theba.core.gui.ThebaGUI Class Reference

List of all members.

Classes
class	HistogramAction
class	MouseClickListener
class	RegCountAction
class	RegionAnalysisAction
Public Member Functions
void	actionPerformed (final ActionEvent e)
void	fiberChordMeasurements ()
void	addChannel (SliceReader reader, String name)
void	addMenuItem (String title, final Runnable action)
void	addMenuSeparator ()
void	addToolbarButton (JComponent customButton)
void	clearChannels ()
synchronized int	currentSlice ()
void	flipVolume ()
short[]	getCurrentPixels ()
ImagePane	getCurrentView ()
ThebaPrefs	getPreferences ()
short[]	getSlice (int z)
Tracker	getCurrentTracker ()
Stack	getStack ()
JFrame	getWindow ()
JCheckBoxMenuItem	hideWhite ()
boolean	isMinimized ()
void	putSlice (short[] data, int z)
void	setPointerLabel (Point p)
void	setProgress (final int val)
void	setProgressComplete ()
void	showImage (final short[] data)
void	showResults (String s)
void	showResults (final StringBuffer results, String title)
void	updateImage ()
void	updateSlice (final int z)
boolean	isStopped ()
void	setIsStopped (boolean isStopped)
void	setProgressbar (int i, int max)
void	releaseFiberId (short val)
short	getNewFiberId ()
void	setLabel (String string)
void	setLoader (PluginLoader loader)
PluginLoader	getPluginLoader ()
Static Public Member Functions
static ThebaGUI	getInstance ()
static void	main (String[] args)
Public Attributes
ArrayList	lumencenters
final int	MAX_FIBERS = 2048
int	width
int	height
int	depth
final short	INVALID = 7
final int	BYTE_TYPE = 0
final int	SHORT_TYPE = 1
Static Package Attributes
static int	count = 0
static short[]	empty
static ThebaGUI	instance = null
static short[]	tmp

Detailed Description

This is the class is responsible for most UI interaction such as menu layout, and listeners.

Author:: jensbw; perchrh

Definition at line 79 of file ThebaGUI.java.

Member Function Documentation

void theba.core.gui.ThebaGUI.actionPerformed ( final ActionEvent e )

This method contains actions for some of the menu elements

Definition at line 220 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.depth, theba.core.gui.ThebaGUI.flipVolume(), theba.core.Plugin.getName(), theba.core.RegionDescriptor.getName(), theba.core.gui.ThebaGUI.getPluginLoader(), theba.core.PluginLoader.getPlugins(), theba.core.PluginLoader.getRegionDescriptors(), theba.core.gui.ThebaGUI.getSlice(), theba.core.PluginLoader.getTrackers(), theba.core.gui.ThebaGUI.setProgress(), theba.core.Tracker.stop(), theba.core.gui.ThebaGUI.tmp, and theba.core.gui.ThebaGUI.updateImage().

Referenced by theba.core.gui.ThebaGUI.addMenuItem(), and theba.core.gui.ThebaGUI.showResults().

void theba.core.gui.ThebaGUI.addChannel	(	SliceReader	reader,
		String	name
	)

Adds a channel to the tabbedview window if it is not already added (based on equal name)

Parameters:

	reader	The input slicereader (or writer)
	name	The tab-name

Definition at line 428 of file ThebaGUI.java.

Referenced by theba.trackers.BackTracker.traceWalls().

void theba.core.gui.ThebaGUI.addMenuItem	(	String	title,
		final Runnable	action
	)

Used by trackers to add menu-items to the track-menu

Parameters:

	title	Title for menu-item
	action	A runnable method containing executable code for this menu-Item

Definition at line 450 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.actionPerformed().

Referenced by theba.trackers.HHTracker.setup(), theba.trackers.FloodTracker3D.setup(), theba.trackers.FiberTracker.setup(), and theba.trackers.BackTracker.setup().

void theba.core.gui.ThebaGUI.addMenuSeparator ( )

Definition at line 468 of file ThebaGUI.java.

Referenced by theba.trackers.HHTracker.setup(), theba.trackers.FiberTracker.setup(), and theba.trackers.BackTracker.setup().

void theba.core.gui.ThebaGUI.addToolbarButton ( JComponent customButton )

Menu used by Trackers to add a button to the toolbar.

Parameters:

customButton

Definition at line 477 of file ThebaGUI.java.

Referenced by theba.trackers.HHTracker.setup(), theba.trackers.FiberTracker.setup(), and theba.trackers.BackTracker.setup().

void theba.core.gui.ThebaGUI.clearChannels ( )

Resets tabbed-pane view

Definition at line 490 of file ThebaGUI.java.

Referenced by theba.trackers.BackTracker.traceWalls().

synchronized int theba.core.gui.ThebaGUI.currentSlice ( )

Returns the depth index of currently selected (by the depthslicer) slice

Returns:: the depth/z-index of the current slice

Definition at line 1040 of file ThebaGUI.java.

Referenced by theba.core.gui.ThebaGUI.getCurrentPixels(), theba.trackers.BackTracker.selectSeed(), theba.core.gui.ThebaGUI.setPointerLabel(), and theba.core.gui.ThebaGUI.updateImage().

void theba.core.gui.ThebaGUI.fiberChordMeasurements ( )

This method generates fiber-chord measurements for the given volume. This involves calculation of the mean distance between porous regions in x,y and z-directions

Definition at line 305 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.count, theba.core.Stack.getDepth(), theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getVoxel(), theba.core.Stack.getWidth(), theba.core.gui.ThebaGUI.isStopped(), theba.core.gui.ThebaGUI.setProgressbar(), and theba.core.gui.ThebaGUI.showResults().

void theba.core.gui.ThebaGUI.flipVolume ( )

Flips the volume 90 degrees by swapping width with depth. Note that the height-dimension is preserved.

Definition at line 1088 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.depth, theba.core.io.VolumeReader.destroy(), theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.height, theba.core.gui.ThebaGUI.isStopped(), theba.core.Tracker.reset(), theba.core.gui.ThebaGUI.setProgress(), theba.core.gui.ThebaGUI.SHORT_TYPE, theba.core.gui.ThebaGUI.tmp, and theba.core.gui.ThebaGUI.width.

Referenced by theba.core.gui.ThebaGUI.actionPerformed(), theba.trackers.FiberTracker.autoSegment(), and theba.trackers.BackTracker.autoSegment().

short [] theba.core.gui.ThebaGUI.getCurrentPixels ( )

Returns the currently selected depth-slice

Returns:: The currently selected image-slice

Definition at line 1134 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.currentSlice(), and theba.core.gui.ThebaGUI.getSlice().

Referenced by theba.trackers.BackTracker.selectSeed(), and theba.core.gui.ThebaGUI.setPointerLabel().

Tracker theba.core.gui.ThebaGUI.getCurrentTracker ( )

Returns:: The currently selected tracker (indicated by the file-open dialog)

Definition at line 1186 of file ThebaGUI.java.

Referenced by theba.core.gui.ImagePane.setData().

ImagePane theba.core.gui.ThebaGUI.getCurrentView ( )

Returns the ImagePane that is currently selected (usually the main view)

Returns:: The selected ImagePane

Definition at line 1143 of file ThebaGUI.java.

Referenced by theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.getStack(), and theba.core.gui.ThebaGUI.updateImage().

static ThebaGUI theba.core.gui.ThebaGUI.getInstance ( ) [static]

Singleton for this class

Returns:: The only instance of ThebaGUI

Definition at line 1616 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.instance.

Referenced by theba.trackers.HHTracker.dilate3d_toWhite(), theba.trackers.FiberTracker.dilate3d_toWhite(), and theba.trackers.BackTracker.dilate3d_toWhite().

short theba.core.gui.ThebaGUI.getNewFiberId ( )

Returns a free fiberlabel from The list is allways updated when the volume is reloaded.

Returns:: A new short that has not yet been used in the data-stack

Definition at line 1958 of file ThebaGUI.java.

Referenced by theba.trackers.HHTracker.track(), theba.trackers.FiberTracker.track(), and theba.trackers.BackTracker.track().

PluginLoader theba.core.gui.ThebaGUI.getPluginLoader ( )

Definition at line 1983 of file ThebaGUI.java.

Referenced by theba.core.gui.ThebaGUI.actionPerformed(), and theba.core.gui.OpenDialog.OpenDialog().

ThebaPrefs theba.core.gui.ThebaGUI.getPreferences ( )

Returns an object containing the current preferences for this application (not that several instances running at once, may use shared properties)

Returns:: The ThebaPrefs object containing preferences relating to FibForks

Definition at line 1159 of file ThebaGUI.java.

Referenced by theba.trackers.BackTracker.removeCrack(), theba.trackers.HHTracker.track(), theba.trackers.FiberTracker.track(), theba.trackers.BackTracker.track(), and theba.core.gui.OpenDialog.validateFields().

short [] theba.core.gui.ThebaGUI.getSlice ( int z )

Returns the short[]-array associated with the current stack-slice width and height dimensions corresponds to the current getStack()-object

Parameters:

The

depth-index in the stack

Returns:: A short[]-array representing the current stack at posistion z

Definition at line 1175 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.getCurrentView(), theba.core.io.VolumeReader.getSlice(), and theba.core.gui.ImagePane.getSliceReader().

Referenced by theba.core.gui.ThebaGUI.actionPerformed(), theba.trackers.BackTracker.findCandidates(), theba.core.gui.ThebaGUI.flipVolume(), theba.core.gui.ThebaGUI.getCurrentPixels(), theba.trackers.BackTracker.removeCrack(), theba.trackers.BackTracker.removeStuff(), theba.core.gui.ThebaGUI.setPointerLabel(), theba.trackers.BackTracker.traceWalls(), theba.trackers.HHTracker.track(), theba.trackers.FiberTracker.track(), and theba.trackers.BackTracker.track().

Stack theba.core.gui.ThebaGUI.getStack ( )

Returns:: The currently active stack-object

Definition at line 1194 of file ThebaGUI.java.

References theba.core.gui.ThebaGUI.getCurrentView(), and theba.core.gui.ImagePane.getVolume().

JFrame theba.core.gui.ThebaGUI.getWindow ( )

Returns the application window

Returns:: The active application window (with associated position, size etc)

Definition at line 1204 of file ThebaGUI.java.

Referenced by theba.core.gui.OpenDialog.OpenDialog(), and theba.core.PluginLoader.PluginLoader().

JCheckBoxMenuItem theba.core.gui.ThebaGUI.hideWhite ( )

Returns:: the hideWhite checkbox-item, that indicates if white voxels should be filtered from view

Definition at line 1212 of file ThebaGUI.java.

boolean theba.core.gui.ThebaGUI.isMinimized ( )

Returns true if the application window is hidden from view

Returns:: true if application should be hidden from view

Definition at line 1221 of file ThebaGUI.java.

Referenced by theba.core.gui.ImagePane.setData(), and theba.core.gui.ThebaGUI.updateSlice().

boolean theba.core.gui.ThebaGUI.isStopped ( )

Returns:: True if any time-consuming tasks should be stopped (this function can be added to any time-consuming tasks such as plugins etc) When the stop-button is selected they should silently be stopped, freeing up the gui for other purposes. Note that there is no guarantee that any of these tasks will leave the system in a stable state...

Definition at line 1853 of file ThebaGUI.java.

Referenced by theba.core.gui.ThebaGUI.fiberChordMeasurements(), and theba.core.gui.ThebaGUI.flipVolume().

static void theba.core.gui.ThebaGUI.main ( String[] args ) [static]

Main method to launch Theba

Parameters:

args

Command-line arguments

Definition at line 1629 of file ThebaGUI.java.

void theba.core.gui.ThebaGUI.putSlice	(	short[]	data,
		int	z
	)

Replaces a particular slice in the stack with new data

Parameters:

	data	A short[]-array with the same width-height dimensionas as the current stack
	z	A depth-index to copy this slice's contents to

Definition at line 1412 of file ThebaGUI.java.

References theba.core.io.VolumeReader.putSlice().

void theba.core.gui.ThebaGUI.releaseFiberId ( short val )

Release up a label This method should be called whenever a region is entirely removed from the stack, such that the label is made available for other purposes

Parameters:

val

The label that is now free to use for otehr purposes

Definition at line 1891 of file ThebaGUI.java.

Referenced by theba.trackers.HHTracker.track(), and theba.trackers.FiberTracker.track().

void theba.core.gui.ThebaGUI.setIsStopped ( boolean isStopped )

Sets the current status of the stop-value

Parameters:

isStopped

Definition at line 1862 of file ThebaGUI.java.

void theba.core.gui.ThebaGUI.setLabel ( String string )

Sets the label-text for the system-toolbar