Package gov.nih.mipav.view.dialogs

Class JDialogReorient

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.JDialogReorient

All Implemented Interfaces:

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

public class JDialogReorient
extends JDialogScriptableBase
implements AlgorithmInterface, ActionDiscovery

Dialog box for basic image processing tools

Version:

April 2006

Author:

Pilou Bazin

See Also:

• 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 AlgorithmTransform	algoTrans
static final int	AXIAL_INDEX
private boolean[]	axisFlip
private int[]	axisOrder
private JComboBox	comboInterpType
private JComboBox	comboResType
private JComboBox	comboTemplate
static final int	CORONAL_INDEX
(package private) FileInfoBase	fileInfo
(package private) FileInfoNIFTI	fileInfoNIFTI
private ModelImage	image
private String	interpType
private String[]	interpTypes
private JLabel	labelInterpType
private JLabel	labelResType
private JLabel	labelTemplate
private JPanel	mainPanel
private int[]	newOr
private JComboBox	newOrientBox
private JComboBox	newOrientBoxX
private JComboBox	newOrientBoxY
private JComboBox	newOrientBoxZ
private String[]	newOrientTypes
private int[]	or
private String[]	orients
private String[]	orientTypes
private JComboBox	presentOrientBoxX
private JComboBox	presentOrientBoxY
private JComboBox	presentOrientBoxZ
private JLabel	presentOrientLabel2
private int	resolutionIndex
private String[]	resolutionTypes
private ModelImage	resultImage
static final int	SAGITTAL_INDEX
private ModelImage	template
static final int	USER_INDEX

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
JDialogReorient()	Empty constructor needed for dynamic instantiation.
JDialogReorient(ModelImage im)
JDialogReorient(Frame theParentFrame, ModelImage im)	Creates dialog for plugin.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent event)	Closes dialog box when the OK button is pressed and calls the algorithm.
void	algorithmPerformed(AlgorithmBase algorithm)	This method is required if the AlgorithmPerformed interface is implemented.
private void	buildTemplateList()
protected void	callAlgorithm()	Once all the necessary variables are set, call the Gaussian Blur algorithm based on what type of image this is and whether or not there is a separate destination image.
protected void	callAlgorithmRun()	For prostate and knees projects, run the re-orientation algorithm to create three orthogonal images from either axial image (prostate) or saggittal image(knees).
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()	Perform any actions required after the running of the algorithm is complete.
void	doRun()	For prostate and knees projects, run the re-orientation algorithm to create three orthogonal images from either axial image (prostate) or saggittal image(knees).
ActionMetadata	getActionMetadata()	Return meta-information about this discoverable action for categorization and labeling purposes.
JComboBox	getNewOrientBox()
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 that returns the image.
private void	init()	Sets up the GUI (panels, buttons, etc) and displays it on the screen.
boolean	isActionComplete()	Returns whether the action has successfully completed its execution.
void	itemStateChanged(ItemEvent e)	Unchanged.
void	set_axial_orientation()	For prostate and knees projects, setting the axail orientation.
void	set_coronal_orientation()	For prostate and knees projects, setting the coronal orientation.
void	set_sagittal_orientation()	For prostate and knees projects, setting the sagittal orientation.
protected void	setGUIFromParams()	Set up the dialog GUI based on the parameters before running the algorithm as part of a script.
void	setParameters()	Accessor that sets the parameters
private boolean	setVariables()	Use the GUI results to set up the variables needed to run the algorithm.
protected void	storeParamsFromGUI()	Store the parameters from the dialog to record the execution of this algorithm.

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

Field Details

algoTrans

private AlgorithmTransform algoTrans

image

private ModelImage image

template

private ModelImage template

resultImage

private ModelImage resultImage

AXIAL_INDEX

public static final int AXIAL_INDEX

See Also:

• Constant Field Values

CORONAL_INDEX

public static final int CORONAL_INDEX

See Also:

• Constant Field Values

SAGITTAL_INDEX

public static final int SAGITTAL_INDEX

See Also:

• Constant Field Values

USER_INDEX

public static final int USER_INDEX

See Also:

• Constant Field Values

orientTypes

private String[] orientTypes

newOrientTypes

private String[] newOrientTypes

resolutionTypes

private String[] resolutionTypes

resolutionIndex

private int resolutionIndex

interpTypes

private String[] interpTypes

interpType

private String interpType

orients

private String[] orients

fileInfo

FileInfoBase fileInfo

fileInfoNIFTI

FileInfoNIFTI fileInfoNIFTI

mainPanel

private JPanel mainPanel

labelResType

private JLabel labelResType

comboResType

private JComboBox comboResType

labelTemplate

private JLabel labelTemplate

comboTemplate

private JComboBox comboTemplate

labelInterpType

private JLabel labelInterpType

comboInterpType

private JComboBox comboInterpType

presentOrientLabel2

private JLabel presentOrientLabel2

presentOrientBoxX

private JComboBox presentOrientBoxX

presentOrientBoxY

private JComboBox presentOrientBoxY

presentOrientBoxZ

private JComboBox presentOrientBoxZ

or

private int[] or

newOrientBox

private JComboBox newOrientBox

newOrientBoxX

private JComboBox newOrientBoxX

newOrientBoxY

private JComboBox newOrientBoxY

newOrientBoxZ

private JComboBox newOrientBoxZ

newOr

private int[] newOr

axisOrder

private int[] axisOrder

axisFlip

private boolean[] axisFlip

Constructor Details

JDialogReorient

public JDialogReorient(Frame theParentFrame,
 ModelImage im)

Creates dialog for plugin.

Parameters:

im - Source image.

parent - Parent frame.

JDialogReorient

public JDialogReorient(ModelImage im)

JDialogReorient

public JDialogReorient()

Empty constructor needed for dynamic instantiation.

Method Details

init

private void init()

Sets up the GUI (panels, buttons, etc) and displays it on the screen.

buildTemplateList

private void buildTemplateList()

getResultImage

public ModelImage getResultImage()

Accessor that returns the image.

Returns:

The result image.

setParameters

public void setParameters()

Accessor that sets the parameters

actionPerformed

public void actionPerformed(ActionEvent event)

Closes dialog box when the OK button is pressed 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 algorithm 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 interface AlgorithmInterface

Parameters:

algorithm - Algorithm that caused the event.

setVariables

private boolean setVariables()

Use the GUI results to set up the variables needed to run the algorithm.

Returns:

true if parameters set successfully, false otherwise.

callAlgorithm

protected void callAlgorithm()

Once all the necessary variables are set, call the Gaussian Blur algorithm based on what type of image this is and whether or not there is a separate destination image.

Specified by:

callAlgorithm in class JDialogScriptableBase

doPostAlgorithmActions

protected void doPostAlgorithmActions()

Perform any actions required after the running of the algorithm is complete.

Overrides:

doPostAlgorithmActions in class JDialogScriptableBase

setGUIFromParams

protected void setGUIFromParams()

Set up the dialog GUI based on the parameters before running the algorithm as part of a script.

Specified by:

setGUIFromParams in class JDialogScriptableBase

storeParamsFromGUI

protected void storeParamsFromGUI()
                           throws ParserException

Store the parameters from the dialog to record the execution of this algorithm.

Specified by:

storeParamsFromGUI in class JDialogScriptableBase

Throws:

ParserException - If there is a problem creating one of the new parameters.

itemStateChanged

public void itemStateChanged(ItemEvent e)

Description copied from class: JDialogBase

Unchanged.

Specified by:

itemStateChanged in interface ItemListener

Overrides:

itemStateChanged in class JDialogBase

Parameters:

e - ItemEvent

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.

getNewOrientBox

public JComboBox getNewOrientBox()

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.

set_axial_orientation

public void set_axial_orientation()

For prostate and knees projects, setting the axail orientation. Auto processing pipeline, which runs from MIPAV plugin commandline or JDialog calling.

set_sagittal_orientation

public void set_sagittal_orientation()

For prostate and knees projects, setting the sagittal orientation. Auto processing pipeline, which runs from MIPAV plugin commandline or JDialog calling.

set_coronal_orientation

public void set_coronal_orientation()

For prostate and knees projects, setting the coronal orientation. Auto processing pipeline, which runs from MIPAV plugin commandline or JDialog calling.

doRun

public void doRun()

For prostate and knees projects, run the re-orientation algorithm to create three orthogonal images from either axial image (prostate) or saggittal image(knees). Auto processing pipeline, which runs from MIPAV plugin commandline or JDialog calling.

callAlgorithmRun

protected void callAlgorithmRun()

For prostate and knees projects, run the re-orientation algorithm to create three orthogonal images from either axial image (prostate) or saggittal image(knees). Auto processing pipeline, which runs from MIPAV plugin commandline or JDialog calling.