Accession
Class AccCALIBwizardPopup

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  Accession.AccCALIBwizardPopup

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

public class AccCALIBwizardPopup
extends java.awt.Frame
implements java.awt.event.ItemListener, java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener

The AccCALIBwizardPopupclass implements a popup GUI to create and edit the image grayscale calibration used in the accessioning program.

 [TODO] Debug Calibration.
 1. The histogram does not correct - bad peak display.
 2. Also check permutations of 
     (no calibration, data, calib. data in Acc DB, has Wedge ROI CW,
      Wedge CW + calibr. data, explict calib w/o wedge, point list
      similar to Flicker). Resolve popup of missing data.
 This is tracked with  calDataMode set from 
   (CAL_WEDGE  CAL_SPOTLIST  CAL_DATA_FILE  CAL_MANUAL).
 3. Validate calibration table that can be used to sepecify 
    calibration values from a file. 
    It may have 1 or more of the following fields 
       "PEAK", "CAL", "GRAY", "CAL-UNIT", "CAL-ABBREV".  

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: 2005/10/20 11:11:05 $ $Revision: 1.13 $

Author:

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

See Also:

Open2Dprot Home, Serialized Form

Nested Class Summary

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

int	activeBin active bin idx [0:nHist-1] else -1
private java.awt.Font	buttonFont
static int	CAL_DATA_FILE get (cal,gray) list calibration from tab-delim data file field names: (PEAK CAL GRAY CAL-UNIT CAL-ABBREV)
static int	CAL_MANUAL Enter calibration manually by typing into the table.
static int	CAL_SPOTLIST Use Spot list values for gray values grayDataList[]
static int	CAL_WEDGE Use ND step wedge ROI for gray values
float[]	calDataList calDataList is calibration value list if not null
int	calDataMode calDataMode of form CAL_WEDGE, CAL_SPOTLIST
private java.awt.Color	calibPeakColor calibration peaks on histogram color
Table	calibTbl calibration data file table
java.lang.String	calTypeStr String name of calDataMode.
java.lang.String	calUnits calUnits is name of calibration units if not null
boolean	changedAccCalibrDataFlag Flag indicating that the accession calibration fields were defined or were edited
Accession	cs instance of the main class
DbSample	dbS link to active sample
java.lang.String	dispName Name of image to display
char[]	dispPixC Picture buffer char[] of image to display .
private boolean	drawIntoImageFlag set if draw plot to GIF file
private java.awt.Menu	editMenu "Edit" pull down Menu list
private java.awt.Menu	fileMenu "File" pull down Menu list
private java.lang.String	fontFamily
int[]	grayDataList grayDataList is peak gray list if not null.
boolean	grayValueListChangedFlag Flag indicating that the accession calibration gray value fields were defined or were edited
private java.awt.Menu	helpMenu "Help" pull down Menu list
private int[]	hist freq hist[0:nHist-1].
private java.awt.Color	histColor
private java.awt.Color	histTopColor
boolean	isVisibleFlag If the Histogram is visible
private java.awt.Color	labelColor
private java.awt.Font	largeFont
boolean	logReportFlag set from "Log report" checkbox menu item
static int	MAX_GRAY # gray values in a pixel
static int	MAXBINS # of histogram into bins
private java.awt.MenuBar	mbar menu bar for the frame
private java.awt.Font	mediumFont
MenuSupport	ms Menu support functions using Hashtables to tack what is active.
private java.awt.TextArea	msgTextArea Text area GUI for message rporting
(package private) static int	N_PCT_PROLOGUE default # of initial rows in the peak wedge calibration table
int	nCalSteps size of calDataList is calibration value list if not null
(package private) static int	NCOLS
int	nGrayPeaks size of the grayDataList is peak gray list if not null
int	nPixels The pixWidth*pixHeight
(package private) static int	NROWS size of the text area in characters
private java.awt.Color	odColor
java.lang.String	oGifFileName Full path of image to "Save image" in
private java.awt.Color	optBkgrdColor
(package private) static int	PEAK_CAL_TBL_COLS default # of editPanel cols
(package private) static int	PEAK_CAL_TBL_ROWS default # of editPanel rows
(package private) static int	peakCalTblCols # of editPanel cols in actual table
(package private) static int	peakCalTblRows # of editPanel rows in actual table
private java.awt.TextField[][]	peakCalTblTF Array of TextFields used in constructing the Peak Calibration Table editPanel.
private java.awt.Color	peakNbrColor peak number color
private int	peakNbrFontSize font size for peak number labels
int	pixHeight The width of the current image
int	pixWidth The width of the current image
(package private) static long	serialVersionUID frame id
private int[]	sHist modified freq sHist[0:nHist-1].
private java.awt.Font	smallFont
private int	textAreaFontSize font size
private java.lang.String	textFontFamily font family for message window
java.awt.Checkbox	useLogCB the "Use log" checkbox
boolean	useLogFlag set from "Use log" checkbox
boolean	useSaveImageFlag set from "Save image" Command
static int	VIEW_HEIGHT Height of the frame
static int	VIEW_WIDTH Width of the frame
int	viewHeight
private java.awt.Menu	viewMenu "View" pull down Menu list
int	viewWidth
private static int[]	xPainted active hit coordinates

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 java.awt.image.ImageObserver

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

Constructor Summary

AccCALIBwizardPopup(Accession cs, DbSample dbS, int calDataMode, float[] calDataList, int[] grayDataList, int nCalSteps, int nGrayPeaks, java.lang.String calUnits, Table calibTbl)
AccCALIBwizardPopup() - Constructor.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle Control panel button clicks
private void	addMenuTree(java.awt.Frame f, java.awt.MenuBar mbar) addMenuTree() - create pull down menus in menu bar
private void	buildHistGUI() buildHistGUI() - build the histogram GUI
void	close(boolean tryToSaveFlag) close() - close this popup and reset flags
private static void	drawFilledBox(java.awt.Graphics g, int xC, int yC, int width, java.awt.Color color) drawFilledBox() - draw plus sign at the specified color.
(package private) boolean	drawGifFile(java.lang.String oGifFileName) drawGifFile() - draw plot into Gif image file if in stand-alone mode.
private boolean	drawHistInCanvas(java.awt.Graphics g) drawHistInCanvas() - draw histogram of hist[].
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the minimum preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - getPreferredSize, needed for sizing frame and ScrollPane correctly.
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	mouseClicked(java.awt.event.MouseEvent e)
void	mouseDragged(java.awt.event.MouseEvent e) mouseDragged() - process mouse event
void	mouseEntered(java.awt.event.MouseEvent e)
void	mouseExited(java.awt.event.MouseEvent e)
boolean	mouseHandler(int x, int y) mouseHandler() - search for the active bin if any
void	mouseMoved(java.awt.event.MouseEvent e)
void	mousePressed(java.awt.event.MouseEvent e)
void	mouseReleased(java.awt.event.MouseEvent e) mouseReleased() - process mouse event
void	paint(java.awt.Graphics g) paint() - draw the histogram
private void	positionHistWindow() positionHistWindow() - position histogram window on the screen
private boolean	reExtrapolateCalibration() reExtrapolateCalibration() - regenerate the mapGrayToCal[] from the peak table
boolean	refreshMapFromTable(boolean updateMapFlag) refreshMapFromTable() - refresh the peak table from the TextFields...
boolean	setCalValueListCalibAccFields() setCalValueListCalibAccFields() - set the accession data calibration values peak list calibration fields
boolean	setGrayPeakListCalibAccFields() setGrayPeakListCalibAccFields() - set the accession data gray value peaks list calibration fields
void	setTitleHist(java.lang.String title) setTitleHist() - set the title
void	setVisible(boolean isVisibleFlag, boolean redoROIhistFlag) setVisible() - set the histogram as visible or not
void	showMsg(java.lang.String msg) showMsg() - display the msg in text area window
void	showMsg(java.lang.String msg, java.awt.Color color) showMsg() - set the status msg
void	update(java.awt.Graphics g) update() - update without background the scrollable canvas
boolean	updateAccTableWithSpotList() updateAccTableWithSpotList() - update accession DB table with spot list data.
void	updateHistogramPlot(boolean redoROIhistFlag) updateHistogramPlot() - set hist state and do repaint to draw it.
private void	updatePeakCalTable() updatePeakCalTable() - update the peak calibration table GUI text field and the dbS.calib cal and gray value arrays with new data from calDataList[] and grayDataList[].
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - close down the window.
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 java.awt.Frame

addNotify, finalize, getAccessibleContext, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, paramString, remove, removeNotify, setCursor, setExtendedState, setIconImage, 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, processWindowEvent, 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, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, 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

cs

public Accession cs

instance of the main class

dbS

public DbSample dbS

link to active sample

CAL_WEDGE

public static final int CAL_WEDGE

Use ND step wedge ROI for gray values

See Also:

Constant Field Values

CAL_SPOTLIST

public static final int CAL_SPOTLIST

Use Spot list values for gray values grayDataList[]

See Also:

Constant Field Values

CAL_DATA_FILE

public static final int CAL_DATA_FILE

get (cal,gray) list calibration from tab-delim data file field names: (PEAK CAL GRAY CAL-UNIT CAL-ABBREV)

See Also:

Constant Field Values

CAL_MANUAL

public static final int CAL_MANUAL

Enter calibration manually by typing into the table.

See Also:

Constant Field Values

calDataMode

public int calDataMode

calDataMode of form CAL_WEDGE, CAL_SPOTLIST

calDataList

public float[] calDataList

calDataList is calibration value list if not null

nCalSteps

public int nCalSteps

size of calDataList is calibration value list if not null

grayDataList

public int[] grayDataList

grayDataList is peak gray list if not null.

nGrayPeaks

public int nGrayPeaks

size of the grayDataList is peak gray list if not null

calUnits

public java.lang.String calUnits

calUnits is name of calibration units if not null

calTypeStr

public java.lang.String calTypeStr

String name of calDataMode.

VIEW_WIDTH

public static final int VIEW_WIDTH

Width of the frame

See Also:

Constant Field Values

VIEW_HEIGHT

public static final int VIEW_HEIGHT

Height of the frame

See Also:

Constant Field Values

viewWidth

public int viewWidth

viewHeight

public int viewHeight

N_PCT_PROLOGUE

static final int N_PCT_PROLOGUE

default # of initial rows in the peak wedge calibration table

See Also:

Constant Field Values

PEAK_CAL_TBL_ROWS

static final int PEAK_CAL_TBL_ROWS

default # of editPanel rows

PEAK_CAL_TBL_COLS

static final int PEAK_CAL_TBL_COLS

default # of editPanel cols

See Also:

Constant Field Values

peakCalTblRows

static final int peakCalTblRows

# of editPanel rows in actual table

peakCalTblCols

static final int peakCalTblCols

# of editPanel cols in actual table

See Also:

Constant Field Values

MAX_GRAY

public static int MAX_GRAY

# gray values in a pixel

MAXBINS

public static int MAXBINS

# of histogram into bins

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

mbar

private java.awt.MenuBar mbar

menu bar for the frame

fileMenu

private java.awt.Menu fileMenu

"File" pull down Menu list

viewMenu

private java.awt.Menu viewMenu

"View" pull down Menu list

editMenu

private java.awt.Menu editMenu

"Edit" pull down Menu list

helpMenu

private java.awt.Menu helpMenu

"Help" pull down Menu list

ms

public MenuSupport ms

Menu support functions using Hashtables to tack what is active.

activeBin

public int activeBin

active bin idx [0:nHist-1] else -1

hist

private int[] hist

freq hist[0:nHist-1].

sHist

private int[] sHist

modified freq sHist[0:nHist-1].

drawIntoImageFlag

private boolean drawIntoImageFlag

set if draw plot to GIF file

msgTextArea

private 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

private java.lang.String fontFamily

smallFont

private java.awt.Font smallFont

mediumFont

private java.awt.Font mediumFont

largeFont

private java.awt.Font largeFont

buttonFont

private java.awt.Font buttonFont

peakNbrFontSize

private int peakNbrFontSize

font size for peak number labels

dispName

public java.lang.String dispName

Name of image to display

dispPixC

public char[] dispPixC

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

pixWidth

public int pixWidth

The width of the current image

pixHeight

public int pixHeight

The width of the current image

nPixels

public int nPixels

The pixWidth*pixHeight

oGifFileName

public java.lang.String oGifFileName

Full path of image to "Save image" in

useLogCB

public java.awt.Checkbox useLogCB

the "Use log" checkbox

useLogFlag

public boolean useLogFlag

set from "Use log" checkbox

useSaveImageFlag

public boolean useSaveImageFlag

set from "Save image" Command

logReportFlag

public boolean logReportFlag

set from "Log report" checkbox menu item

optBkgrdColor

private java.awt.Color optBkgrdColor

histColor

private java.awt.Color histColor

histTopColor

private java.awt.Color histTopColor

odColor

private java.awt.Color odColor

calibPeakColor

private java.awt.Color calibPeakColor

calibration peaks on histogram color

labelColor

private java.awt.Color labelColor

peakNbrColor

private java.awt.Color peakNbrColor

peak number color

peakCalTblTF

private java.awt.TextField[][] peakCalTblTF

Array of TextFields used in constructing the Peak Calibration Table editPanel. Not all entries are used. It is of size [0:peakCalTblRows-1][0:peakCalTblCols-1].

xPainted

private static int[] xPainted

active hit coordinates

isVisibleFlag

public boolean isVisibleFlag

If the Histogram is visible

changedAccCalibrDataFlag

public boolean changedAccCalibrDataFlag

Flag indicating that the accession calibration fields were defined or were edited

grayValueListChangedFlag

public boolean grayValueListChangedFlag

Flag indicating that the accession calibration gray value fields were defined or were edited

calibTbl

public Table calibTbl

calibration data file table

Constructor Detail

AccCALIBwizardPopup

public AccCALIBwizardPopup(Accession cs,
                           DbSample dbS,
                           int calDataMode,
                           float[] calDataList,
                           int[] grayDataList,
                           int nCalSteps,
                           int nGrayPeaks,
                           java.lang.String calUnits,
                           Table calibTbl)

AccCALIBwizardPopup() - Constructor. Note: need to call setSampleDatabase() and setNameValueEditGUI() to do repaint. Note: data structures used by this class are validated and may pass one or more (calibration values, corresponding gray values, units, calibTable).

Parameters:

cs - is an instance of the main class

dbS - is sample to calibrate

calDataMode - is CAL_WEDGE, CAL_SPOTLIST, CAL_DATA_FILE, or CAL_MANUAL

calDataList - is calibration value list [0:nCalSteps-1] if not null. These are the target values corresponding to each of the gray values. E.G., they could be OD values for an OD step wedge, etc.

grayDataList - is peak gray list [0:nGrayPeaks-1] if not null. These are the gray values corresponding to calibration data.

nCalSteps - size of calDataList[]

nGrayPeaks - size of grayDataList[]

calUnits - is name of calibration units if not null

calibTbl - is calibration Table if doing CAL_DATA_FILE

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

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the minimum preferred size

Overrides:

getMinimumSize in class java.awt.Container

Returns:

window size

positionHistWindow

private void positionHistWindow()

positionHistWindow() - position histogram window on the screen

buildHistGUI

private void buildHistGUI()

buildHistGUI() - build the histogram GUI

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

showMsg

public void showMsg(java.lang.String msg)

showMsg() - display the msg in text area window

Parameters:

msg - to display

showMsg

public void showMsg(java.lang.String msg,
                    java.awt.Color color)

showMsg() - set the status msg

Parameters:

msg - is the status window msg

color - to draw it

setTitleHist

public void setTitleHist(java.lang.String title)

setTitleHist() - set the title

Parameters:

title - is window title

setVisible

public void setVisible(boolean isVisibleFlag,
                       boolean redoROIhistFlag)

setVisible() - set the histogram as visible or not

Parameters:

redoROIhistFlag - will reompute thie iData.hist[] from the ROI window in the image.

drawGifFile

boolean drawGifFile(java.lang.String oGifFileName)

drawGifFile() - draw plot into Gif image file if in stand-alone mode. This sets it up and lets paint() to the heavy lifting...

Parameters:

oGifFileName - is the full path GIF output file

Returns:

true if successful

setCalValueListCalibAccFields

public boolean setCalValueListCalibAccFields()

setCalValueListCalibAccFields() - set the accession data calibration values peak list calibration fields

Returns:

true if succeed

setGrayPeakListCalibAccFields

public boolean setGrayPeakListCalibAccFields()

setGrayPeakListCalibAccFields() - set the accession data gray value peaks list calibration fields

Returns:

true if succeed

updatePeakCalTable

private void updatePeakCalTable()

updatePeakCalTable() - update the peak calibration table GUI text field and the dbS.calib cal and gray value arrays with new data from calDataList[] and grayDataList[].

 Array of TextFields used in constructing the editable
 Peak Calibration Table.
 It is of size [0:peakCalTblRows-1][0:peakCalTblCols-1].
 holding the N_PCT_PROLOGUE rows plus the MAX_WEDGE_STEPS.
 The following is an example:
  -------------------------------------------------------------
  col #0             col #1      col #2     col #3
  -------------------------------------------------------------
 0  Calibration units ["optical density" / "Grayvalue" / "CPM", etc.]
 1  Wedge window      [calCWx1:calCWx2, calCWy1:calCWy2] - set by ROI
 2  Wedge identifier  ["manufacturer and part #"]
 3  Step #1 OD        [od value] Gray peak [gray value]
    Step #2 OD        [od value] Gray peak [gray value]
           . . .
 n  Step #n OD        [od value] Gray peak [gray value]
  -------------------------------------------------------------  

refreshMapFromTable

public boolean refreshMapFromTable(boolean updateMapFlag)

refreshMapFromTable() - refresh the peak table from the TextFields...

Parameters:

updateMapFlag - to apply the new table to updating mapGrayToCal[].

Returns:

true if succeed

reExtrapolateCalibration

private boolean reExtrapolateCalibration()

reExtrapolateCalibration() - regenerate the mapGrayToCal[] from the peak table

Returns:

true if the extrapolate succeeds

updateAccTableWithSpotList

public boolean updateAccTableWithSpotList()

updateAccTableWithSpotList() - update accession DB table with spot list data. It will save the spot size in table field "SpotMeasSize" and the list of nGrayPeaks spot centroids in field "SpotXYlist" as "x1,y1,s1,x2,y2,s2, ...xn,yn,sn" where (xi,yi) is spot i's centroid and si is its size (square of odd size centered at xi,yi). Note could use Util.cvs2iArray(xysListValue, 60, ",") to parse this and then disect out the (x,y,x) triples. If the accession DB table does not have these fields, it will add it. Then it updates the columns.

Returns:

true if updated

updateHistogramPlot

public void updateHistogramPlot(boolean redoROIhistFlag)

updateHistogramPlot() - set hist state and do repaint to draw it.

Parameters:

redoROIhistFlag - will reompute thie iData.hist[] from the ROI window in the image.

drawFilledBox

private static final void drawFilledBox(java.awt.Graphics g,
                                        int xC,
                                        int yC,
                                        int width,
                                        java.awt.Color color)

drawFilledBox() - draw plus sign at the specified color.

Parameters:

g - is graphics context

x - is center of object

y - is center of object

width - is width of object

color - is color to draw

drawHistInCanvas

private boolean drawHistInCanvas(java.awt.Graphics g)

drawHistInCanvas() - draw histogram of hist[].

Parameters:

g - is graphics context

paint

public void paint(java.awt.Graphics g)

paint() - draw the histogram

Overrides:

paint in class java.awt.Container

Parameters:

g - is graphics context

See Also:

drawHistInCanvas(java.awt.Graphics)

actionPerformed

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

actionPerformed() - Handle Control panel button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - is ActionEvent for buttons in control panel

close

public void close(boolean tryToSaveFlag)

close() - close this popup and reset flags

Parameters:

tryToSaveFlag - try to save calibration if needed

update

public void update(java.awt.Graphics g)

update() - update without background the scrollable canvas

Overrides:

update in class java.awt.Container

Parameters:

g - is graphics context

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

mouseHandler

public boolean mouseHandler(int x,
                            int y)

mouseHandler() - search for the active bin if any

Parameters:

x - mouse position

y - mouse position

Returns:

true if found it in the xPainted[] list and set activeBin to the index i in [0:255] else set activeBin to -1.

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent e)

mouseDragged() - process mouse event

Specified by:

mouseDragged in interface java.awt.event.MouseMotionListener

Parameters:

e - is mouse pressed event

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)

mouseReleased() - process mouse event

Specified by:

mouseReleased in interface java.awt.event.MouseListener

Parameters:

e - is mouse pressed event

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)

Specified by:

mouseExited in interface java.awt.event.MouseListener

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent e)

Specified by:

mouseMoved in interface java.awt.event.MouseMotionListener

windowClosing

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

windowClosing() - close down the window.

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - is window closing event

See Also:

close(boolean)

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