mtb_cellcounter

Class CellCntrRegionFilterFrame

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Frame

javax.swing.JFrame

mtb_cellcounter.CellCntrRegionFilterFrame

All Implemented Interfaces:

ij.measure.Measurements, ActionListener, ImageObserver, MenuContainer, Serializable, Runnable, EventListener, Accessible, RootPaneContainer, WindowConstants

public class CellCntrRegionFilterFrame
extends JFrame
implements ij.measure.Measurements, Runnable, ActionListener

Adjusts the lower and upper thresholds for size and intensity of regions.

Author:

ImageJ 1.0 Team (see notice on top), Birgit Moeller

See Also:

Serialized Form

Nested Class Summary

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

JFrame.AccessibleJFrame

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

Frame.AccessibleAWTFrame

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 and Description
private CellCounter	cc Reference to the corresponding plugin object.
private static String	CLOSE Label and command of close button.
private JButton	closeButton Window close button.
private CellCntrMarkerVector	currentMarkers Current markers.
private int	currentStackZ Z index of current slice in stack.
private static String	DARK_BACKGROUND
private int[]	histogramRegionIntensities Histogram of region average intensities with 256 bins.
private int[]	histogramRegionSizes Histogram of region sizes with 256 bins.
private ij.ImageJ	ij Reference to running ImageJ instance.
private static String	LOC_KEY
private int	maxRegIntensity Intensity of brightest region in current segmentation.
private int	maxRegSize Size of biggest region in current segmentation.
private int	minRegIntensity Intensity of darkest region in current segmentation.
private int	minRegSize Size of smallest region in current segmentation.
private static String	MODE_KEY
private JPanel	panel Main panel of the frame.
private CellCntrRegionFilterAdjustPanel	panelFilterIntensity Panel to filter regions according to average intensity.
private CellCntrRegionFilterAdjustPanel	panelFilterSize Panel to filter regions according to size.
private Thread	thread The main thread of this application.

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 ij.measure.Measurements

ADD_TO_OVERLAY, ALL_STATS, AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, NaN_EMPTY_CELLS, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV

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

Constructors

Constructor and Description
CellCntrRegionFilterFrame(CellCounter counter, CellCntrMarkerVector markers, MTBImage image, int stackZ) Default constructor.

Method Summary

Modifier and Type	Method and Description
void	actionPerformed(ActionEvent e)
static void	filterMarkerRegions(CellCntrMarkerVector markers, int z, int minSize, int maxSize, int minIntensity, int maxIntensity) Function to filter given set of markers with region shape.
int	getCurrentMarkerType() Request type ID of currently given set of marker vectors.
int	getMaxIntensityValue() Returns the upper threshold for the region intensity.
int	getMaxSizeValue() Returns the upper threshold for the region size.
int	getMinIntensityValue() Returns the lower threshold for the region intensity.
int	getMinSizeValue() Returns the lower threshold for the region size.
void	run()
private void	setMarkers(CellCntrMarkerVector data, MTBImage image, int stackZ) Set new markers.
void	updateMarkerData(CellCntrMarkerVector data, MTBImage image, int stackZ, boolean ignoreHistory) Update marker data.
void	updateRegionFiltering() Updates the region filter.

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, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

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, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, 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, 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, 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, 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, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, 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 java.awt.MenuContainer

getFont, postEvent

Field Detail

ij

private ij.ImageJ ij

Reference to running ImageJ instance.

LOC_KEY

private static final String LOC_KEY

See Also:

Constant Field Values

MODE_KEY

private static final String MODE_KEY

See Also:

Constant Field Values

DARK_BACKGROUND

private static final String DARK_BACKGROUND

See Also:

Constant Field Values

thread

private Thread thread

The main thread of this application.

panel

private JPanel panel

Main panel of the frame.

CLOSE

private static final String CLOSE

Label and command of close button.

See Also:

Constant Field Values

cc

private CellCounter cc

Reference to the corresponding plugin object.

panelFilterSize

private CellCntrRegionFilterAdjustPanel panelFilterSize

Panel to filter regions according to size.

panelFilterIntensity

private CellCntrRegionFilterAdjustPanel panelFilterIntensity

Panel to filter regions according to average intensity.

closeButton

private JButton closeButton

Window close button.

currentMarkers

private CellCntrMarkerVector currentMarkers

Current markers.

currentStackZ

private int currentStackZ

Z index of current slice in stack.

maxRegSize

private int maxRegSize

Size of biggest region in current segmentation.

minRegSize

private int minRegSize

Size of smallest region in current segmentation.

maxRegIntensity

private int maxRegIntensity

Intensity of brightest region in current segmentation.

minRegIntensity

private int minRegIntensity

Intensity of darkest region in current segmentation.

histogramRegionSizes

private int[] histogramRegionSizes

Histogram of region sizes with 256 bins.

histogramRegionIntensities

private int[] histogramRegionIntensities

Histogram of region average intensities with 256 bins.

Constructor Detail

CellCntrRegionFilterFrame

public CellCntrRegionFilterFrame(CellCounter counter,
                                 CellCntrMarkerVector markers,
                                 MTBImage image,
                                 int stackZ)

Default constructor.

Parameters:

counter - Reference to associated cell counter.

markers - Markers to filter.

image - Image from which segmentation data originates.

stackZ - Coordinate of image in complete z-stack.

Method Detail

setMarkers

private void setMarkers(CellCntrMarkerVector data,
                        MTBImage image,
                        int stackZ)

Set new markers.

This methods initializes all internal member variables related to marker data, e.g., minimal and maximal values of size and intensity ranges, and data histograms.

Parameters:

data - New data.

image - Image from where segmentation data originates.

stackZ - Coordinate of image in complete z-stack.

updateMarkerData

public void updateMarkerData(CellCntrMarkerVector data,
                             MTBImage image,
                             int stackZ,
                             boolean ignoreHistory)

Update marker data.

Parameters:

data - New marker data.

image - New image.

stackZ - Coordinate of image in complete z-stack.

ignoreHistory - If true, markers are treated as first seen.

getCurrentMarkerType

public int getCurrentMarkerType()

Request type ID of currently given set of marker vectors.

Returns:

Type ID of current markers.

getMinSizeValue

public int getMinSizeValue()

Returns the lower threshold for the region size.

Returns:

Minimal region size.

getMaxSizeValue

public int getMaxSizeValue()

Returns the upper threshold for the region size.

Returns:

Maximal region size.

getMinIntensityValue

public int getMinIntensityValue()

Returns the lower threshold for the region intensity.

Returns:

Minimal region intensity.

getMaxIntensityValue

public int getMaxIntensityValue()

Returns the upper threshold for the region intensity.

Returns:

Maximal region intensity.

actionPerformed

public void actionPerformed(ActionEvent e)

Specified by:

actionPerformed in interface ActionListener

run

public void run()

Specified by:

run in interface Runnable

updateRegionFiltering

public void updateRegionFiltering()

Updates the region filter.

This function is called in case of changes in threshold settings.

filterMarkerRegions

public static void filterMarkerRegions(CellCntrMarkerVector markers,
                                       int z,
                                       int minSize,
                                       int maxSize,
                                       int minIntensity,
                                       int maxIntensity)

Function to filter given set of markers with region shape.

Markers not coinciding with the given criteria are set inactive after filtering. Note that markers not located in given z-slice are skipped.

Parameters:

markers - Set of markers to filter.

z - Z-coordinate of image/slice in stack.

minSize - Minimal size of valid markers.

maxSize - Maximal size of valid markers.

minIntensity - Minimal intensity of valid markers.

maxIntensity - Maximal intensity of valid markers.