Seg2Dgel
Class Sg2showImage

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      Seg2Dgel.Sg2showImage

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class Sg2showImage
extends javax.swing.JFrame
implements java.awt.event.ItemListener, java.awt.event.ActionListener, java.awt.event.WindowListener

Class Sg2showImage implements a popup GUI to show images used in the 2D Gel Spot Segmenter.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.

Version:

$Date: 2005/10/23 12:44:54 $ $Revision: 1.33 $

Author:

P. Lemkin, NCI-Frederick, Frederick, MD, 21702

See Also:

Open2Dprot Home, 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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

java.awt.Checkbox	allSpotsCB the "All spots" Checkbox
boolean	allSpotsFlag set from "All spots" checkbox
java.lang.String	baseImageFile base name of the image for use in the title
boolean	changeGuiFlag flag to indicating that the GUI may have changed and that it should be rebuilt.
javax.swing.JPanel	controlPanel Control panel for the main frame
java.lang.String	dataUnits Data type as fct of histogram data type
java.lang.String	dispName Name of image to display after a segmentation
char[]	dispPixC Picture buffer char[] of image to display after a segmentation.
java.awt.Choice	dispPixChoice Selector for image to display after a segmentation
java.lang.String	dispPixFile File of image to display after a segmentation.
char[]	dispPixWorking Picture buffer char[] of image to display after a segmentation.
(package private) static int	DIST_THR Distance threshold in pixels from mouse (x,y) to spot centroid to find spot \
boolean	drawHorizSliceFlag menu CB item to display horizontal slice
boolean	drawVertSliceFlag menu CB item to display vertical slice
static boolean	ENABLE_ZOOM Enable zoom of images
java.awt.Menu	fileMenu "File" pull down Menu list
boolean	filterGEQactiveBinFlag menu CB item to test spots for GEQ activeBin value, else LEQ activeBin value fromt the selected histogram bin for the histogram histType spot data.
java.lang.String	fontFamily
boolean	hasHistGUIflag flag to indicate that the GUI contains the Histogram sub-GUI
Sg2drawHistogram	hCanvas Histogram Canvas to hold the image
int[]	hist full input unscaled histogram data [0:nHist-1]
static int	HIST_HEIGHT Height of the histogram
static int	HIST_IMAGE_DENSITY types of histogram data allowed
static int	HIST_NONE types of histogram data allowed
static int	HIST_SPOT_AREA types of histogram data allowed
static int	HIST_SPOT_MAX_DENSITY types of histogram data allowed
static int	HIST_SPOT_MIN_DENSITY types of histogram data allowed
static int	HIST_SPOT_MNBKGRD types of histogram data allowed
static int	HIST_SPOT_MNDENSITY types of histogram data allowed
static int	HIST_SPOT_SX_SY_RATIO_RANGE types of histogram data allowed
static int	HIST_SPOT_TOT_DENSITY types of histogram data allowed
static int	HIST_SPOT_TOT_DENSITY_PRIME types of histogram data allowed
static int	HIST_SPOT_TOT_DENSITY_RANGE types of histogram data allowed
static int	HIST_SPOT_VOLUME types of histogram data allowed
static int	HIST_WIDTH Width of the histogram
java.awt.Choice	histChoice "Histogram" Choice list
java.awt.Menu	histMenu "Histogram" pull down Menu list
static java.lang.String[]	histNames list of histogram data types
int	histType type of data to use with the histogram
static int	IS_HEIGHT Height of the img scroller
static int	IS_WIDTH Width of the img scroller
boolean	isVisibleFlag Set true if window is visible
java.awt.Font	largeFont
java.awt.Checkbox	logReportCB the "Log report" checkbox
boolean	logReportFlag set from "Log report" checkbox
float	maxDataValue Maximum value expected for current hist[] data
int	maxGrayPixel Maximum gray value for pixel
(package private) java.awt.MenuBar	mbar menu bar for the frame
java.awt.Font	mediumFont
float	minDataValue Minimum value expected for current hist[] data
MenuSupport	ms Menu support functions using Hashtables to tack what is active
java.awt.TextArea	msgTextArea Text area GUI for message rporting
int	nbrPassedFilter # of spots passing filter
(package private) static int	NCOLS
int	nHist size of input unscaled histogram[] data
int	nPixels The pixWidth*pixHeight
int	nPixList
(package private) static int	NROWS size of the text area in characters
java.awt.Image	pImg Image to display
char[][]	pixClist List of display pix associate char[] images
java.lang.String[]	pixFileList
int[]	pixGrayBits list of max gray pixel sizes of pixClist pixels
int	pixHeight The height of the image
java.lang.String[]	pixMenuList list of display picture menu commands for choices
java.lang.String[]	pixNameList list of display picture names for choices
int	pixWidth The width of the image
java.awt.Dimension	preferedCanvasSize
int	radix Code for winDump radix
java.awt.Choice	radixChoice Selector for windmp radix
java.lang.String	radixName Name winDump radix
int	ROI_CW Computing Window ROI code
int	ROI_DBUG Debugging region ROI code
int	ROI_ND Step Wedge ROI code
int	ROI_NONE No ROI code
int	ROI_PIXDUMP Picture dump region ROI code
int	ROI_WORKING Working ROI code.
java.awt.Choice	roiChoice Selector for show ROI CW overlay
int	roiCode code for show ROI CW overlay
Roi	roiCW
Roi	roiDBUG "DBUG",ROI_DBUG instance
java.awt.Menu	roiMenu "RegionOfInterest" pull down Menu list
java.lang.String	roiName name for show ROI CW overlay
Roi	roiND ""ND",ROI_ND instance
Roi	roiPIXDUMP "PIXDUMP",ROI_PIXDUMP instance
Roi	roiWORKING Internal "WORKING",ROI_WORKING instance that can be used to set the CW, DBUG or PIXDUMP (not the ND) Rois
int	selImgIdx image index
(package private) static long	serialVersionUID frame id
Seg2Dgel	sg2 instance of the main class
private Sg2viewImage	sg2Vi Sg2ViewImage to hold the image
boolean	showCWflag
boolean	showDbugCWflag
boolean	showNDCWflag
boolean	showPixdumpCWflag
boolean	showSpotNbrsFlag set from "View spot numbers" checkbox
java.awt.Font	smallFont
boolean	splitPanelFlag to use spiltPane or not
private int	textAreaFontSize font size
private java.lang.String	textFontFamily font family for message window
java.awt.Checkbox	useDragCB the "Use drag" checkbox
boolean	useDragFlag set from "Use drag" checkbox
boolean	useFilterByBinFlag menu CB item to filter spots by testing if the histogram active bin is selected and histogram spot feature meets the active bin test
boolean	useHistGUIflag flag to use simple ImageViewer w/o histogram or full GUI with the histogram
int	VIEW_HEIGHT Height of the frame with and without histogram
int	VIEW_WIDTH_NO_HIST Width of the frame without histogram
int	VIEW_WIDTH_WITH_HIST Width of the frame with histogram
int	viewHeight
java.awt.Menu	viewMenu "View" pull down Menu list
int	viewWidth
int	windmpSize Code for winDump size
java.awt.Choice	windmpSizeChoice Selector for winDump size
java.lang.String	windmpSizeName Name windump size
java.awt.Choice	zoomChoice "Zoom" Choice list
int	zoomVal

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

Sg2showImage(Seg2Dgel sg2, boolean useHistGUIflag, java.lang.String baseImageFile)
Sg2showImage() - Constructor

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle button clicks
void	addHistogramGUI() addHistogramGUI() - Add the histogram GUI to the ImageViewer GUI
private void	addMenuTree(java.awt.Frame f, java.awt.MenuBar mbar) addMenuTree() - create pull down menus in menu bar
boolean	buildImageGUI(java.awt.Image img) buildImageGUI() - Build the ImageViewer GUI from scratch
boolean	calcHistogram() calcHistogram() - compute histogram from image data.
boolean	calcSpotDataMaxMinValues() calcSpotDataMaxMinValues() - calc maxDataValue and minDataValue from the spotList[] data that is inside of the ROI if used.
void	close() close() - close this popup and reset flags
void	displayImageGUI() displayImageGUI() - show the Image Viewer, used only have already initialized before.
java.awt.Dimension	getPreferredSize() getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.
private boolean	initImageGUI(java.lang.String dName) initImageGUI() - init the image gui.
void	itemStateChanged(java.awt.event.ItemEvent e) itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
void	positionImageWindow() positionImageWindow() - position image window on the screen
void	removeHistogramGUI() removeHistogramGUI() - Remove the histogram GUI from the ImageViewer GUI
boolean	setCurrentROI() setCurrentROI() - set the current ROI if both ULHC and LRHC are not -1
boolean	setHistDataGUI(int histDataType) setHistDataGUI() - set checkbox radio button and choice selected for histogram data type
boolean	setImageGUI(java.lang.String imgName) setImageGUI() - set checkbox radio button and choice selected for image to be displayed
boolean	setPixDatabase(java.lang.String[] pixNameList, java.lang.String[] pixMenuList, java.lang.String[] pixFileList, char[][] pixClist, int[] pixGrayBits, int nPixList, java.lang.String defaultPixName, int pixWidth, int pixHeight, boolean useHistGUIflag) setPixDatabase() - setup the list of predefined images available to the ImageViewer.
void	setRadixGUI(int r) setRadixGUI() - set checkbox radio button and choice selected for radix type
void	setROItypeGUI(int code) setROItypeGUI() - set checkbox radio button and choice selected for ROI type
boolean	setSg2ImageGUI(java.lang.String dName) setSg2ImageGUI() - reset the Image Viewer GUI window only
void	setWindmpSizeGUI(int size) setWindmpSizeGUI() - set checkbox radio button and Choice selected and process event for windmp size checkboxes
void	setZoom(int zoomValue) setZoom() - set the image size/zoom and create a new internalCanvas
boolean	showImageGUI(java.lang.String dName) showImageGUI() - show the Image Viewer GUI window
void	showImgMsg(java.lang.String msg) showImgMsg() - display the msg in text area window
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - closing down the window, get rid of the frame.
void	windowDeactivated(java.awt.event.WindowEvent e)
void	windowDeiconified(java.awt.event.WindowEvent e)
void	windowIconified(java.awt.event.WindowEvent e)
void	windowOpened(java.awt.event.WindowEvent e)

Methods inherited from class javax.swing.JFrame

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

Methods inherited from class java.awt.Frame

addNotify, finalize, 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, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, 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, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, 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, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, 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, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

serialVersionUID

static final long serialVersionUID

frame id

See Also:

Constant Field Values

sg2

public Seg2Dgel sg2

instance of the main class

ENABLE_ZOOM

public static final boolean ENABLE_ZOOM

Enable zoom of images

See Also:

Constant Field Values

useHistGUIflag

public boolean useHistGUIflag

flag to use simple ImageViewer w/o histogram or full GUI with the histogram

baseImageFile

public java.lang.String baseImageFile

base name of the image for use in the title

changeGuiFlag

public boolean changeGuiFlag

flag to indicating that the GUI may have changed and that it should be rebuilt.

hasHistGUIflag

public boolean hasHistGUIflag

flag to indicate that the GUI contains the Histogram sub-GUI

VIEW_WIDTH_NO_HIST

public final int VIEW_WIDTH_NO_HIST

Width of the frame without histogram

See Also:

Constant Field Values

VIEW_WIDTH_WITH_HIST

public final int VIEW_WIDTH_WITH_HIST

Width of the frame with histogram

See Also:

Constant Field Values

VIEW_HEIGHT

public final int VIEW_HEIGHT

Height of the frame with and without histogram

See Also:

Constant Field Values

HIST_WIDTH

public static final int HIST_WIDTH

Width of the histogram

See Also:

Constant Field Values

HIST_HEIGHT

public static final int HIST_HEIGHT

Height of the histogram

See Also:

Constant Field Values

IS_WIDTH

public static final int IS_WIDTH

Width of the img scroller

See Also:

Constant Field Values

IS_HEIGHT

public static final int IS_HEIGHT

Height of the img scroller

See Also:

Constant Field Values

NROWS

static final int NROWS

size of the text area in characters

See Also:

Constant Field Values

NCOLS

static final int NCOLS

See Also:

Constant Field Values

DIST_THR

static final int DIST_THR

Distance threshold in pixels from mouse (x,y) to spot centroid to find spot \

See Also:

Constant Field Values

ROI_NONE

public final int ROI_NONE

No ROI code

See Also:

Constant Field Values

ROI_CW

public final int ROI_CW

Computing Window ROI code

See Also:

Constant Field Values

ROI_ND

public final int ROI_ND

Step Wedge ROI code

See Also:

Constant Field Values

ROI_DBUG

public final int ROI_DBUG

Debugging region ROI code

See Also:

Constant Field Values

ROI_PIXDUMP

public final int ROI_PIXDUMP

Picture dump region ROI code

See Also:

Constant Field Values

ROI_WORKING

public final int ROI_WORKING

Working ROI code. This ROI may then be copied to the CW, DBUG or PIXDUMP ROIs

See Also:

Constant Field Values

mbar

java.awt.MenuBar mbar

menu bar for the frame

fileMenu

public java.awt.Menu fileMenu

"File" pull down Menu list

roiMenu

public java.awt.Menu roiMenu

"RegionOfInterest" pull down Menu list

viewMenu

public java.awt.Menu viewMenu

"View" pull down Menu list

histMenu

public java.awt.Menu histMenu

"Histogram" pull down Menu list

histChoice

public java.awt.Choice histChoice

"Histogram" Choice list

zoomChoice

public java.awt.Choice zoomChoice

"Zoom" Choice list

controlPanel

public javax.swing.JPanel controlPanel

Control panel for the main frame

ms

public MenuSupport ms

Menu support functions using Hashtables to tack what is active

sg2Vi

private Sg2viewImage sg2Vi

Sg2ViewImage to hold the image

msgTextArea

public java.awt.TextArea msgTextArea

Text area GUI for message rporting

textAreaFontSize

private int textAreaFontSize

font size

textFontFamily

private java.lang.String textFontFamily

font family for message window

fontFamily

public java.lang.String fontFamily

smallFont

public java.awt.Font smallFont

mediumFont

public java.awt.Font mediumFont

largeFont

public java.awt.Font largeFont

dispPixChoice

public java.awt.Choice dispPixChoice

Selector for image to display after a segmentation

pixHeight

public int pixHeight

The height of the image

pixWidth

public int pixWidth

The width of the image

radixChoice

public java.awt.Choice radixChoice

Selector for windmp radix

radixName

public java.lang.String radixName

Name winDump radix

radix

public int radix

Code for winDump radix

windmpSizeChoice

public java.awt.Choice windmpSizeChoice

Selector for winDump size

windmpSizeName

public java.lang.String windmpSizeName

Name windump size

windmpSize

public int windmpSize

Code for winDump size

roiChoice

public java.awt.Choice roiChoice

Selector for show ROI CW overlay

roiName

public java.lang.String roiName

name for show ROI CW overlay

roiCode

public int roiCode

code for show ROI CW overlay

roiWORKING

public Roi roiWORKING

Internal "WORKING",ROI_WORKING instance that can be used to set the CW, DBUG or PIXDUMP (not the ND) Rois

roiCW

public Roi roiCW

roiND

public Roi roiND

""ND",ROI_ND instance

roiDBUG

public Roi roiDBUG

"DBUG",ROI_DBUG instance

roiPIXDUMP

public Roi roiPIXDUMP

"PIXDUMP",ROI_PIXDUMP instance

allSpotsCB

public java.awt.Checkbox allSpotsCB

the "All spots" Checkbox

allSpotsFlag

public boolean allSpotsFlag

set from "All spots" checkbox

showSpotNbrsFlag

public boolean showSpotNbrsFlag

set from "View spot numbers" checkbox

isVisibleFlag

public boolean isVisibleFlag

Set true if window is visible

drawHorizSliceFlag

public boolean drawHorizSliceFlag

menu CB item to display horizontal slice

drawVertSliceFlag

public boolean drawVertSliceFlag

menu CB item to display vertical slice

filterGEQactiveBinFlag

public boolean filterGEQactiveBinFlag

menu CB item to test spots for GEQ activeBin value, else LEQ activeBin value fromt the selected histogram bin for the histogram histType spot data.

useFilterByBinFlag

public boolean useFilterByBinFlag

menu CB item to filter spots by testing if the histogram active bin is selected and histogram spot feature meets the active bin test

nbrPassedFilter

public int nbrPassedFilter

# of spots passing filter

useDragCB

public java.awt.Checkbox useDragCB

the "Use drag" checkbox

useDragFlag

public boolean useDragFlag

set from "Use drag" checkbox

logReportCB

public java.awt.Checkbox logReportCB

the "Log report" checkbox

logReportFlag

public boolean logReportFlag

set from "Log report" checkbox

viewWidth

public int viewWidth

viewHeight

public int viewHeight

zoomVal

public int zoomVal

showCWflag

public boolean showCWflag

showNDCWflag

public boolean showNDCWflag

showDbugCWflag

public boolean showDbugCWflag

showPixdumpCWflag

public boolean showPixdumpCWflag

hCanvas

public Sg2drawHistogram hCanvas

Histogram Canvas to hold the image

hist

public int[] hist

full input unscaled histogram data [0:nHist-1]

nHist

public int nHist

size of input unscaled histogram[] data

histType

public int histType

type of data to use with the histogram

HIST_NONE

public static final int HIST_NONE

types of histogram data allowed

See Also:

Constant Field Values

HIST_IMAGE_DENSITY

public static final int HIST_IMAGE_DENSITY

types of histogram data allowed

See Also:

Constant Field Values

HIST_SPOT_AREA

public static final int HIST_SPOT_AREA

types of histogram data allowed

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Constant Field Values

HIST_SPOT_MNBKGRD

public static final int HIST_SPOT_MNBKGRD

types of histogram data allowed

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Constant Field Values

HIST_SPOT_MNDENSITY

public static final int HIST_SPOT_MNDENSITY

types of histogram data allowed

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Constant Field Values

HIST_SPOT_TOT_DENSITY

public static final int HIST_SPOT_TOT_DENSITY

types of histogram data allowed

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Constant Field Values

HIST_SPOT_TOT_DENSITY_PRIME

public static final int HIST_SPOT_TOT_DENSITY_PRIME

types of histogram data allowed

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Constant Field Values

HIST_SPOT_VOLUME

public static final int HIST_SPOT_VOLUME

types of histogram data allowed

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Constant Field Values

HIST_SPOT_MIN_DENSITY

public static final int HIST_SPOT_MIN_DENSITY

types of histogram data allowed

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Constant Field Values

HIST_SPOT_MAX_DENSITY

public static final int HIST_SPOT_MAX_DENSITY

types of histogram data allowed

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Constant Field Values

HIST_SPOT_TOT_DENSITY_RANGE

public static final int HIST_SPOT_TOT_DENSITY_RANGE

types of histogram data allowed

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Constant Field Values

HIST_SPOT_SX_SY_RATIO_RANGE

public static final int HIST_SPOT_SX_SY_RATIO_RANGE

types of histogram data allowed

See Also:

Constant Field Values

histNames

public static final java.lang.String[] histNames

list of histogram data types

dataUnits

public java.lang.String dataUnits

Data type as fct of histogram data type

minDataValue

public float minDataValue

Minimum value expected for current hist[] data

maxDataValue

public float maxDataValue

Maximum value expected for current hist[] data

maxGrayPixel

public int maxGrayPixel

Maximum gray value for pixel

dispPixC

public char[] dispPixC

Picture buffer char[] of image to display after a segmentation. Note this is read either from the pix? variable or from the file if the pix? variable is null.

dispName

public java.lang.String dispName

Name of image to display after a segmentation

nPixels

public int nPixels

The pixWidth*pixHeight

dispPixFile

public java.lang.String dispPixFile

File of image to display after a segmentation. Used if dispPixC is null.

dispPixWorking

public char[] dispPixWorking

Picture buffer char[] of image to display after a segmentation. Note this is read either from the pix? variable or from the file if the pix? variable is null.

selImgIdx

public int selImgIdx

image index

nPixList

public int nPixList

pixNameList

public java.lang.String[] pixNameList

list of display picture names for choices

pixMenuList

public java.lang.String[] pixMenuList

list of display picture menu commands for choices

pixFileList

public java.lang.String[] pixFileList

pixClist

public char[][] pixClist

List of display pix associate char[] images

pixGrayBits

public int[] pixGrayBits

list of max gray pixel sizes of pixClist pixels

pImg

public java.awt.Image pImg

Image to display

preferedCanvasSize

public java.awt.Dimension preferedCanvasSize

splitPanelFlag

public boolean splitPanelFlag

to use spiltPane or not

Constructor Detail

Sg2showImage

public Sg2showImage(Seg2Dgel sg2,
                    boolean useHistGUIflag,
                    java.lang.String baseImageFile)

Sg2showImage() - Constructor

Parameters:

sg2 - is an instance of the main class

useHistGUIflag - to bring up the histogram GUI as well.

baseImageFile - is the base name of the image

Method Detail

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.

Overrides:

getPreferredSize in class java.awt.Container

Returns:

frame size

setPixDatabase

public boolean setPixDatabase(java.lang.String[] pixNameList,
                              java.lang.String[] pixMenuList,
                              java.lang.String[] pixFileList,
                              char[][] pixClist,
                              int[] pixGrayBits,
                              int nPixList,
                              java.lang.String defaultPixName,
                              int pixWidth,
                              int pixHeight,
                              boolean useHistGUIflag)

setPixDatabase() - setup the list of predefined images available to the ImageViewer. All images must be the same heightXwidth.

Parameters:

pixNameList - is the list of display picture names for choices/menus

pixMenuList - is the list of display picture menu cmds

pixFileList - is list of associated file names if any

pixClist - is list of the associate char[] images

nPixList - is size of the lists in case list contents is less than size

defaultPixName - is the default pix name

pixWidth - is width of all images

pixHeight - is height of all images

useHistGUIflag - to bring up the histogram GUI as well.

Returns:

true if succeed

initImageGUI

private boolean initImageGUI(java.lang.String dName)

initImageGUI() - init the image gui. This sets the dispName, dispPixWorking, dispPixFile, and selImgIdx.

Parameters:

dName - is the image to display

Returns:

true if succeed

displayImageGUI

public void displayImageGUI()

displayImageGUI() - show the Image Viewer, used only have already initialized before. Should leave everything the way it was before window was closed.

showImageGUI

public boolean showImageGUI(java.lang.String dName)

showImageGUI() - show the Image Viewer GUI window

Returns:

true if succeed

setSg2ImageGUI

public boolean setSg2ImageGUI(java.lang.String dName)

setSg2ImageGUI() - reset the Image Viewer GUI window only

Returns:

true if succeed

addHistogramGUI

public void addHistogramGUI()

addHistogramGUI() - Add the histogram GUI to the ImageViewer GUI

removeHistogramGUI

public void removeHistogramGUI()

removeHistogramGUI() - Remove the histogram GUI from the ImageViewer GUI

buildImageGUI

public boolean buildImageGUI(java.awt.Image img)

buildImageGUI() - Build the ImageViewer GUI from scratch

addMenuTree

private void addMenuTree(java.awt.Frame f,
                         java.awt.MenuBar mbar)

addMenuTree() - create pull down menus in menu bar

Parameters:

f - is frame

mbar - is MenuBar

showImgMsg

public void showImgMsg(java.lang.String msg)

showImgMsg() - display the msg in text area window

Parameters:

msg - to display

positionImageWindow

public void positionImageWindow()

positionImageWindow() - position image window on the screen

setCurrentROI

public boolean setCurrentROI()

setCurrentROI() - set the current ROI if both ULHC and LRHC are not -1

close

public void close()

close() - close this popup and reset flags

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

windowClosing() - closing down the window, get rid of the frame.

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - is window closing event

See Also:

close()

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener

calcSpotDataMaxMinValues

public boolean calcSpotDataMaxMinValues()

calcSpotDataMaxMinValues() - calc maxDataValue and minDataValue from the spotList[] data that is inside of the ROI if used. This range is for ALL spots - not just VALID spots. Filtering for valid spots is done elsewhere.

calcHistogram

public boolean calcHistogram()

calcHistogram() - compute histogram from image data. The dynamic range is determined by the actual data.

setWindmpSizeGUI

public void setWindmpSizeGUI(int size)

setWindmpSizeGUI() - set checkbox radio button and Choice selected and process event for windmp size checkboxes

Parameters:

size - is the size X size window in the range of 5 to 21.

setROItypeGUI

public void setROItypeGUI(int code)

setROItypeGUI() - set checkbox radio button and choice selected for ROI type

Parameters:

code - is the ROI_xxxx code

setZoom

public void setZoom(int zoomValue)

setZoom() - set the image size/zoom and create a new internalCanvas

Parameters:

zoomValue -

setRadixGUI

public void setRadixGUI(int r)

setRadixGUI() - set checkbox radio button and choice selected for radix type

Parameters:

r - is the radix code

setImageGUI

public boolean setImageGUI(java.lang.String imgName)

setImageGUI() - set checkbox radio button and choice selected for image to be displayed

Parameters:

imgName - is the name name

Returns:

true if found image to be displayed

setHistDataGUI

public boolean setHistDataGUI(int histDataType)

setHistDataGUI() - set checkbox radio button and choice selected for histogram data type

Parameters:

r - is the radix code

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)

itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

Parameters:

e - is ItemEvent

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

actionPerformed() - Handle button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - is action evet