Class DrawHistogram

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

All Implemented Interfaces:

java.awt.event.ActionListener, 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, javax.swing.RootPaneContainer, javax.swing.WindowConstants

 class DrawHistogram
extends javax.swing.JFrame
implements java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener

The DrawHistogram class is used to draw an image intensity histogram in a popup frame. It is used for both the a) ROI region intensity histogram, and b) the ND step wedge calibraion (grayscale to OD) histogram. It is created on a per image (left or right) basis.

 NOTES:
 =====
 - The this.calibHistFlag indicates if it is a calibration or ROI
   histogram.
 - The instance lives in iData[12].dwHist and in iData[12].dwCalHist.
 - The histogram lives in iData.hist[] and is computed by 
   iData.calcHistogramROI() and iData.calcHistogram()
 - The (Quantify | Region Of Interest | Show ROI histogram (C-H))
   creates the histogram and computes the ROI data.
   i.e., (Quantify | Region of interest (ROI) | Capture measurement
   by ROI (C-R)) will also update the histogram if it exists.
 - Popup the calibration histogram from the menu
   (Quantify | Calibrate | Optical density).
 - There are different menu buttons in this popup depending on the
   functionality: either computing window ROI histogram or calibration
   (ND step wedge) histogram.

 The ND step wedge or spot-list grayscale to OD calibration procedure
============================--------------============================
 If a cal/{imageFile}.cal file exists when the image is loaded into
 flicker, it was read in at that time. Then when the Calibrate OD
 histogram was started, it uses those values in the Calibration Peaks
 table. Otherwise, the table will be null.
 NOTE: if you are using one of the four demo Leukemia gels, it will
 preload the OD values for demonstration purposes. 
 
 1. If you are using the step wedge, define a well-define ROI region 
    around the ND step wedge in the image using C-U (ULHC) and C-L
    (LRHC). Then compute the histogram using C-R.
 1.1 If instead, you are using the getPeaksByMeasFlag option, then do 
    NOT import the ROI histogram, but instead get the data from the 
    iData.spotList[] to save in a new histogram and the gray-peaks
    table as the mean spot values.
 2. If there are no OD data in the peaks table, then enter the OD 
    calibration values into the red Optical Density TextFields. [If the
    calibration was set previously and we read them in from the .cal 
    file, then preset these fields.] Also preset the corresponding 
    grayscale Gray-peak TextField values if you know what the values are.
    Special hack: If the current gel is not calibrated and the other
    gel has a calibration step list calib.ndWedgeODvalues[0:maxNDsteps-1]
    for maxNDsteps>0, then use it to save time typing it in.
 3. To force it to analyze the ROI wedge area, click on the
    "Analyze wedge ROI" button. This recomputes the histogram on
    the ROI (which may have changed) and the recomputes the calibration
    curve. 
 4. This will also update the Calibration Peak Table and generate the
    extrapolated mapGrayToOD[] calibration. The new histogram will show
    the Gray-peak values cooresponding to the OD values with red tick
    marks on the peaks. 
 4.1 It calls calib.findPeaks() to find the peaks and copies the peaks 
    into the Calibration Peak Table Gray-peak TextFields.
 4.2  It calls calib.extrapolateNDwedge() to compute calib.mapGrayToOD[] 
 4.3 It redraws the histogram plot with
     a) overlay calibration curve calib.mapGrayToOD[]
     b) Peaks table of (OD values, peak gray values)
 5. You can edit the peak list, by selecting a peak with the mouse and
    then pressing either throws "Add peak" or "Delete peak" button in 
    which case it redoes steps 4 through 4.3.
 6. When you are done editing you can save the calibration by pressing
    the "Save calibration state" button. This saves the calibration data
    in the cal/{imageFile}.cal file and copies the calib.mapGrayToOD[] 
    to the iData instance which you can then use for making calibrated
    measurements.
 7. Press "Done" to exit the calibration wizard.

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 Flicker Mozilla and Legal files are available on http://open2dprot.sourceforge.net/Flicker.

Version:

$Date$ $Revision$

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

Flicker Home, ShowHistPopup

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

(package private) int	activeBin active bin idx [0:nHist-1] else -1
private java.lang.String	activeImage active image name is "left" or "right"
(package private) static int	CAL_POPUP_HEIGHT default frame size height of popup
(package private) static int	CAL_POPUP_WIDTH default frame size width of popup
private CalibrateOD	calib link to working data related CalibrateOD instance
private CalibrateOD	calibBKUP Backup copy of the initial CalibrateOD instance that can be used for restoring the calibration.
private boolean	calibChangedFlag The calibration peak table changed
private boolean	calibHistFlag The histogram is a calibration histogram
private java.awt.Color	calibPeakColor calibration peaks on histogram color
private int	cHeight working canvas height
private int	cWidth working canvas width
private boolean	drawIntoImageFlag set if draw plot to GIF file
private java.awt.Panel	editPanel Array of TextFields used in constructing the editable Peak Calibration Table.
private static Flicker	flk link to global Flicker instance
private java.lang.String	fontFamily Font family
(package private) java.awt.Dimension	frameSize size of frame
private boolean	getPeaksByMeasFlag Get the peaks from the circular mask measurement spot list using the mean circle measurement grayscale values not corrected for background (since we do not know what background is).
private int[]	hist freq hist[0:nHist-1].
private java.awt.Color	histColor
private int	histMode The histogram mode is either: MODE_CW_ROI_HIST, MODE_CALIB_ND_ROI_HIST, or MODE_CALIB_SPOTLIST_HIST
private java.awt.Color	histTopColor
private java.lang.String	horizCaption horizontal caption
private ImageData	iData link to data related ImageData instance
private java.lang.String	imageFile current image file name
boolean	isVisibleFlag If the Histogram is visible
private java.awt.Color	labelColor
private java.awt.Font	largeFont medium font used for labeling
private java.awt.Color	lightWhite
(package private) static int	MAX_GRAY # gray values in a pixel
(package private) static int	MAX_ND_STEPS default # of peak wedge calibration table steps
(package private) static int	MAXBINS # of histogram into bins
private java.awt.Font	mediumFont medium font used for labeling
(package private) static int	MODE_CALIB_ND_ROI_HIST Draw histogram mode - draw calibration ND wedge histogram based on ND ROI region.
(package private) static int	MODE_CALIB_SPOTLIST_HIST Draw histogram mode - draw calibration histogram based on spot list data.
(package private) static int	MODE_CW_ROI_HIST Draw histogram mode - draw CW ROI histogram
(package private) static int	N_PCT_PROLOGUE default # of initial rows in the peak wedge calibration table
private java.awt.Color	odColor
private java.lang.String	oGifFileName full Gif file path name
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
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
(package private) java.lang.String	r1 extra sample data
(package private) java.lang.String	r2 extra sample data
(package private) java.lang.String	r3 extra sample data
(package private) static int	ROI_POPUP_HEIGHT default frame size height of popup
(package private) static int	ROI_POPUP_WIDTH default frame size width of popup
private int[]	sHist modified freq sHist[0:nHist-1].
private java.awt.Font	smallFont small font used for labeling
private java.awt.Label	statusLabel status Label
private java.awt.Color	textInputColor
private java.lang.String	title current canvas title
private static Util	util link to global CalibrateOD instance
private java.lang.String	vertCaption vertical caption
private static int[]	xPainted active hit coordinates
private static int[]	yPainted active y hit coordinates

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

DrawHistogram(Flicker flk, java.lang.String title, java.lang.String horizCaption, java.lang.String vertCaption, int histMode)
DrawHistogram() - create a histogram plot for left or right selected image.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle Control panel button clicks
private void	buildHistGUI() buildHistGUI() - build the histogram GUI
void	close() close() - close this popup and reset flags if needed [TODO] If they edited the calibration and peak calibration table, and they did not save the calibration (i.e.
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[].
private static void	drawPlus(java.awt.Graphics g, int x, int y, java.awt.Color color) drawPlus() - draw plus sign at the specified color.
boolean	genPeaksFromMeasSpotList() genPeaksFromMeasSpotList() - get the peak list from the circular mask measurement spot list using the mean circle measurement grayscale values.
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the minimum preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - getPreferredSize, needed for sizing frame correctly.
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 mapGrayToOD[] from the peak table
boolean	refreshPeakTable(boolean updateMapFlag) refreshPeakTable() - refresh the peak table from the TextFields...
void	setExtraInfo(java.lang.String r1, java.lang.String r2, java.lang.String r3) setExtraInfo() - set the extra info fields (r1,r2,f3)
void	setHorizCaption(java.lang.String horizCaption) setHorizCaption() - set the horizontal caption
void	setStatusMsg(java.lang.String msg) setStatusMsg() - set the status msg
void	setStatusMsg(java.lang.String msg, java.awt.Color color) setStatusMsg() - set the status msg
void	setTitleHist(java.lang.String title) setTitleHist() - set the title
void	setVertCaption(java.lang.String vertCaption) setVertCaption() - set the vertical caption
void	setVisible(boolean isVisibleFlag, boolean redoROIhistFlag) setVisible() - set the histogram as visible or not
void	updateHistogramPlot(boolean redoROIhistFlag) updateHistogramPlot() - set hist state and do repaint to draw it.
private void	updatePeakCalTable() updatePeakCalTable() - update the peak calibration table with new data from the calib od and gray value arrays.
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 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, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, 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

MAX_GRAY

static final int MAX_GRAY

# gray values in a pixel

See Also:

Constant Field Values

MAXBINS

static final int MAXBINS

# of histogram into bins

See Also:

Constant Field Values

MODE_CW_ROI_HIST

static final int MODE_CW_ROI_HIST

Draw histogram mode - draw CW ROI histogram

See Also:

Constant Field Values

MODE_CALIB_ND_ROI_HIST

static final int MODE_CALIB_ND_ROI_HIST

Draw histogram mode - draw calibration ND wedge histogram based on ND ROI region.

See Also:

Constant Field Values

MODE_CALIB_SPOTLIST_HIST

static final int MODE_CALIB_SPOTLIST_HIST

Draw histogram mode - draw calibration histogram based on spot list data.

See Also:

Constant Field Values

ROI_POPUP_WIDTH

static final int ROI_POPUP_WIDTH

default frame size width of popup

See Also:

Constant Field Values

ROI_POPUP_HEIGHT

static final int ROI_POPUP_HEIGHT

default frame size height of popup

See Also:

Constant Field Values

CAL_POPUP_WIDTH

static final int CAL_POPUP_WIDTH

default frame size width of popup

See Also:

Constant Field Values

CAL_POPUP_HEIGHT

static final int CAL_POPUP_HEIGHT

default frame size height of popup

See Also:

Constant Field Values

N_PCT_PROLOGUE

static final int N_PCT_PROLOGUE

default # of initial rows in the peak wedge calibration table

See Also:

Constant Field Values

MAX_ND_STEPS

static final int MAX_ND_STEPS

default # of peak wedge calibration table steps

See Also:

Constant Field Values

PEAK_CAL_TBL_ROWS

static final int PEAK_CAL_TBL_ROWS

default # of editPanel rows

See Also:

Constant Field Values

PEAK_CAL_TBL_COLS

static final int PEAK_CAL_TBL_COLS

default # of editPanel cols

See Also:

Constant Field Values

flk

private static Flicker flk

link to global Flicker instance

util

private static Util util

link to global CalibrateOD instance

calib

private CalibrateOD calib

link to working data related CalibrateOD instance

calibBKUP

private CalibrateOD calibBKUP

Backup copy of the initial CalibrateOD instance that can be used for restoring the calibration.

iData

private ImageData iData

link to data related ImageData instance

imageFile

private java.lang.String imageFile

current image file name

activeImage

private java.lang.String activeImage

active image name is "left" or "right"

histMode

private int histMode

The histogram mode is either: MODE_CW_ROI_HIST, MODE_CALIB_ND_ROI_HIST, or MODE_CALIB_SPOTLIST_HIST

calibHistFlag

private boolean calibHistFlag

The histogram is a calibration histogram

calibChangedFlag

private boolean calibChangedFlag

The calibration peak table changed

getPeaksByMeasFlag

private boolean getPeaksByMeasFlag

Get the peaks from the circular mask measurement spot list using the mean circle measurement grayscale values not corrected for background (since we do not know what background is). Otherwise the ND step wedge histogram peak analysis is used.

frameSize

java.awt.Dimension frameSize

size of frame

cWidth

private int cWidth

working canvas width

cHeight

private int cHeight

working canvas height

oGifFileName

private java.lang.String oGifFileName

full Gif file path name

title

private java.lang.String title

current canvas title

vertCaption

private java.lang.String vertCaption

vertical caption

horizCaption

private java.lang.String horizCaption

horizontal caption

r1

java.lang.String r1

extra sample data

r2

java.lang.String r2

extra sample data

r3

java.lang.String r3

extra sample data

activeBin

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

smallFont

private java.awt.Font smallFont

small font used for labeling

mediumFont

private java.awt.Font mediumFont

medium font used for labeling

largeFont

private java.awt.Font largeFont

medium font used for labeling

fontFamily

private java.lang.String fontFamily

Font family

peakNbrFontSize

private int peakNbrFontSize

font size for peak number labels

lightWhite

private java.awt.Color lightWhite

optBkgrdColor

private java.awt.Color optBkgrdColor

textInputColor

private java.awt.Color textInputColor

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

editPanel

private java.awt.Panel editPanel

Array of TextFields used in constructing the editable Peak Calibration Table.

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:PEAK_CAL_TBL_ROWS-1][0:PEAK_CAL_TBL_COLS-1].

statusLabel

private java.awt.Label statusLabel

status Label

xPainted

private static int[] xPainted

active hit coordinates

yPainted

private static int[] yPainted

active y hit coordinates

isVisibleFlag

public boolean isVisibleFlag

If the Histogram is visible

Constructor Detail

DrawHistogram

public DrawHistogram(Flicker flk,
                     java.lang.String title,
                     java.lang.String horizCaption,
                     java.lang.String vertCaption,
                     int histMode)

DrawHistogram() - create a histogram plot for left or right selected image. If the image is not selected, it is not valid and the this.activeImage is set to null. The histogram data is in iData.hist[] and depends on the left or right image being selected. If calibHistFlag is set, then present a calibration histogram GUI.

Parameters:

flk - is the Flicker instance

title - is window title

horizCaption - is horizontal caption

vertCaption - is vertical caption (generally frequency)

histMode - is either MODE_CW_ROI_HIST, MODE_CALIB_ND_ROI_HIST, or MODE_CALIB_SPOTLIST_HIST

Method Detail

buildHistGUI

private void buildHistGUI()

buildHistGUI() - build the histogram GUI

getPreferredSize

public java.awt.Dimension getPreferredSize()

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

Overrides:

getPreferredSize in class java.awt.Container

Returns:

frame size

positionHistWindow

private void positionHistWindow()

positionHistWindow() - position histogram window on the screen

setStatusMsg

public void setStatusMsg(java.lang.String msg)

setStatusMsg() - set the status msg

Parameters:

msg - is the status window msg

setStatusMsg

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

setStatusMsg() - 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

setHorizCaption

public void setHorizCaption(java.lang.String horizCaption)

setHorizCaption() - set the horizontal caption

Parameters:

horizCaption - is horizontal caption

setVertCaption

public void setVertCaption(java.lang.String vertCaption)

setVertCaption() - set the vertical caption

Parameters:

vertCaption - is vertical caption (generally frequency)

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

setExtraInfo

public void setExtraInfo(java.lang.String r1,
                         java.lang.String r2,
                         java.lang.String r3)

setExtraInfo() - set the extra info fields (r1,r2,f3)

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the minimum preferred size

Overrides:

getMinimumSize in class java.awt.Container

Returns:

window size

updatePeakCalTable

private void updatePeakCalTable()

updatePeakCalTable() - update the peak calibration table with new data from the calib od and gray value arrays.

 Array of TextFields used in constructing the editable
 Peak Calibration Table.
 It is of size [0:PEAK_CAL_TBL_ROWS-1][0:PEAK_CAL_TBL_COLS-1].
 holding the N_PCT_PROLOGUE rows plus the MAX_ND_STEPS.
  -------------------------------------------------------------
  col #0             col #1      col #2     col #3
  -------------------------------------------------------------
 0  Calibration units ["optical density" / "Grayvalue" / "CPM", etc.]
 1  Wedge window      [ndcwx1 : ndcwx2, ndcwy1 : ndcwy2] - 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]
  -------------------------------------------------------------  

refreshPeakTable

public boolean refreshPeakTable(boolean updateMapFlag)

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

Parameters:

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

Returns:

true if succeed

reExtrapolateCalibration

private boolean reExtrapolateCalibration()

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

Returns:

true if the extrapolate succeeds

genPeaksFromMeasSpotList

public boolean genPeaksFromMeasSpotList()

genPeaksFromMeasSpotList() - get the peak list from the circular mask measurement spot list using the mean circle measurement grayscale values. These values are not corrected for background (since we do not know what background is).

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.

drawPlus

private static final void drawPlus(java.awt.Graphics g,
                                   int x,
                                   int y,
                                   java.awt.Color color)

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

Parameters:

g - is graphics context

x - is center of object

y - is center of object

color - is color to draw

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

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.

close

public void close()

close() - close this popup and reset flags if needed [TODO] If they edited the calibration and peak calibration table, and they did not save the calibration (i.e. calibChangedFlag is true), then ask them here and save it if they say yes. If not, then restore the previous calibration.

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()

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