Package gov.nih.mipav.view.dialogs

Class JDialogCorrectSpacing

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.JDialogCorrectSpacing

All Implemented Interfaces:

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

public class JDialogCorrectSpacing
extends JDialogScriptableBase
implements AlgorithmInterface

Algorithm to adjust image volume for cases when the slice spacing is not equal to the slice thickness. When spacing > thickness: repeat images from original image set insert blank images (so that in the final image volume, all images will have the same slice thickness and the image volume will be to proper scale. When spacing < thickness: set thickness = spacing. Only works for DICOM or XML files, since they include the sliceSpacing field.

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 AlgorithmCorrectSpacing	correctSpaceAlgo	DOCUMENT ME!
private int[]	extents	DOCUMENT ME!
private FileInfoBase	fileInfoBuffer	DOCUMENT ME!
private float	gap	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private int	newNumIm	DOCUMENT ME!
private float	newThick	DOCUMENT ME!
private float	newZStart	DOCUMENT ME!
private int	numBlank	DOCUMENT ME!
private int	numIm	DOCUMENT ME!
private int	numRepIm	DOCUMENT ME!
private ModelImage	resultImage	DOCUMENT ME!
private static final long	serialVersionUID	Use serialVersionUID for interoperability.
private float	space	DOCUMENT ME!
private float	thick	DOCUMENT ME!
private String[]	titles	DOCUMENT ME!
private float	zStart	DOCUMENT ME!

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
JDialogCorrectSpacing()	Empty constructor needed for dynamic instantiation (used during scripting).
JDialogCorrectSpacing(JFrame parent, ModelImage image)	Constructor that creates new dialog for Correct Spacing.

Method Summary

Modifier and Type	Method	Description
void	algorithmPerformed(AlgorithmBase algorithm)	This method is required if the AlgorithmInterface is implemented.
void	callAlgorithm()	Call algorithm to copy appropriate images from original, and double where necessary.
private void	correctSpaceLTthick(ModelImage im, float newThickVal)	This method corrects spacing for cases where the space is less than the thickness.
protected void	doPostAlgorithmActions()	Store the result image in the script runner's image table now that the action execution is finished.
private void	generateNewImages()	Generates new images.
private void	getNewInfo()	Calculates the new slice thickness (newThick), number of times to repeat each original image (numRepIm), the number of blanks to insert between the image duplicates (numBlank), and the new z coordinate origin for the image volume (newZStart).
ModelImage	getResultImage()	Accessor that returns the image.
protected void	setGUIFromParams()	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
protected void	storeParamsFromGUI()	Record the parameters just used to run this algorithm in a script.

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

actionPerformed, buildApplyButton, buildButtons, buildCancelButton, buildCancelButton, buildCloseButton, buildHelpButton, buildImageComboBox, buildOKButton, buildOKButton, buildOKCancelButtons, buildTitledBorder, buildTitledBorder, createLabel, createProgressBar, createProgressBar, createTextField, focusGained, focusLost, getDialogName, isCancelled, isQuietRunning, isRunInSeparateThread, isScriptRunning, itemStateChanged, loadDefaults, loadDefaults, makeImageName, makeString, openNewFrame, saveDefaults, saveDefaults, setLeftHandSystem, setQuietRunning, setScriptRunning, setSeparateThread, setVisible, setVisible, setVisibleMenuBar, setVisibleStandard, setVOIManager, setWCSystem, testParameter, testParameterMin, updateFFTFileInfo, updateFileInfo, updateFileInfoOtherModality, updateFileInfoStatic, updateFileInfoStatic, updateFileTypeInfo, updateFileTypeInfo, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

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

Field Details

serialVersionUID

private static final long serialVersionUID

Use serialVersionUID for interoperability.

See Also:

• Constant Field Values

correctSpaceAlgo

private AlgorithmCorrectSpacing correctSpaceAlgo

DOCUMENT ME!

extents

private int[] extents

DOCUMENT ME!

fileInfoBuffer

private FileInfoBase fileInfoBuffer

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

numIm

private int numIm

DOCUMENT ME!

numRepIm

private int numRepIm

DOCUMENT ME!

numBlank

private int numBlank

DOCUMENT ME!

newNumIm

private int newNumIm

DOCUMENT ME!

resultImage

private ModelImage resultImage

DOCUMENT ME!

thick

private float thick

DOCUMENT ME!

space

private float space

DOCUMENT ME!

gap

private float gap

DOCUMENT ME!

newThick

private float newThick

DOCUMENT ME!

zStart

private float zStart

DOCUMENT ME!

newZStart

private float newZStart

DOCUMENT ME!

titles

private String[] titles

DOCUMENT ME!

Constructor Details

JDialogCorrectSpacing

public JDialogCorrectSpacing()

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

JDialogCorrectSpacing

public JDialogCorrectSpacing(JFrame parent,
 ModelImage image)

Constructor that creates new dialog for Correct Spacing. No dialog will be displayed.

Parameters:

parent - Parent frame of this dialog.

image - Active image in parent frame.

Method Details

algorithmPerformed

public void algorithmPerformed(AlgorithmBase algorithm)

This method is required if the AlgorithmInterface is implemented.

Specified by:

algorithmPerformed in interface AlgorithmInterface

Parameters:

algorithm - Algorithm that caused the event.

callAlgorithm

public void callAlgorithm()

Call algorithm to copy appropriate images from original, and double where necessary.

Specified by:

callAlgorithm in class JDialogScriptableBase

getResultImage

public ModelImage getResultImage()

Accessor that returns the image.

Returns:

The result image

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.

correctSpaceLTthick

private void correctSpaceLTthick(ModelImage im,
 float newThickVal)

This method corrects spacing for cases where the space is less than the thickness.

Parameters:

im - DOCUMENT ME!

newThickVal - DOCUMENT ME!

generateNewImages

private void generateNewImages()

Generates new images. Calculates the new total number of images (newNumIm) and then generates new images with that dimension. Calls callAgorithm, passing it the resultImage.

getNewInfo

private void getNewInfo()

Calculates the new slice thickness (newThick), number of times to repeat each original image (numRepIm), the number of blanks to insert between the image duplicates (numBlank), and the new z coordinate origin for the image volume (newZStart).