCUMENT ME!
private JTextField	yscaleText	Brute-force registration parameters:.

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

displayInNewFrame, isComplete, scriptParameters

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

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

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

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Constructor Summary

Constructors

Constructor	Description
JDialogRegistrationOAR2D()	Empty constructor needed for dynamic instantiation (used during scripting).
JDialogRegistrationOAR2D(Frame theParentFrame, ModelImage im)	Creates new dialog for user to choose type of 2D image registration algorithm to run.
JDialogRegistrationOAR2D(Frame theParentFrame, ModelImage ref, ModelImage match, int iCost, int iDOF, int iInterp, float fRotateBegin, float fRotateEnd, float fCoarseRate, float fFineRate, boolean bDoSubsample, int iMaxIterations, int iNumMin, int iInterp2, boolean bDisplayTransform, float fRotateBF, float fXScaleBF, float fYScaleBF, int iScaleStepsBF, int iTranslationBF)	Creates new dialog for user to choose type of 2D image registration algorithm to run.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent event)	Closes dialog box when the OK button is pressed, sets the variables, and calls the algorithm.
void	algorithmPerformed(AlgorithmBase algorithm)	This method is required if the AlgorithmPerformed interface is implemented.
private JDialog	buildAdvancedDialog(int maxIter, int numMinima)	Build advanced settings dialog.
private JDialog	buildBruteForceDialog()	Builds the bruteForceDialog so the user can set the brute-force registration parameters:
private JComboBox	buildImgComboBox(ModelImage image)	Builds a list of images.
protected void	callAlgorithm()	Calls the algorithm with the set-up parameters.
ParameterTable	createInputParameters()	Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in setGUIFromParams()).
ParameterTable	createOutputParameters()	Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
protected void	doPostAlgorithmActions()	Store the result image in the script runner's image table now that the action execution is finished.
ActionMetadata	getActionMetadata()	Return meta-information about this discoverable action for categorization and labeling purposes.
boolean	getBruteForce()	Accessor to get whether or not to do the brute-force registration.
float	getCoarseBegin()	Accessor to get the coarse sample begin.
float	getCoarseEnd()	Accessor to get the coarse sample end.
float	getCoarseRate()	Accessor to get the coarse sample rate.
int	getCostChoice()	Accessor to get the choice of cost function.
boolean	getDisplayTransform()	Accessor to get the display transform flag.
int	getDOF()	Accessor to get the degrees of freedom.
float	getFineRate()	Accessor to get the fine sample rate.
int	getInterp()	Accessor to get the initial interpolation.
int	getInterp2()	Accessor to get the final interpolation.
int	getMaxIterations()	Accessor to get maxIterations.
int	getNumMinima()	Accessor to get numMinima.
String	getOutputImageName(String imageParamName)	Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).
ModelImage	getResultImage()	Accessor to get the result image.
float	getRotationBruteForce()	Accessor to get the rotation range for brute force registration:
int	getScaleStepsBruteForce()	Accessor to get the y scale range for brute force registration:
boolean	getSubsample()	Accessor to get whether or not subsampling occurs.
int	getTranslationBruteForce()	Accessor to get the translation range for brute force registration:
float	getXScaleBruteForce()	Accessor to get the x scale range for brute force registration:
float	getYScaleBruteForce()	Accessor to get the y scale range for brute force registration:
private void	init()	Initializes the GUI components and displays the dialog.
private void	initPresets()	Initializes the GUI components, based on the preset values set by the class calling the constructor.
boolean	isActionComplete()	Returns whether the action has successfully completed its execution.
void	itemStateChanged(ItemEvent event)	Changes the interpolation box to enabled or disabled depending on if the transform box is checked or not.
void	setCoarseBegin(float x)	Accessor to set the coarse sample begin.
void	setCoarseEnd(float x)	Accessor to set the coarse sample end.
void	setCoarseRate(float x)	Accessor to set the coarse sample rate.
void	setCostChoice(int x)	Accessor to set the choice of cost function.
void	setDisplayTransform(boolean flag)	Accessor to set the display transform flag.
void	setDOF(int x)	Accessor to set the degrees of freedom.
void	setFillValue(float fillValue)	Accessor to set intensity value for out of bounds data
void	setFineRate(float x)	Accessor to set the fine sample rate.
protected void	setGUIFromParams()	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
void	setInputWeightImage(ModelImage im)	Accessor to set the input weight image.
void	setInterp(int x)	Accessor to set the initial interpolation.
void	setInterp2(int x)	Accessor to set the final interpolation.
void	setMatrixDirectory(String matrixDirectory)	Accessor to set directory in which the matrix file is stored
void	setMultiThread(boolean doMultiThread)	Accessor to set whether or not powell's algorithm uses multithreading
void	setOutOfBoundsIndex(int outOfBoundsIndex)	tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image max
void	setReferenceImage(ModelImage im)	Accessor to set the reference image.
void	setReferenceWeightImage(ModelImage im)	Accessor to set the reference weight image.
void	setSearchAlgorithm(int searchAlgorithm)
void	setSubsample(boolean doSubsample)	Accessor to set whether or not subsampling occurs.
private boolean	setVariables()	Sets the variables needed to call the registration algorithm based on the values entered in the dialog.
void	setVoisOnly(boolean flag)	Accessor to set the VOIs only flag.
void	setWeighted(boolean flag)	Accessor to set the weighted images flag.
protected void	storeParamsFromGUI()	Record the parameters just used to run this algorithm in a script.
private boolean	testType(int type, float value)	Determine if the value is in the image type range and within the float range since AlgorithmTransform does not use double buffers.

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

getDialogActionString, insertScriptLine, isComplete, scriptRun, setComplete

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, 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

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

Methods inherited from class java.awt.Dialog

addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack

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

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

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface gov.nih.mipav.view.dialogs.ActionDiscovery

scriptRun

Methods inherited from interface gov.nih.mipav.model.scripting.ScriptableActionInterface

insertScriptLine, scriptRun

Field Details

serialVersionUID

private static final long serialVersionUID

Use serialVersionUID for interoperability.

See Also:

• Constant Field Values

POWELL

private final int POWELL

See Also:

• Constant Field Values

ELSUNC

private final int ELSUNC

See Also:

• Constant Field Values

LEVENBERG_MARQUARDT

private final int LEVENBERG_MARQUARDT

See Also:

• Constant Field Values

NL2SOL

private final int NL2SOL

See Also:

• Constant Field Values

searchAlgorithm

private int searchAlgorithm

advancedDialog

private JDialog advancedDialog

Variables for Advanced Settings dialog.

maxIterationsText

private JTextField maxIterationsText

DOCUMENT ME!

numMinText

private JTextField numMinText

DOCUMENT ME!

bruteForceCheckBox

private JCheckBox bruteForceCheckBox

CheckBox to turn brute-force registration on or off:.

bruteForceDialog

private JDialog bruteForceDialog

Dialog to set the brute-force registration parameters:.

buttonWeightInput

private JButton buttonWeightInput

DOCUMENT ME!

buttonWeightRef

private JButton buttonWeightRef

DOCUMENT ME!

coarseRateText

private JTextField coarseRateText

DOCUMENT ME!

comboBoxCostFunct

private JComboBox comboBoxCostFunct

DOCUMENT ME!

comboBoxSearchAlgo

private JComboBox comboBoxSearchAlgo

comboBoxDOF

private JComboBox comboBoxDOF

DOCUMENT ME!

comboBoxImage

private JComboBox comboBoxImage

DOCUMENT ME!

comboBoxInterp

private JComboBox comboBoxInterp

DOCUMENT ME!

comboBoxInterp2

private JComboBox comboBoxInterp2

DOCUMENT ME!

cost

private int cost

DOCUMENT ME!

interp

private int interp

DOCUMENT ME!

interp2

private int interp2

DOCUMENT ME!

DOF

private int DOF

DOCUMENT ME!

displayTransform

private boolean displayTransform

DOCUMENT ME!

doColor

private boolean doColor

DOCUMENT ME!

doColorCheckBox

private JCheckBox doColorCheckBox

CheckBox to turn color registration on or off:.

doSubsample

private boolean doSubsample

DOCUMENT ME!

doJTEM

private boolean doJTEM

doMultiThread

private boolean doMultiThread

fileNameWRef

private String fileNameWRef

DOCUMENT ME!

directoryWRef

private String directoryWRef

DOCUMENT ME!

fileNameWInput

private String fileNameWInput

DOCUMENT ME!

directoryWInput

private String directoryWInput

DOCUMENT ME!

fineRateText

private JTextField fineRateText

DOCUMENT ME!

inputWeightImage

private ModelImage inputWeightImage

DOCUMENT ME!

refWeightImage

private ModelImage refWeightImage

DOCUMENT ME!

labelCoarse

private JLabel labelCoarse

DOCUMENT ME!

labelCoarseDegrees

private JLabel labelCoarseDegrees

DOCUMENT ME!

labelFine

private JLabel labelFine

DOCUMENT ME!

labelFineDegrees

private JLabel labelFineDegrees

DOCUMENT ME!

labelInterp2

private JLabel labelInterp2

DOCUMENT ME!

labelRotateDegrees

private JLabel labelRotateDegrees

DOCUMENT ME!

labelRotateRange

private JLabel labelRotateRange

DOCUMENT ME!

labelRotateRangeTo

private JLabel labelRotateRangeTo

DOCUMENT ME!

m_bSubsetDialog

private boolean m_bSubsetDialog

If true the dialog for this instance of JDialogRegistrationOAR2D will not activate the AlgorithmRegOAR2D:.

matchImage

private ModelImage matchImage

DOCUMENT ME!

maxIterations_def

private int maxIterations_def

DOCUMENT ME!

numMinima_def

private int numMinima_def

DOCUMENT ME!

maxIterations

private int maxIterations

DOCUMENT ME!

noneRadio

private JRadioButton noneRadio

DOCUMENT ME!

numMinima

private int numMinima

DOCUMENT ME!

refImage

private ModelImage refImage

DOCUMENT ME!

reg2

private AlgorithmRegOAR2D reg2

DOCUMENT ME!

reg2E

private AlgorithmRegELSUNCOAR2D reg2E

resultImage

private ModelImage resultImage

DOCUMENT ME!

rotateBegin

private float rotateBegin

DOCUMENT ME!

rotateEnd

private float rotateEnd

DOCUMENT ME!

coarseRate

private float coarseRate

DOCUMENT ME!

fineRate

private float fineRate

DOCUMENT ME!

rotateBeginText

private JTextField rotateBeginText

DOCUMENT ME!

rotateEndText

private JTextField rotateEndText

DOCUMENT ME!

rotationBF

private float rotationBF

DOCUMENT ME!

xscaleBF

private float xscaleBF

DOCUMENT ME!

yscaleBF

private float yscaleBF

DOCUMENT ME!

rotationText

private JTextField rotationText

Brute-force registration parameters:.

translationText

private JTextField translationText

Brute-force registration parameters:.

xscaleText

private JTextField xscaleText

Brute-force registration parameters:.

yscaleText

private JTextField yscaleText

Brute-force registration parameters:.

scaleStepsText

private JTextField scaleStepsText

Brute-force registration parameters:.

sampleCheckBox

private JCheckBox sampleCheckBox

DOCUMENT ME!

jtemCheckBox

private JCheckBox jtemCheckBox

DOCUMENT ME!

multiThreadCheckBox

private JCheckBox multiThreadCheckBox

scaleStepsBF

private int scaleStepsBF

DOCUMENT ME!

textInput

private JTextField textInput

DOCUMENT ME!

textRef

private JTextField textRef

DOCUMENT ME!

transformCheckbox

private JCheckBox transformCheckbox

DOCUMENT ME!

translationBF

private int translationBF

DOCUMENT ME!

UI

private ViewUserInterface UI

DOCUMENT ME!

voiRadio

private JRadioButton voiRadio

DOCUMENT ME!

voisOnly

private boolean voisOnly

DOCUMENT ME!

weighted

private boolean weighted

DOCUMENT ME!

weightRadio

private JRadioButton weightRadio

DOCUMENT ME!

outOfBoundsLabel

private JLabel outOfBoundsLabel

outOfBoundsComboBox

private JComboBox outOfBoundsComboBox

valueLabel

private JLabel valueLabel

valueText

private JTextField valueText

imageMin

private double imageMin

imageMax

private double imageMax

dataType

private int dataType

outOfBoundsIndex

private int outOfBoundsIndex

Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

fillValue

private float fillValue

matrixLabel

private JLabel matrixLabel

matrixComboBox

private JComboBox matrixComboBox

matrixDirectory

private String matrixDirectory

userDirectoryLabel

private JLabel userDirectoryLabel

userDirectoryText

private JTextField userDirectoryText

Constructor Details

JDialogRegistrationOAR2D

public JDialogRegistrationOAR2D()

Empty constructor needed for dynamic instantiation (used during scripting).

JDialogRegistrationOAR2D

public JDialogRegistrationOAR2D(Frame theParentFrame,
 ModelImage im)

Creates new dialog for user to choose type of 2D image registration algorithm to run.

Parameters:

theParentFrame - Parent frame.

im - Source image.

JDialogRegistrationOAR2D

public JDialogRegistrationOAR2D(Frame theParentFrame,
 ModelImage ref,
 ModelImage match,
 int iCost,
 int iDOF,
 int iInterp,
 float fRotateBegin,
 float fRotateEnd,
 float fCoarseRate,
 float fFineRate,
 boolean bDoSubsample,
 int iMaxIterations,
 int iNumMin,
 int iInterp2,
 boolean bDisplayTransform,
 float fRotateBF,
 float fXScaleBF,
 float fYScaleBF,
 int iScaleStepsBF,
 int iTranslationBF)

Creates new dialog for user to choose type of 2D image registration algorithm to run.

Parameters:

theParentFrame - Parent frame.

ref - Reference image.

match - Match image.

iCost - default cost choice.

iDOF - default degrees of freedom choice.

iInterp - default image interpolation choice.

fRotateBegin - default rotation range choice.

fRotateEnd - default rotation range choice.

fCoarseRate - default rotation coarse rate choice.

fFineRate - default rotation fine rate choice.

bDoSubsample - default subsampling choice.

iMaxIterations - default max iterations choice.

iNumMin - default number of minima choice.

iInterp2 - default display interpolation choice.

bDisplayTransform - default display transformed image choice.

fRotateBF - default rotation angle range for brute-force registration.

fXScaleBF - default scale in x range for brute-force registration.

fYScaleBF - default scale in x range for brute-force registration.

iScaleStepsBF - default number of steps to divide scale range brute-force registration.

iTranslationBF - default translation range for brute-force registration.

Method Details

actionPerformed

public void actionPerformed(ActionEvent event)

Closes dialog box when the OK button is pressed, sets the variables, and calls the algorithm.

Specified by:

actionPerformed in interface ActionListener

Overrides:

actionPerformed in class JDialogBase

Parameters:

event - Event that triggers function.

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 complete.

Specified by:

algorithmPerformed in interface AlgorithmInterface

Parameters:

algorithm - Algorithm that caused the event.

getBruteForce

public boolean getBruteForce()

Accessor to get whether or not to do the brute-force registration.

Returns:

bruteForceCheckBox.isSelected()

getCoarseBegin

public float getCoarseBegin()

Accessor to get the coarse sample begin.

Returns:

rotateBegon Coarse begin

getCoarseEnd

public float getCoarseEnd()

Accessor to get the coarse sample end.

Returns:

rotateEnd Coarse end

getCoarseRate

public float getCoarseRate()

Accessor to get the coarse sample rate.

Returns:

coarseRate, Coarse rate

getCostChoice

public int getCostChoice()

Accessor to get the choice of cost function.

Returns:

cost, Cost function.

getDisplayTransform

public boolean getDisplayTransform()

Accessor to get the display transform flag.

Returns:

displayTransform flag true means display the transformed image.

getDOF

public int getDOF()

Accessor to get the degrees of freedom.

Returns:

DOF, Degrees of freedom

getFineRate

public float getFineRate()

Accessor to get the fine sample rate.

Returns:

fineRate, Fine rate

getInterp

public int getInterp()

Accessor to get the initial interpolation.

Returns:

interp, Interpolation

getInterp2

public int getInterp2()

Accessor to get the final interpolation.

Returns:

interp2, Interpolation

getMaxIterations

public int getMaxIterations()

Accessor to get maxIterations.

Returns:

maxIterations

getNumMinima

public int getNumMinima()

Accessor to get numMinima.

Returns:

numMinima

getResultImage

public ModelImage getResultImage()

Accessor to get the result image.

Returns:

Result image.

getRotationBruteForce

public float getRotationBruteForce()

Accessor to get the rotation range for brute force registration:

Returns:

rotationBF, range of rotations

getScaleStepsBruteForce

public int getScaleStepsBruteForce()

Accessor to get the y scale range for brute force registration:

Returns:

scaleStepsBF, number of divisions for scale

getSubsample

public boolean getSubsample()

Accessor to get whether or not subsampling occurs.

Returns:

doSubsample

getTranslationBruteForce

public int getTranslationBruteForce()

Accessor to get the translation range for brute force registration:

Returns:

translationBF, range of x,y translations

getXScaleBruteForce

public float getXScaleBruteForce()

Accessor to get the x scale range for brute force registration:

Returns:

xscaleBF, range of scales in x

getYScaleBruteForce

public float getYScaleBruteForce()

Accessor to get the y scale range for brute force registration:

Returns:

yscaleBF, range of scales in y

itemStateChanged

public void itemStateChanged(ItemEvent event)

Changes the interpolation box to enabled or disabled depending on if the transform box is checked or not.

Specified by:

itemStateChanged in interface ItemListener

Overrides:

itemStateChanged in class JDialogBase

Parameters:

event - Event that triggered this function.

setCoarseBegin

public void setCoarseBegin(float x)

Accessor to set the coarse sample begin.

Parameters:

x - Coarse begin

setCoarseEnd

public void setCoarseEnd(float x)

Accessor to set the coarse sample end.

Parameters:

x - Coarse end

setCoarseRate

public void setCoarseRate(float x)

Accessor to set the coarse sample rate.

Parameters:

x - Coarse rate

setCostChoice

public void setCostChoice(int x)

Accessor to set the choice of cost function.

Parameters:

x - Cost function.

setDisplayTransform

public void setDisplayTransform(boolean flag)

Accessor to set the display transform flag.

Parameters:

flag - true means display the transformed image.

setDOF

public void setDOF(int x)

Accessor to set the degrees of freedom.

Parameters:

x - Degrees of freedom

setFineRate

public void setFineRate(float x)

Accessor to set the fine sample rate.

Parameters:

x - Fine rate

setInputWeightImage

public void setInputWeightImage(ModelImage im)

Accessor to set the input weight image.

Parameters:

im - Input weight image.

setInterp

public void setInterp(int x)

Accessor to set the initial interpolation.

Parameters:

x - Interpolation

setInterp2

public void setInterp2(int x)

Accessor to set the final interpolation.

Parameters:

x - Interpolation

setReferenceImage

public void setReferenceImage(ModelImage im)

Accessor to set the reference image.

Parameters:

im - Reference image.

setReferenceWeightImage

public void setReferenceWeightImage(ModelImage im)

Accessor to set the reference weight image.

Parameters:

im - Reference weight image.

setSubsample

public void setSubsample(boolean doSubsample)

Accessor to set whether or not subsampling occurs.

Parameters:

doSubsample - DOCUMENT ME!

setSearchAlgorithm

public void setSearchAlgorithm(int searchAlgorithm)

Parameters:

searchAlgorithm -

setMultiThread

public void setMultiThread(boolean doMultiThread)

Accessor to set whether or not powell's algorithm uses multithreading

Parameters:

doMultiThread -

setVoisOnly

public void setVoisOnly(boolean flag)

Accessor to set the VOIs only flag.

Parameters:

flag - true then only register the parts of the images in the VOIs.

setWeighted

public void setWeighted(boolean flag)

Accessor to set the weighted images flag.

Parameters:

flag - true means there are weighted images.

setOutOfBoundsIndex

public void setOutOfBoundsIndex(int outOfBoundsIndex)

tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image max

Parameters:

outOfBoundsIndex -

setFillValue

public void setFillValue(float fillValue)

Accessor to set intensity value for out of bounds data

Parameters:

fillValue -

setMatrixDirectory

public void setMatrixDirectory(String matrixDirectory)

Accessor to set directory in which the matrix file is stored

Parameters:

matrixDirectory -

callAlgorithm

protected void callAlgorithm()

Calls the algorithm with the set-up parameters.

Specified by:

callAlgorithm in class JDialogScriptableBase

doPostAlgorithmActions

protected void doPostAlgorithmActions()

Store the result image in the script runner's image table now that the action execution is finished.

Overrides:

doPostAlgorithmActions in class JDialogScriptableBase

setGUIFromParams

protected void setGUIFromParams()

Set the dialog GUI using the script parameters while running this algorithm as part of a script.

Specified by:

setGUIFromParams in class JDialogScriptableBase

storeParamsFromGUI

protected void storeParamsFromGUI()
                           throws ParserException

Record the parameters just used to run this algorithm in a script.

Specified by:

storeParamsFromGUI in class JDialogScriptableBase

Throws:

ParserException - If there is a problem creating/recording the new parameters.

buildAdvancedDialog

private JDialog buildAdvancedDialog(int maxIter,
 int numMinima)

Build advanced settings dialog. Returns JDialog.

Parameters:

maxIter - DOCUMENT ME!

numMinima - DOCUMENT ME!

Returns:

DOCUMENT ME!

buildBruteForceDialog

private JDialog buildBruteForceDialog()

Builds the bruteForceDialog so the user can set the brute-force registration parameters:

Returns:

bruteForceDialog

buildImgComboBox

private JComboBox buildImgComboBox(ModelImage image)

Builds a list of images. Returns combobox.

Parameters:

image - DOCUMENT ME!

Returns:

Newly created combo box.

init

private void init()

Initializes the GUI components and displays the dialog.

initPresets

private void initPresets()

Initializes the GUI components, based on the preset values set by the class calling the constructor. Then displays the dialog.

setVariables

private boolean setVariables()

Sets the variables needed to call the registration algorithm based on the values entered in the dialog.

Returns:

true if the variables are properly set, false otherwise.

testType

private boolean testType(int type,
 float value)

Determine if the value is in the image type range and within the float range since AlgorithmTransform does not use double buffers.

Parameters:

type - image type

value - value tested

Returns:

true if value is within acceptable range

getActionMetadata

public ActionMetadata getActionMetadata()

Return meta-information about this discoverable action for categorization and labeling purposes.

Specified by:

getActionMetadata in interface ActionDiscovery

Returns:

Metadata for this action.

createInputParameters

public ParameterTable createInputParameters()

Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in setGUIFromParams()).

Specified by:

createInputParameters in interface ActionDiscovery

Returns:

A parameter table listing the inputs of this algorithm.

createOutputParameters

public ParameterTable createOutputParameters()

Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).

Specified by:

createOutputParameters in interface ActionDiscovery

Returns:

A parameter table listing the outputs of this algorithm.

getOutputImageName

public String getOutputImageName(String imageParamName)

Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).

Specified by:

getOutputImageName in interface ActionDiscovery

Parameters:

imageParamName - The output image parameter label for which to get the image name.

Returns:

The image name of the requested output image parameter label.

isActionComplete

public boolean isActionComplete()

Returns whether the action has successfully completed its execution.

Specified by:

isActionComplete in interface ActionDiscovery

Returns:

True, if the action is complete. False, if the action failed or is still running.