com.xinapse.dynamic
Class AbstractDynamicFrame

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      com.xinapse.util.ImageOrganiserFrame
                          com.xinapse.util.MultiContrastAnalysisFrame
                              com.xinapse.dynamic.AbstractDynamicFrame

All Implemented Interfaces:

MessageShower, PreferencesSettable, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public abstract class AbstractDynamicFrame
extends com.xinapse.util.MultiContrastAnalysisFrame

AbstractDynamicFrame - a GUI for performing general image dynamic analysis.

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JFrame.AccessibleJFrame

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

java.awt.Frame.AccessibleAWTFrame

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

static java.lang.String	APPLY_SPATIAL_FILTER_PREFERENCE_NAME The Preference name for whether to apply a spatial smoothing filter.
static int	DEFAULT_N_STEADY_STATES The default number of steady state images, if not set in user preferences.
protected javax.swing.JPanel	dynamicModelPanel The JPanel that contains the analysis setup.
protected com.xinapse.util.XinapseFormattedTextField	fwhmTextField A JFormattedTextField to set the FWHM of the smoothing filter.
protected com.xinapse.dynamic.DynamicMaskSelectorWorker.Panel	maskSelectorPanel A JPanel for selecting an image mask.
protected static int	MAX_N_TIMES The maximum number of time points that can be selected in various spinners.
static java.lang.String	N_STEADY_STATES_PREFERENCE_NAME The Preference name for the number of steady-state images.
ImageSelectionPanel	outputImageSelectionPanel ImageSelectionPanel used to select the output images basename.
protected javax.swing.JCheckBox	registerCheckBox A check box to turn on registration.
static java.lang.String	REGISTRATION_PREFERENCE_NAME The Preference name for whether to perform registration.
protected javax.swing.JCheckBox	smoothingFilterCheckBox A check box to turn on spatial filtering.
static java.lang.String	SPATIAL_FILTER_FWHM_PREFERENCE_NAME The Preference name for smoothing filter FWHM in mm.
static java.lang.String	THRESHOLD_PREFERENCE_NAME The Preference name for the intensity threshold.
static java.lang.String	TIME_BETWEEN_IMAGES_PREFERENCE_NAME The Preference name for the time between images.
protected javax.swing.JTextField	timeBetweenImagesField The JTextField to set the time between images in seconds.

Fields inherited from class com.xinapse.util.MultiContrastAnalysisFrame

imageInputPanel, roamingResponseDialog

Fields inherited from class com.xinapse.util.ImageOrganiserFrame

bottomPanel, defaultCursor, doItButton, doneButton, imageDisplayer, loadResultButton, outputPanel, quitMe, saveToDiskButton, statusText, waitCursor

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

protected	AbstractDynamicFrame(com.xinapse.displayer.ImageDisplayer parent, java.lang.String frameTitle, java.awt.Image iconImage, java.lang.String preferencesNodeName) Creates new DynamicFrame for use with Jim.
protected	AbstractDynamicFrame(java.lang.String frameTitle, java.awt.Image iconImage, java.lang.String preferencesNodeName) Creates new DynamicFrame for a stand-alone image dynamic analysis application.

Method Summary

void	busyCursors() Sets the cursor for this MessageShower to indicate that an operation is in progress.
float	getDeltaX() For the purposes of plotting data, returns the step between values of the independent variable.
MultiSliceImage	getMaskImage() Returns the mask image if masking by an image has been selected.
int	getNSteadyStates() Returns the number of pre-steady-state images set in the GUI.
java.lang.String	getOutputImagesBaseName() Returns the basename for the output images.
java.io.File	getROIMaskFile() Returns the mask ROI file if masking by a ROIs has been selected.
float	getSmoothingFWHMmm() Returns the full-width-at-half-maximum for the smoothing filter.
java.lang.Double	getThreshold() Returns the intensity threshold for pixel processing.
float	getTimeBetweenImages() Returns the time between images set in the GUI.
boolean	getUseBrainFinder() Returns whether the Brain Finder option has been set in the GUI.
java.lang.String	getXAxisLabel() For the purposes of plotting data, returns the x-axis label.
float	getXStart() For the purposes of plotting data, returns the starting value of the independent variable.
void	readyCursors() Sets the cursor for this MessageShower to indicate that it is ready for user input.
void	savePreferences(java.util.prefs.Preferences prefs) Save the current settings to the user Preferences at the given node name.
void	setDefaults() Set the default values.
void	setThreshold(java.lang.Double thr) Sets the intensity threshold for pixel processing.
void	setTimeBetweenImages(java.lang.Float timeBetweenImages) Sets the time between images in the GUI.
void	setVisible(boolean b)
void	showStatus(java.lang.String s) Shows a status message in the GUI.

Methods inherited from class com.xinapse.util.MultiContrastAnalysisFrame

addChangeListener, drawRoamingResponseGraphs, getContiguousContrasts, getDynamicModel, getInputImages, getNContrasts, getNContrasts, getNSliceLocations, getNSliceLocations, getSliceDataType, getSlicePix, isSingleInputImage, putSlicePix, removeChangeListener, setNContrasts, showRoamingResponseDialog, unloadImage, updateRoamingResponse

Methods inherited from class com.xinapse.util.ImageOrganiserFrame

addActionWorker, doIt, getDisplayer, getJFrame, getParentComponent, getScrollPane, hasActionWorkers, removeActionWorker, setActionDescription, setEnabled, setScrollableContent, showError, showError, showStatus, showSuppressibleError, showSuppressibleError, showWarning, stopActionWorkers

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

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, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, show, toBack, 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, transferFocusBackward, 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, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, 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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

TIME_BETWEEN_IMAGES_PREFERENCE_NAME

public static final java.lang.String TIME_BETWEEN_IMAGES_PREFERENCE_NAME

The Preference name for the time between images.

See Also:

Constant Field Values

THRESHOLD_PREFERENCE_NAME

public static final java.lang.String THRESHOLD_PREFERENCE_NAME

The Preference name for the intensity threshold.

See Also:

Constant Field Values

REGISTRATION_PREFERENCE_NAME

public static final java.lang.String REGISTRATION_PREFERENCE_NAME

The Preference name for whether to perform registration.

See Also:

Constant Field Values

APPLY_SPATIAL_FILTER_PREFERENCE_NAME

public static final java.lang.String APPLY_SPATIAL_FILTER_PREFERENCE_NAME

The Preference name for whether to apply a spatial smoothing filter.

See Also:

Constant Field Values

SPATIAL_FILTER_FWHM_PREFERENCE_NAME

public static final java.lang.String SPATIAL_FILTER_FWHM_PREFERENCE_NAME

The Preference name for smoothing filter FWHM in mm.

See Also:

Constant Field Values

N_STEADY_STATES_PREFERENCE_NAME

public static final java.lang.String N_STEADY_STATES_PREFERENCE_NAME

The Preference name for the number of steady-state images.

See Also:

Constant Field Values

DEFAULT_N_STEADY_STATES

public static final int DEFAULT_N_STEADY_STATES

The default number of steady state images, if not set in user preferences.

See Also:

Constant Field Values

MAX_N_TIMES

protected static final int MAX_N_TIMES

The maximum number of time points that can be selected in various spinners.

See Also:

Constant Field Values

timeBetweenImagesField

protected javax.swing.JTextField timeBetweenImagesField

The JTextField to set the time between images in seconds.

registerCheckBox

protected final javax.swing.JCheckBox registerCheckBox

A check box to turn on registration.

smoothingFilterCheckBox

protected final javax.swing.JCheckBox smoothingFilterCheckBox

A check box to turn on spatial filtering.

fwhmTextField

protected final com.xinapse.util.XinapseFormattedTextField fwhmTextField

A JFormattedTextField to set the FWHM of the smoothing filter.

maskSelectorPanel

protected final com.xinapse.dynamic.DynamicMaskSelectorWorker.Panel maskSelectorPanel

A JPanel for selecting an image mask.

dynamicModelPanel

protected final javax.swing.JPanel dynamicModelPanel

The JPanel that contains the analysis setup. Components for the analysis model should be added to this JPanel.

outputImageSelectionPanel

public ImageSelectionPanel outputImageSelectionPanel

ImageSelectionPanel used to select the output images basename.

Constructor Detail

AbstractDynamicFrame

protected AbstractDynamicFrame(java.lang.String frameTitle,
                               java.awt.Image iconImage,
                               java.lang.String preferencesNodeName)

Creates new DynamicFrame for a stand-alone image dynamic analysis application.

AbstractDynamicFrame

protected AbstractDynamicFrame(com.xinapse.displayer.ImageDisplayer parent,
                               java.lang.String frameTitle,
                               java.awt.Image iconImage,
                               java.lang.String preferencesNodeName)

Creates new DynamicFrame for use with Jim.

Method Detail

showStatus

public void showStatus(java.lang.String s)

Shows a status message in the GUI.

Specified by:

showStatus in interface MessageShower

Specified by:

showStatus in class com.xinapse.util.ImageOrganiserFrame

Parameters:

s - the status message to show.

getUseBrainFinder

public boolean getUseBrainFinder()

Returns whether the Brain Finder option has been set in the GUI.

Returns:

true of the Brain Finder option has been set; false otherwise.

getMaskImage

public MultiSliceImage getMaskImage()
                             throws com.xinapse.util.InvalidArgumentException

Returns the mask image if masking by an image has been selected.

Returns:

the mask image if masking by an image has been selected, or null if masking by an image has not been selected.

Throws:

com.xinapse.util.InvalidArgumentException - if masking by an image has been selected, but the mask image has not been set or cannot be opened.

getROIMaskFile

public java.io.File getROIMaskFile()
                            throws com.xinapse.util.InvalidArgumentException

Returns the mask ROI file if masking by a ROIs has been selected.

Returns:

the ROI File if masking by a ROIs has been selected, or null if masking by a ROIs has not been selected.

Throws:

com.xinapse.util.InvalidArgumentException - if masking by ROIs has been selected, but the mask ROIs File has not been set or cannot be opened.

getThreshold

public java.lang.Double getThreshold()
                              throws com.xinapse.util.InvalidArgumentException

Returns the intensity threshold for pixel processing.

Returns:

the intensity threshold or null if no threshold has been set.

Throws:

com.xinapse.util.InvalidArgumentException - if the threshold value cannot be interpreset from what has been set in the GUI.

setThreshold

public void setThreshold(java.lang.Double thr)

Sets the intensity threshold for pixel processing.

Parameters:

thr - the intensity threshold or null if no threshold is to be set.

getXStart

public float getXStart()

For the purposes of plotting data, returns the starting value of the independent variable.

Specified by:

getXStart in class com.xinapse.util.MultiContrastAnalysisFrame

Returns:

1 which is the scan number of the first image.

getDeltaX

public float getDeltaX()
                throws com.xinapse.util.InvalidArgumentException

For the purposes of plotting data, returns the step between values of the independent variable.

Specified by:

getDeltaX in class com.xinapse.util.MultiContrastAnalysisFrame

Returns:

1 which is the step between scans.

Throws:

com.xinapse.util.InvalidArgumentException - never.

getXAxisLabel

public java.lang.String getXAxisLabel()

For the purposes of plotting data, returns the x-axis label.

Specified by:

getXAxisLabel in class com.xinapse.util.MultiContrastAnalysisFrame

Returns:

"scan number".

getTimeBetweenImages

public float getTimeBetweenImages()
                           throws com.xinapse.util.InvalidArgumentException

Returns the time between images set in the GUI.

Returns:

the time (in seconds) between images.

Throws:

com.xinapse.util.InvalidArgumentException - if the time between images has not been set by the user, or if the time between images cannot be interpreted, or is not positive.

setTimeBetweenImages

public void setTimeBetweenImages(java.lang.Float timeBetweenImages)

Sets the time between images in the GUI.

Parameters:

timeBetweenImages - the time between images. If null, this method has not effect.

getSmoothingFWHMmm

public float getSmoothingFWHMmm()
                         throws com.xinapse.util.InvalidArgumentException

Returns the full-width-at-half-maximum for the smoothing filter.

Returns:

the full-width-at-half-maximum for the smoothing filter.

Throws:

com.xinapse.util.InvalidArgumentException - if the FWHM has not been set by the user, or the FWHM cannot be interpreted, or is not positive.

getOutputImagesBaseName

public java.lang.String getOutputImagesBaseName()
                                         throws com.xinapse.util.InvalidArgumentException

Returns the basename for the output images.

Returns:

the basename for the output images.

Throws:

com.xinapse.util.InvalidArgumentException - if the basename has not been set by the user.

getNSteadyStates

public int getNSteadyStates()

Returns the number of pre-steady-state images set in the GUI.

Returns:

the number of pre-steady-state images set in the GUI.

setDefaults

public void setDefaults()

Description copied from interface: PreferencesSettable

Set the default values.

Specified by:

setDefaults in interface PreferencesSettable

Overrides:

setDefaults in class com.xinapse.util.MultiContrastAnalysisFrame

savePreferences

public void savePreferences(java.util.prefs.Preferences prefs)
                     throws com.xinapse.util.InvalidArgumentException

Description copied from interface: PreferencesSettable

Save the current settings to the user Preferences at the given node name.

Specified by:

savePreferences in interface PreferencesSettable

Overrides:

savePreferences in class com.xinapse.util.MultiContrastAnalysisFrame

Parameters:

prefs - the java.util.prefs.Preferences to which the current settings will be saved.

Throws:

InvalidArgumentException - if the current settings are invalid and cannot be saved to the preferences.

busyCursors

public void busyCursors()

Description copied from interface: MessageShower

Sets the cursor for this MessageShower to indicate that an operation is in progress.

Specified by:

busyCursors in interface MessageShower

Overrides:

busyCursors in class com.xinapse.util.MultiContrastAnalysisFrame

readyCursors

public void readyCursors()

Description copied from interface: MessageShower

Sets the cursor for this MessageShower to indicate that it is ready for user input.

Specified by:

readyCursors in interface MessageShower

Overrides:

readyCursors in class com.xinapse.util.MultiContrastAnalysisFrame

setVisible

public void setVisible(boolean b)

Overrides:

setVisible in class com.xinapse.util.MultiContrastAnalysisFrame