Class Flicker

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by java.awt.Window
              extended by java.awt.Frame
                  extended by javax.swing.JFrame
                      extended by Flicker
All Implemented Interfaces:
java.awt.event.ComponentListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.lang.Runnable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class Flicker
extends javax.swing.JFrame
implements java.lang.Runnable, java.awt.image.ImageObserver, java.awt.event.WindowListener, java.awt.event.ComponentListener

See Also:
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
 boolean abortFlag
          set true if run into problems when exiting and do not want to write out the state as we may corrupt it.
 java.lang.String activeImage
          active image "left", "right", "both" === was both
 Affine aff
          Affine instance
 java.awt.Color alertColor
          Color to use for background of alert messages
 boolean allowXformFlag
          transforms are allowed
 java.lang.String[] args
           
static java.lang.String baseFlkServer
          Base URL of Flicker server containing documentation and resources
 BuildGUI bGui
          BuildGUI instance of user interface
 java.awt.Color bkgrdCircleColor
          Adjustable measurement circle color
 int bkgrdCircleRadius
          "background" circle radius.
 CalibrateOD cal
          Calibrate OD instance
static int CANVAS_INCR
          Canvas change increment size - empirically determined
static int CANVAS_SIZE
          canvas size used in all canvas image windows
 int canvasSize
          size for left and right image canvases.
 int[][] circleMask
          "measurement" circle mask of size nCirMask X nCirMask
 java.lang.String clickableCGIbaseURL1
           is clickable to get DB entry
 java.lang.String clickableCGIbaseURL1pix
           is clickable to get DB entry
 java.lang.String clickableCGIbaseURL2
           is clickable to get DB entry
 java.lang.String clickableCGIbaseURL2pix
           is clickable to get DB entry
 int colorMode
          method to use when filter RBG in ImageScroller
 boolean composeXformFlag
          Replace(Preserve) orig imgs w/ xforms
(package private) static boolean CONSOLE_FLAG
          Debugging flag - Always TRUE
 java.lang.String currentPRIbaseURL
          Base URL for currently selected PIR server for accessing spot data using the previously looked up SWISS-PROT ID.
 SliderState curState
          This is the working SliderState instance which will be either the "base-state" or the I1 or I2 instance.
(package private) static java.lang.String DATE
           
 boolean DBUG_NTSC_RGB2GRAY
          DEBUGGING convert color RGB image to grayscale using NTSC algor.
 boolean dbugFlag
          true if debug printout, set by GUI
 int DEF_CIRCLE_MASK_RADIUS
          The radius is used to determine the size of the circle mask circleMask[nCirMask][nCirMask].
static int DEFAULT_TARGET_SIZE
          NOTE: set to 512 to enable if do image resizing
 int defaultFlickerDelay
           default delay if not flickering
 boolean displayInfoFlag
          if TRUE then display enter/exit info
 boolean doingXformFlag
          doing the transform
 boolean doMeasureProtIDlookupAndPopupFlag
          Do spot measurement adding it to the spotList, protein lookup for that spot, and popup current access server Web page in one operation when the user clicks on a spot in an active image.
 java.lang.String[] efMnuName
          what appears in menu
 java.lang.String[] efName
          name of command
 int[] efNbr
          function number 1 to MAX_EXTERN_FCTS
 EventKbd ekb
          get kbd event handler
static java.lang.String EP97PAPER_FILE
          Popup HTML browser additional documentation for related to Flicker.
 boolean errorLoadingImageFlag
          set by ImageObserver imageUpdate()
 java.lang.String errStr
          error string if not ""
 EventMenu evMu
           
 EventScroller evs
          instance of event scroller handler
 FlkDemo fDemo
          FlkDemo database
static java.lang.String fileSeparator
          File separator
 boolean finished1
          flag that finished transform 1
 boolean finished2
          finished transform 2
 FileIO fio
          FileIO utilities
 boolean firstTimeThruFlag
          first time to load img at start up, need to fix bug in ImgMeasure
static java.lang.String FLICKER_HOME
          Popup HTML browser documentation for Flicker.
 boolean flickerFlag
          enable flickering, set by GUI also from if set
static java.lang.String FLK_BASE_URL
          Flicker server Base URL
 int flkCanvasSize
          size for flicker canvas which does not include scrollbars etc.
 ImageScroller flkIS
          (non-scrollable) image canvas for drawing flicker images.
 java.lang.String flkStateFile
          current Flicker .flk state file that lives in "DB/".
 FlkMap fm
          FlkMap database
static int FRAME_HEIGHT
          Frame height
static int FRAME_INCR
          Frame change increment size - empirically determined
static int FRAME_WIDTH
          Frame width
 int frameHeight
          main frame height
 int frameWidth
          main frame width
 FlkRecent fRecent
          FlkRecent database
 FlkUser fUser
          FlkUser database
 boolean GC_MEMORY_DBUG
          Enable pretty-printing GC Memory debugging
static java.lang.String GOOGLE_2D_SEARCH
          Popup HTML browser additional documentation for finding 2D gels on the Internet
 java.awt.Color guardRegionColor
          Adjustable guard region color
 ImageScroller i1IS
          scrollable image 1 scrollable image (left)
 ImageScroller i2IS
          scrollable image 2 scrollable image (right)
 ImageData iData1
          image 1 picture data associated with ImageScroller i1IS (left)
 ImageData iData2
          image 2 picture data associated with ImageScroller i2IS (right)
static java.lang.String IMAGE_FILE1
          default left image1 file
static java.lang.String IMAGE_FILE2
          default right image2 file
 java.lang.String imageFile1
          full path of image 1 (left) file or URL
 java.lang.String imageFile2
          full path of image 2 (right) file or URL
 java.awt.Font imageFont
          image font for overlay
 boolean imageLoadErrorFlag
          true if image loading error
 int imagesToProcess
          CountDown to determine if finished.
 ImageIO imgIO
          Flicker image I/O and conversion functions
private  java.awt.Point imgPos
          position of the image for flickering
 ImageXform imgXform
          current image transform if any
 Info info
          Info status region
static java.lang.String IPROCLASS
          Popup HTML browser additional documentation for finding 2D gels on \ the Internet
static java.lang.String IPROLINK
          Popup HTML browser additional documentation for finding 2D gels on \ the Internet
 boolean isClickableDBflag
          flag set if currently selected image is clickable
 boolean isSuspendedFlag
          Threads were suspended by stop()
 ImageXform ix
          image transform
 ImageXform ixf1
          image transform for image 1 if any
 ImageXform ixf2
          image transform for image 2 if any
 ImageScroller lastIS
          last selected image canvas - used in an operation and is selected by clicking on either throws left or right (I1 or I2) images.
 java.lang.String lastISName
          last IS that was clicked on
 java.awt.Color lastMsgColor
          save last message color state
 java.lang.String lastMsgStr
          save last message state
static int LINES_REPORT_STATUS
          # lines to compute before status report
 Landmark lms
          list of landmarks
 java.awt.Color lmsColor
          Adjustable landmark color
static int MAX_CANVAS_SIZE
          Maximum canvas size used in all canvas image windows
(package private) static int MAX_CIRCLE_RADIUS
          maximum circle mask radius.
static int MAX_EXTERN_FCTS
          maximum # of external Fcts (10 or 20 is nice)
static int MAX_KEEPALIVE_TIME
          5 min.
(package private) static int MAX_SPOTS
          Maximum # of spots that can be measured/gel image and saved in .spt file
static int MAX_TARGET_SIZE
          max target size if do initial image resizing
 int maxColsToPrint
          WinDump window size in pixels
 java.awt.Color measCircleColor
          Adjustable measurement circle color
 int measCircleRadius
          "measurement" circle radius.
static int MIN_CANVAS_SIZE
          Minimum canvas size used in all canvas image windows
(package private) static int MIN_CIRCLE_RADIUS
          maximum circle mask radius.
static int MIN_TARGET_SIZE
          min target size if do initial image resizing
 float minLSQcolinearity1
          for image 1 w.r.t landmarks
 float minLSQcolinearity2
          for image 2 w.r.t landmarks
 int nbrUniqueAFT
          set to # of unique non-colinear affine transform
 int nCirMask
          The radius determines the size of circle mask circleMask[nCirMask][nCirMask].
(package private) static boolean NEVER
          Debugging flag - Always FALSE
static int NORM_COLOR
          normal color mapping, no change
 int NOT_AVAIL_YET
          This is not available yet if it is set to -1, for DEBUGGING, set it to 0.
private  boolean notDoneFlag
          Set to kill the run loop
private  java.awt.Point objPos
          position of the object for flickering
static java.lang.String OLD_FLICKER_HOME
          Popup HTML browser additional documentation for related to Flicker.
static java.lang.String osName
          name of this operating system
 PluginMgr piMgr
          Plugin manager
 java.lang.String popupWindowName
          default name of popup window
static java.lang.String POSTER_FILE1
          Popup HTML browser additional documentation for related to Flicker.
static java.lang.String POSTER_FILE2
          Popup HTML browser additional documentation for related to Flicker.
static java.lang.String POSTER_FILE3
          Popup HTML browser additional documentation for related to Flicker.
static java.lang.String POSTER_FILE4
          Popup HTML browser additional documentation for related to Flicker.
 boolean prevFlickerFlag
          previous state of flickerFlag saved when start ain ImageXform
static int PSEUDO_COLOR
          Pseudo color hsv2rgb mapping
static java.lang.String QUICK_START
          Popup HTML browser documentation for Flicker.
 boolean readyFlag
          finished reading images.
static java.lang.String REF_MAN_ADDUSERIMAGES
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_CHECKBOX
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_KEYSTROKES
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_MENUS
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_MOUSE
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_PUTATIVESPOTID
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_SLIDERS
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_SPOTLISTS_ANNOTATE
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_SPOTLISTS_CREATE
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_TRANSFORMS
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MAN_UPDATING
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_MANUAL
          Popup HTML browser documentation for Flicker.
static java.lang.String REF_VERSION_NBR
          Popup HTML browser documentation for Flicker.
 boolean repaintLockFlag
          xForm sync
 boolean resizeFrameFlag
          allow dragging the frame to cause it to resize
static int RGB_TO_GRAY_COLOR
          RGB to gray color using .33*r+.5*g+.17*b
 java.awt.Color roiColor
           
 java.lang.Thread runT
          Flicker thread
 boolean saveOimagesWhenSaveStateflag
          Save oImgs when do a "Save(As) state" if they exist and allowXformFlag is enabled.
 int scrHeight
          min (FRAME_HEIGHT, screenHeight)
 int scrWidth
          min (FRAME_WIDTH, screenWidth)
 boolean showI1flag
          flag to indicate that I1 is being displayed in flkIS else I2 is being displayed.
 boolean spotsListModeFlag
          C-J Toggle between list-of-spots else trial-spot measurement mode.
 Spot spt
          Spot structures
 java.util.Date startupDate
           
 boolean stopAnnotationUpdateFlag
          Flag to stop spot list annotation lookup from proteomics Web server.
static java.lang.String SUN_JAI_LICENSE
          Popup HTML browser additional documentation for related to Flicker.
static java.lang.String SWISS_2DPAGE
          Popup HTML browser additional documentation for finding 2D gels on the Internet
 java.lang.String sWorking
          incremental loading message
 SpatialXform sxf
          poly warp spatial transform
(package private) static java.awt.Color targetColor
          adjustable cross-hairs color
 java.awt.Font textFont
          text font for messages
 float thrColinearity
          co-linearity threshold for testing LMS
(package private)  java.lang.String title
          Title of program
 TiffLoader tr
          Tiff image reader
 java.awt.Color trialObjColor
          Adjustable trial object color
static java.lang.String TWO_D_HUNT
          Popup HTML browser additional documentation for finding 2D gels on the Internet
static java.lang.String UNIPROT
          Popup HTML browser additional documentation for finding 2D gels on \ the Internet
 boolean USE_AWT_ZOOM
          Enable using AWT implemented zoom only does positive integer zoom
 boolean USE_DE_ZOOM
          Enable using de_zoom transform over 1/N to NX zoom (-N to +N)
 boolean USE_GANG_BC
          DEBUGGING Enable using "View Gang Brightness/Contrast"
 boolean USE_GUARD
          Enable guard region in the menu
 boolean USE_PLUGINS
          Enable plugins in the menu
 boolean useDemoLeukemiaCalPreFlag
          Use demo leukemia gels ND wedge calibration preloads.
 boolean useGuardRegionImageFlag
           
 boolean useLogInputFlag
          "Use log of pixels if > 8-bits grayscale image"
 boolean useMeasCtrFlag
          "Use measurement counters" in measurements
 boolean useNTSCrgbTograyCvtFlag
          use NTSC RGB to grayscale when read in color image when generate the iData.iPix[] pixel array.
 boolean usePIRiProClassServerFlag
          Enable access to the PIR iProClass server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.
 boolean usePIRiProLinkFlag
          Enable access to the PIR iProLink server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.
 boolean usePIRUniprotServerFlag
          Enable access to the PIR UniProt server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.
 boolean useProteinDBbrowserFlag
          Use protein DB browser, else lookup ID and name on active images.
static java.lang.String userCalDir
          User calibration "cal/" directory used for saving .cal files
 boolean userClickableImageDBflag
          User enabled image as clickable DB checkbox to get DB entry
static java.lang.String userDir
          User directory
static java.lang.String userSptDir
          User spot data "spt/" directory used for saving .spt files
static java.lang.String userTmpDir
          User temporary "tmp/" directory used for misc.
 boolean useSwiss2DpageServerFlag
          Enable access to the Swiss-2DPAGE server for accessing spot data.
 boolean useThresholdInsideFlag
          Use threshold inside/outside filter [t1:t2] else outside of [t1:t2]
 boolean useTotDensityFlag
          "Use sum density else mean" in measurements
 Util util
          misc utility methods
 boolean validAffineFlag
          set when do valid affine xform
(package private) static java.lang.String VERSION
          Compiled Version constant for use in version comparison etc.
 boolean viewBoundaryFlag
          view boundary overlay
 boolean viewDispGrayValuesFlag
          view display image RGB as gray values
 boolean viewDrawSpotAnnIdFlag
          view measurement annotation as 'spot nbr' overlay
 boolean viewDrawSpotAnnNbrFlag
          view measurement annotation as 'spot nbr' overlay
 boolean viewDrawSpotLocCircleFlag
          view measurement location as 'circle'{annotation} overlay
 boolean viewDrawSpotLocPlusFlag
          view measurement location as '+'{annotation} overlay
 boolean viewGangBCFlag
          gang brightnessContrast both images
 boolean viewGangScrollFlag
          gang scroll both images
 boolean viewGangZoomFlag
          gang zoom both images
 boolean viewLMSflag
          view landmarks overlay
 boolean viewMeasCircleFlag
          view measurement circle overlay
 boolean viewMultPopups
          view multiple popups
 boolean viewNormalizedColorFlag
          view normalized color
 boolean viewPseudoColorFlag
          view pseudo color display
 boolean viewReportPopupFlag
          view Report popup window
 boolean viewRGB2GrayFlag
          RGB to gray color .33*r+.5*g+.17*b image display
 boolean viewRoiFlag
          view ROI overlay
 boolean viewTargetFlag
          view target overlay
 boolean viewTrialObjFlag
          view trial objects overlay
static java.lang.String VIGNETTES
          Popup HTML browser documentation for Flicker.
static java.lang.String WALKER_BOOK_CHAPTER_2005
          Popup HTML browser additional documentation for related to Flicker.
 Windump windmp
          Window digital data dump
 int winDumpRadix
          WinDump data printing radix
static java.lang.String WORLD_2DPAGE
          Popup HTML browser additional documentation for finding 2D gels on the Internet
 java.lang.String xformName
          current transform
 int xformThreadCtr
          test and set thread counter.
 
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 java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE
 
Constructor Summary
Flicker()
          Flicker() - constructor for Class Flicker
 
Method Summary
 boolean changeCanvasSize(java.lang.String cmd)
          changeCanvasSize() - change the canvas size by the specified + or - increment command.
 boolean checkIfSaveFlkFile()
          checkIfSaveFlkFile() - test if need to save the .flk file If so, ask them if they want to do it.
 void chkDoneWithTransform()
          chkDoneWithTransform() - called by run() thread when xform completed and the xformThreadCtr was incremented by softDoneWithTransform().
 boolean chkIfClickableDB(boolean showMsgFlag)
          chkIfClickableDB() - check if currently selected image is a clickable active map data base in that it has a valid url.
 void componentHidden(java.awt.event.ComponentEvent componentEvent)
           
 void componentMoved(java.awt.event.ComponentEvent componentEvent)
           
 void componentResized(java.awt.event.ComponentEvent componentEvent)
          componentResized() - resize canvases to proper sizes when frame is resized.
 void componentShown(java.awt.event.ComponentEvent componentEvent)
           
 void doFullRepaint()
          doFullRepaint() - repaint flkIS, i1IS, i2IS and their canvases as well as flk.repaint().
 void finalize()
          finalize() - total stop and kill Flicker threads.Write out the "Flicker.properties" file to save user preferences.
 void init(java.lang.String[] args)
          init() - init Flicker state variables.
private  void initialImageLoad()
          initialImageLoad() - load the initial images when first enter run().
private  void initState(java.lang.String[] args)
          initState() - init Flicker state variables.
(package private)  ImageData lookupCurrentImageData()
          lookupCurrentImageData() - lookup the current active ImageData if it is left or right
(package private)  ImageScroller lookupCurrentImageScroller()
          lookupCurrentImageScroller() - lookup the current active ImageData if it is left or right
static void main(java.lang.String[] args)
          main() - for Flicker application CMD LINE: java Flicker [image1] [image2]
 void paintComponent(java.awt.Graphics g)
          paintComponent() - paint Flicker
 void reInitStateVars()
          reInitStateVars() - reinitialize the state variables
 void resetDefaultView()
          resetDefaultView() - Reset default state of views, colors, etc.
 void run()
          run() - Flicker method to run threads and perform timing dependent operators.
 boolean setCanvasAndFrameSize(int newCanvasSize, int newFrameWidth, int newFrameHeight)
          setCanvasAndFrameSize() - change the canvas and frame sizes
 void start()
          start() - start new Flicker threads
 void stop()
          stop() - stop or suspend Flicker threads
 void testAndSetThreadCounter()
          testAndSetThreadCounter() - safe test and set of thread counter
 void updateFlickerImage()
          updateFlickerImage() - update the flicker image.
 void windowActivated(java.awt.event.WindowEvent windowEvent)
           
 void windowClosed(java.awt.event.WindowEvent windowEvent)
           
 void windowClosing(java.awt.event.WindowEvent windowEvent)
           
 void windowDeactivated(java.awt.event.WindowEvent windowEvent)
           
 void windowDeiconified(java.awt.event.WindowEvent windowEvent)
           
 void windowIconified(java.awt.event.WindowEvent windowEvent)
           
 void windowOpened(java.awt.event.WindowEvent windowEvent)
           
 
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, 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, getPreferredSize, 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.image.ImageObserver
imageUpdate
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Field Detail

VERSION

static final java.lang.String VERSION
Compiled Version constant for use in version comparison etc.

See Also:
Constant Field Values

DATE

static final java.lang.String DATE
See Also:
Constant Field Values

CONSOLE_FLAG

static boolean CONSOLE_FLAG
Debugging flag - Always TRUE


NEVER

static boolean NEVER
Debugging flag - Always FALSE


NOT_AVAIL_YET

public int NOT_AVAIL_YET
This is not available yet if it is set to -1, for DEBUGGING, set it to 0. It is used in both the menu generation and the messages for unimplemented code.


USE_GUARD

public final boolean USE_GUARD
Enable guard region in the menu

See Also:
Constant Field Values

USE_PLUGINS

public final boolean USE_PLUGINS
Enable plugins in the menu

See Also:
Constant Field Values

USE_GANG_BC

public final boolean USE_GANG_BC
DEBUGGING Enable using "View Gang Brightness/Contrast"

See Also:
Constant Field Values

DBUG_NTSC_RGB2GRAY

public final boolean DBUG_NTSC_RGB2GRAY
DEBUGGING convert color RGB image to grayscale using NTSC algor.

See Also:
Constant Field Values

USE_AWT_ZOOM

public final boolean USE_AWT_ZOOM
Enable using AWT implemented zoom only does positive integer zoom

See Also:
Constant Field Values

USE_DE_ZOOM

public final boolean USE_DE_ZOOM
Enable using de_zoom transform over 1/N to NX zoom (-N to +N)

See Also:
Constant Field Values

GC_MEMORY_DBUG

public final boolean GC_MEMORY_DBUG
Enable pretty-printing GC Memory debugging

See Also:
Constant Field Values

osName

public static java.lang.String osName
name of this operating system


fileSeparator

public static java.lang.String fileSeparator
File separator


userDir

public static java.lang.String userDir
User directory


userTmpDir

public static java.lang.String userTmpDir
User temporary "tmp/" directory used for misc. output and SaveAs files.


userCalDir

public static java.lang.String userCalDir
User calibration "cal/" directory used for saving .cal files


userSptDir

public static java.lang.String userSptDir
User spot data "spt/" directory used for saving .spt files


FLK_BASE_URL

public static final java.lang.String FLK_BASE_URL
Flicker server Base URL

See Also:
Constant Field Values

baseFlkServer

public static java.lang.String baseFlkServer
Base URL of Flicker server containing documentation and resources


FLICKER_HOME

public static final java.lang.String FLICKER_HOME
Popup HTML browser documentation for Flicker.


QUICK_START

public static final java.lang.String QUICK_START
Popup HTML browser documentation for Flicker.


REF_MANUAL

public static final java.lang.String REF_MANUAL
Popup HTML browser documentation for Flicker.


REF_MAN_KEYSTROKES

public static final java.lang.String REF_MAN_KEYSTROKES
Popup HTML browser documentation for Flicker.


REF_MAN_MOUSE

public static final java.lang.String REF_MAN_MOUSE
Popup HTML browser documentation for Flicker.


REF_MAN_SLIDERS

public static final java.lang.String REF_MAN_SLIDERS
Popup HTML browser documentation for Flicker.


REF_MAN_CHECKBOX

public static final java.lang.String REF_MAN_CHECKBOX
Popup HTML browser documentation for Flicker.


REF_MAN_MENUS

public static final java.lang.String REF_MAN_MENUS
Popup HTML browser documentation for Flicker.


REF_MAN_TRANSFORMS

public static final java.lang.String REF_MAN_TRANSFORMS
Popup HTML browser documentation for Flicker.


REF_MAN_SPOTLISTS_CREATE

public static final java.lang.String REF_MAN_SPOTLISTS_CREATE
Popup HTML browser documentation for Flicker.


REF_MAN_SPOTLISTS_ANNOTATE

public static final java.lang.String REF_MAN_SPOTLISTS_ANNOTATE
Popup HTML browser documentation for Flicker.


REF_MAN_PUTATIVESPOTID

public static final java.lang.String REF_MAN_PUTATIVESPOTID
Popup HTML browser documentation for Flicker.


REF_MAN_UPDATING

public static final java.lang.String REF_MAN_UPDATING
Popup HTML browser documentation for Flicker.


REF_MAN_ADDUSERIMAGES

public static final java.lang.String REF_MAN_ADDUSERIMAGES
Popup HTML browser documentation for Flicker.


REF_VERSION_NBR

public static final java.lang.String REF_VERSION_NBR
Popup HTML browser documentation for Flicker.


VIGNETTES

public static final java.lang.String VIGNETTES
Popup HTML browser documentation for Flicker.


WALKER_BOOK_CHAPTER_2005

public static final java.lang.String WALKER_BOOK_CHAPTER_2005
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

OLD_FLICKER_HOME

public static final java.lang.String OLD_FLICKER_HOME
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

EP97PAPER_FILE

public static final java.lang.String EP97PAPER_FILE
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

POSTER_FILE1

public static final java.lang.String POSTER_FILE1
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

POSTER_FILE2

public static final java.lang.String POSTER_FILE2
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

POSTER_FILE3

public static final java.lang.String POSTER_FILE3
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

POSTER_FILE4

public static final java.lang.String POSTER_FILE4
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

SUN_JAI_LICENSE

public static final java.lang.String SUN_JAI_LICENSE
Popup HTML browser additional documentation for related to Flicker.

See Also:
Constant Field Values

SWISS_2DPAGE

public static final java.lang.String SWISS_2DPAGE
Popup HTML browser additional documentation for finding 2D gels on the Internet

See Also:
Constant Field Values

WORLD_2DPAGE

public static final java.lang.String WORLD_2DPAGE
Popup HTML browser additional documentation for finding 2D gels on the Internet

See Also:
Constant Field Values

TWO_D_HUNT

public static final java.lang.String TWO_D_HUNT
Popup HTML browser additional documentation for finding 2D gels on the Internet

See Also:
Constant Field Values

GOOGLE_2D_SEARCH

public static final java.lang.String GOOGLE_2D_SEARCH
Popup HTML browser additional documentation for finding 2D gels on the Internet

See Also:
Constant Field Values

UNIPROT

public static final java.lang.String UNIPROT
Popup HTML browser additional documentation for finding 2D gels on \ the Internet

See Also:
Constant Field Values

IPROCLASS

public static final java.lang.String IPROCLASS
Popup HTML browser additional documentation for finding 2D gels on \ the Internet

See Also:
Constant Field Values

IPROLINK

public static final java.lang.String IPROLINK
Popup HTML browser additional documentation for finding 2D gels on \ the Internet

See Also:
Constant Field Values

IMAGE_FILE1

public static java.lang.String IMAGE_FILE1
default left image1 file


IMAGE_FILE2

public static java.lang.String IMAGE_FILE2
default right image2 file


NORM_COLOR

public static final int NORM_COLOR
normal color mapping, no change

See Also:
Constant Field Values

PSEUDO_COLOR

public static final int PSEUDO_COLOR
Pseudo color hsv2rgb mapping

See Also:
Constant Field Values

RGB_TO_GRAY_COLOR

public static final int RGB_TO_GRAY_COLOR
RGB to gray color using .33*r+.5*g+.17*b

See Also:
Constant Field Values

LINES_REPORT_STATUS

public static final int LINES_REPORT_STATUS
# lines to compute before status report

See Also:
Constant Field Values

MAX_KEEPALIVE_TIME

public static final int MAX_KEEPALIVE_TIME
5 min. Max # seconds for keepalive

See Also:
Constant Field Values

CANVAS_SIZE

public static final int CANVAS_SIZE
canvas size used in all canvas image windows

See Also:
Constant Field Values

MIN_CANVAS_SIZE

public static int MIN_CANVAS_SIZE
Minimum canvas size used in all canvas image windows


MAX_CANVAS_SIZE

public static int MAX_CANVAS_SIZE
Maximum canvas size used in all canvas image windows


CANVAS_INCR

public static int CANVAS_INCR
Canvas change increment size - empirically determined


FRAME_HEIGHT

public static final int FRAME_HEIGHT
Frame height

See Also:
Constant Field Values

FRAME_WIDTH

public static final int FRAME_WIDTH
Frame width

See Also:
Constant Field Values

FRAME_INCR

public static int FRAME_INCR
Frame change increment size - empirically determined


DEFAULT_TARGET_SIZE

public static final int DEFAULT_TARGET_SIZE
NOTE: set to 512 to enable if do image resizing

See Also:
Constant Field Values

MIN_TARGET_SIZE

public static final int MIN_TARGET_SIZE
min target size if do initial image resizing

See Also:
Constant Field Values

MAX_TARGET_SIZE

public static final int MAX_TARGET_SIZE
max target size if do initial image resizing

See Also:
Constant Field Values

MAX_CIRCLE_RADIUS

static final int MAX_CIRCLE_RADIUS
maximum circle mask radius. filter is 2N+1, 7 is 15x15 15 is 31x31, 25 is 51x51.

See Also:
Constant Field Values

MIN_CIRCLE_RADIUS

static final int MIN_CIRCLE_RADIUS
maximum circle mask radius. A value of 0 is a single pixel

See Also:
Constant Field Values

DEF_CIRCLE_MASK_RADIUS

public int DEF_CIRCLE_MASK_RADIUS
The radius is used to determine the size of the circle mask circleMask[nCirMask][nCirMask]. The value nCirMask = (2*radius+1). So a radius of 5 is 11x11, etc. A radius= 0 is a single pixel.


MAX_SPOTS

static final int MAX_SPOTS
Maximum # of spots that can be measured/gel image and saved in .spt file

See Also:
Constant Field Values

aff

public Affine aff
Affine instance


bGui

public BuildGUI bGui
BuildGUI instance of user interface


cal

public CalibrateOD cal
Calibrate OD instance


ekb

public EventKbd ekb
get kbd event handler


evs

public EventScroller evs
instance of event scroller handler


evMu

public EventMenu evMu

fio

public FileIO fio
FileIO utilities


fDemo

public FlkDemo fDemo
FlkDemo database


fUser

public FlkUser fUser
FlkUser database


fm

public FlkMap fm
FlkMap database


fRecent

public FlkRecent fRecent
FlkRecent database


imgIO

public ImageIO imgIO
Flicker image I/O and conversion functions


ix

public ImageXform ix
image transform


info

public Info info
Info status region


lms

public Landmark lms
list of landmarks


piMgr

public PluginMgr piMgr
Plugin manager


sxf

public SpatialXform sxf
poly warp spatial transform


spt

public Spot spt
Spot structures


tr

public TiffLoader tr
Tiff image reader


util

public Util util
misc utility methods


windmp

public Windump windmp
Window digital data dump


lastIS

public ImageScroller lastIS
last selected image canvas - used in an operation and is selected by clicking on either throws left or right (I1 or I2) images.


flkIS

public ImageScroller flkIS
(non-scrollable) image canvas for drawing flicker images. When flickering, this will switch between containing data from iData1 and iData2 depending on the flicker state variable showI1flag that is toggled in the run() method.


i1IS

public ImageScroller i1IS
scrollable image 1 scrollable image (left)


i2IS

public ImageScroller i2IS
scrollable image 2 scrollable image (right)


iData1

public ImageData iData1
image 1 picture data associated with ImageScroller i1IS (left)


iData2

public ImageData iData2
image 2 picture data associated with ImageScroller i2IS (right)


imgXform

public ImageXform imgXform
current image transform if any


ixf1

public ImageXform ixf1
image transform for image 1 if any


ixf2

public ImageXform ixf2
image transform for image 2 if any


runT

public java.lang.Thread runT
Flicker thread


notDoneFlag

private boolean notDoneFlag
Set to kill the run loop


args

public java.lang.String[] args

flkStateFile

public java.lang.String flkStateFile
current Flicker .flk state file that lives in "DB/". This may be the initial startup file or may be the result of "Open state file" or "SaveAs state file".


lastISName

public java.lang.String lastISName
last IS that was clicked on


startupDate

public java.util.Date startupDate

title

java.lang.String title
Title of program


activeImage

public java.lang.String activeImage
active image "left", "right", "both" === was both


sWorking

public java.lang.String sWorking
incremental loading message


errStr

public java.lang.String errStr
error string if not ""


colorMode

public int colorMode
method to use when filter RBG in ImageScroller


alertColor

public java.awt.Color alertColor
Color to use for background of alert messages


lastMsgColor

public java.awt.Color lastMsgColor
save last message color state


lastMsgStr

public java.lang.String lastMsgStr
save last message state


popupWindowName

public java.lang.String popupWindowName
default name of popup window


imageFile1

public java.lang.String imageFile1
full path of image 1 (left) file or URL


imageFile2

public java.lang.String imageFile2
full path of image 2 (right) file or URL


xformName

public java.lang.String xformName
current transform


imageFont

public java.awt.Font imageFont
image font for overlay


textFont

public java.awt.Font textFont
text font for messages


showI1flag

public boolean showI1flag
flag to indicate that I1 is being displayed in flkIS else I2 is being displayed.


finished1

public boolean finished1
flag that finished transform 1


finished2

public boolean finished2
finished transform 2


xformThreadCtr

public int xformThreadCtr
test and set thread counter. Increment when transform completes of it aborts. It is tested in the run() loop and cleared by testAndSetThreadCounter().


validAffineFlag

public boolean validAffineFlag
set when do valid affine xform


errorLoadingImageFlag

public boolean errorLoadingImageFlag
set by ImageObserver imageUpdate()


displayInfoFlag

public boolean displayInfoFlag
if TRUE then display enter/exit info


doingXformFlag

public boolean doingXformFlag
doing the transform


isSuspendedFlag

public boolean isSuspendedFlag
Threads were suspended by stop()


readyFlag

public boolean readyFlag
finished reading images.


imageLoadErrorFlag

public boolean imageLoadErrorFlag
true if image loading error


abortFlag

public boolean abortFlag
set true if run into problems when exiting and do not want to write out the state as we may corrupt it.


stopAnnotationUpdateFlag

public boolean stopAnnotationUpdateFlag
Flag to stop spot list annotation lookup from proteomics Web server. The flag is set by typing C-Q and tested in the lookup loop.


viewLMSflag

public boolean viewLMSflag
view landmarks overlay


viewTargetFlag

public boolean viewTargetFlag
view target overlay


viewTrialObjFlag

public boolean viewTrialObjFlag
view trial objects overlay


viewBoundaryFlag

public boolean viewBoundaryFlag
view boundary overlay


viewRoiFlag

public boolean viewRoiFlag
view ROI overlay


viewMeasCircleFlag

public boolean viewMeasCircleFlag
view measurement circle overlay


viewDrawSpotLocCircleFlag

public boolean viewDrawSpotLocCircleFlag
view measurement location as 'circle'{annotation} overlay


viewDrawSpotLocPlusFlag

public boolean viewDrawSpotLocPlusFlag
view measurement location as '+'{annotation} overlay


viewDrawSpotAnnNbrFlag

public boolean viewDrawSpotAnnNbrFlag
view measurement annotation as 'spot nbr' overlay


viewDrawSpotAnnIdFlag

public boolean viewDrawSpotAnnIdFlag
view measurement annotation as 'spot nbr' overlay


viewMultPopups

public boolean viewMultPopups
view multiple popups


viewGangScrollFlag

public boolean viewGangScrollFlag
gang scroll both images


viewGangZoomFlag

public boolean viewGangZoomFlag
gang zoom both images


viewGangBCFlag

public boolean viewGangBCFlag
gang brightnessContrast both images


viewDispGrayValuesFlag

public boolean viewDispGrayValuesFlag
view display image RGB as gray values


firstTimeThruFlag

public boolean firstTimeThruFlag
first time to load img at start up, need to fix bug in ImgMeasure


viewNormalizedColorFlag

public boolean viewNormalizedColorFlag
view normalized color


viewPseudoColorFlag

public boolean viewPseudoColorFlag
view pseudo color display


viewRGB2GrayFlag

public boolean viewRGB2GrayFlag
RGB to gray color .33*r+.5*g+.17*b image display


viewReportPopupFlag

public boolean viewReportPopupFlag
view Report popup window


useGuardRegionImageFlag

public boolean useGuardRegionImageFlag

useNTSCrgbTograyCvtFlag

public boolean useNTSCrgbTograyCvtFlag
use NTSC RGB to grayscale when read in color image when generate the iData.iPix[] pixel array.


doMeasureProtIDlookupAndPopupFlag

public boolean doMeasureProtIDlookupAndPopupFlag
Do spot measurement adding it to the spotList, protein lookup for that spot, and popup current access server Web page in one operation when the user clicks on a spot in an active image. The use must have enabled one of the (Edit | Select access to active DB server | ...) options. If doMeasureProtIDlookupAndPopupFlag is NOT set, the user must set the "Click to access DB" checkbox to have Flicker popup the browser.


useSwiss2DpageServerFlag

public boolean useSwiss2DpageServerFlag
Enable access to the Swiss-2DPAGE server for accessing spot data.


usePIRUniprotServerFlag

public boolean usePIRUniprotServerFlag
Enable access to the PIR UniProt server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.


usePIRiProClassServerFlag

public boolean usePIRiProClassServerFlag
Enable access to the PIR iProClass server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.


usePIRiProLinkFlag

public boolean usePIRiProLinkFlag
Enable access to the PIR iProLink server for accessing spot data using the previously looked up SWISS-PROT Accession Name Spot.id.


currentPRIbaseURL

public java.lang.String currentPRIbaseURL
Base URL for currently selected PIR server for accessing spot data using the previously looked up SWISS-PROT ID. It may be UNIPROT, IPROCLASS, or IPROLINK.


useDemoLeukemiaCalPreFlag

public boolean useDemoLeukemiaCalPreFlag
Use demo leukemia gels ND wedge calibration preloads. If this flag is set PRIOR to loading the demo Leukemia gels, It sets up the calibration (ROI, OD list) and then when you invoke (Quantify | Calibrate | Calibrate OD by step wedge) you get to practice editing the calibrating and then saving it. NOTE: this switch is NOT saved in the state since it would wipe out the calibration next time it is read.


useThresholdInsideFlag

public boolean useThresholdInsideFlag
Use threshold inside/outside filter [t1:t2] else outside of [t1:t2]


saveOimagesWhenSaveStateflag

public boolean saveOimagesWhenSaveStateflag
Save oImgs when do a "Save(As) state" if they exist and allowXformFlag is enabled.


useProteinDBbrowserFlag

public boolean useProteinDBbrowserFlag
Use protein DB browser, else lookup ID and name on active images. For now, use popup Swiss-2DPAGE browser, else parse the data from the web site.


userClickableImageDBflag

public boolean userClickableImageDBflag
User enabled image as clickable DB checkbox to get DB entry


allowXformFlag

public boolean allowXformFlag
transforms are allowed


composeXformFlag

public boolean composeXformFlag
Replace(Preserve) orig imgs w/ xforms


dbugFlag

public boolean dbugFlag
true if debug printout, set by GUI


prevFlickerFlag

public boolean prevFlickerFlag
previous state of flickerFlag saved when start ain ImageXform


flickerFlag

public boolean flickerFlag
enable flickering, set by GUI also from if set


clickableCGIbaseURL1

public java.lang.String clickableCGIbaseURL1
is clickable to get DB entry


clickableCGIbaseURL2

public java.lang.String clickableCGIbaseURL2
is clickable to get DB entry


clickableCGIbaseURL1pix

public java.lang.String clickableCGIbaseURL1pix
is clickable to get DB entry


clickableCGIbaseURL2pix

public java.lang.String clickableCGIbaseURL2pix
is clickable to get DB entry


isClickableDBflag

public boolean isClickableDBflag
flag set if currently selected image is clickable


curState

public SliderState curState
This is the working SliderState instance which will be either the "base-state" or the I1 or I2 instance.


defaultFlickerDelay

public int defaultFlickerDelay
default delay if not flickering


flkCanvasSize

public int flkCanvasSize
size for flicker canvas which does not include scrollbars etc. This is derived from canvasSize.


canvasSize

public int canvasSize
size for left and right image canvases. The flkCanvasSize is derived from this size.


frameWidth

public int frameWidth
main frame width


frameHeight

public int frameHeight
main frame height


scrWidth

public int scrWidth
min (FRAME_WIDTH, screenWidth)


scrHeight

public int scrHeight
min (FRAME_HEIGHT, screenHeight)


resizeFrameFlag

public boolean resizeFrameFlag
allow dragging the frame to cause it to resize


winDumpRadix

public int winDumpRadix
WinDump data printing radix


maxColsToPrint

public int maxColsToPrint
WinDump window size in pixels


useLogInputFlag

public boolean useLogInputFlag
"Use log of pixels if > 8-bits grayscale image"


useTotDensityFlag

public boolean useTotDensityFlag
"Use sum density else mean" in measurements


useMeasCtrFlag

public boolean useMeasCtrFlag
"Use measurement counters" in measurements


spotsListModeFlag

public boolean spotsListModeFlag
C-J Toggle between list-of-spots else trial-spot measurement mode. This will set the overlay view to the measured list of spots. If this is set, then (C-M) pushes spots into the iData.spotList[] and they can be displayed together on the screen as numbered circles or "+" with optional spot id annotation. If it is NOT set, then do NOT save spots in the spot list and treat C-M commands as trial measurements.


bkgrdCircleRadius

public int bkgrdCircleRadius
"background" circle radius. At the time the background measurement is made, it is set to be the current measCircleRadius size. It is only changed when the (C-B) command is used.


measCircleRadius

public int measCircleRadius
"measurement" circle radius. This is set to the value from the curState.measCircleRadius value.


circleMask

public int[][] circleMask
"measurement" circle mask of size nCirMask X nCirMask


nCirMask

public int nCirMask
The radius determines the size of circle mask circleMask[nCirMask][nCirMask]. The value nCirMask = (2*radius+1). So a radius of 5 is 11x11, etc. A radius= 0 is a single pixel.


imgPos

private java.awt.Point imgPos
position of the image for flickering


objPos

private java.awt.Point objPos
position of the object for flickering


imagesToProcess

public int imagesToProcess
CountDown to determine if finished. 1 or 2 transforms


nbrUniqueAFT

public int nbrUniqueAFT
set to # of unique non-colinear affine transform


thrColinearity

public float thrColinearity
co-linearity threshold for testing LMS


minLSQcolinearity1

public float minLSQcolinearity1
for image 1 w.r.t landmarks


minLSQcolinearity2

public float minLSQcolinearity2
for image 2 w.r.t landmarks


roiColor

public java.awt.Color roiColor

targetColor

static java.awt.Color targetColor
adjustable cross-hairs color


trialObjColor

public java.awt.Color trialObjColor
Adjustable trial object color


lmsColor

public java.awt.Color lmsColor
Adjustable landmark color


bkgrdCircleColor

public java.awt.Color bkgrdCircleColor
Adjustable measurement circle color


measCircleColor

public java.awt.Color measCircleColor
Adjustable measurement circle color


guardRegionColor

public java.awt.Color guardRegionColor
Adjustable guard region color


MAX_EXTERN_FCTS

public static final int MAX_EXTERN_FCTS
maximum # of external Fcts (10 or 20 is nice)

See Also:
Constant Field Values

efName

public java.lang.String[] efName
name of command


efMnuName

public java.lang.String[] efMnuName
what appears in menu


efNbr

public int[] efNbr
function number 1 to MAX_EXTERN_FCTS


repaintLockFlag

public boolean repaintLockFlag
xForm sync

Constructor Detail

Flicker

public Flicker()
Flicker() - constructor for Class Flicker

Method Detail

main

public static void main(java.lang.String[] args)
main() - for Flicker application CMD LINE: java Flicker [image1] [image2]

Parameters:
args - is the command line arg list

initState

private void initState(java.lang.String[] args)
initState() - init Flicker state variables.


resetDefaultView

public void resetDefaultView()
resetDefaultView() - Reset default state of views, colors, etc. We also have to change the menu checkboxes so they are synced as well.


reInitStateVars

public void reInitStateVars()
reInitStateVars() - reinitialize the state variables


init

public void init(java.lang.String[] args)
init() - init Flicker state variables.


start

public void start()
start() - start new Flicker threads


stop

public void stop()
stop() - stop or suspend Flicker threads


run

public void run()
run() - Flicker method to run threads and perform timing dependent operators. It first loads the images and then enters the thread based timing loop.

Specified by:
run in interface java.lang.Runnable

chkDoneWithTransform

public void chkDoneWithTransform()
chkDoneWithTransform() - called by run() thread when xform completed and the xformThreadCtr was incremented by softDoneWithTransform(). ImageXform operates on iData to either iData1 or iData2 and . At that point we can create an image from the output iData.oImg and repaint it. Note: If composeXformFlag is set, then if we were using the original image, it may have changed.

See Also:
ImageXform.softDoneWithTransform(ImageData, java.lang.String, java.lang.String)

checkIfSaveFlkFile

public boolean checkIfSaveFlkFile()
checkIfSaveFlkFile() - test if need to save the .flk file If so, ask them if they want to do it.

Returns:
true if no problems.

finalize

public void finalize()
finalize() - total stop and kill Flicker threads.Write out the "Flicker.properties" file to save user preferences. NOTE: add other termination stuff here...

Overrides:
finalize in class java.awt.Frame

initialImageLoad

private void initialImageLoad()
initialImageLoad() - load the initial images when first enter run(). [NOTE] This code has a bug if the initial input images can not be found and loadBlankImageData() is called. loadBlankImageData() does not work.


changeCanvasSize

public boolean changeCanvasSize(java.lang.String cmd)
changeCanvasSize() - change the canvas size by the specified + or - increment command. If no increment command is used, then just resize it to the current setting.

Returns:
true if resize it.

setCanvasAndFrameSize

public boolean setCanvasAndFrameSize(int newCanvasSize,
                                     int newFrameWidth,
                                     int newFrameHeight)
setCanvasAndFrameSize() - change the canvas and frame sizes

Parameters:
newCanvasSize -
newFramWidth -
newFrameHeight -
Returns:
true if resize it.

doFullRepaint

public void doFullRepaint()
doFullRepaint() - repaint flkIS, i1IS, i2IS and their canvases as well as flk.repaint().


updateFlickerImage

public void updateFlickerImage()
updateFlickerImage() - update the flicker image. Show iData1.?Img else iData2.?Img in the flkIS canvas where ?Img is either bcImg, zImg, oImg or iImg in that order depending on the transform, zoom, and B-C status.


testAndSetThreadCounter

public void testAndSetThreadCounter()
testAndSetThreadCounter() - safe test and set of thread counter


chkIfClickableDB

public boolean chkIfClickableDB(boolean showMsgFlag)
chkIfClickableDB() - check if currently selected image is a clickable active map data base in that it has a valid url. Then set the isClickableDBflag. Also enable/disable the "Clickable DB" checkbox depending on whether the data exists.

Parameters:
showMsgFlag - to also report a message if true
Returns:
true if clickable

lookupCurrentImageScroller

ImageScroller lookupCurrentImageScroller()
lookupCurrentImageScroller() - lookup the current active ImageData if it is left or right

Returns:
either flk.iData1 or flk.iData2, else null if not selected.

lookupCurrentImageData

ImageData lookupCurrentImageData()
lookupCurrentImageData() - lookup the current active ImageData if it is left or right

Returns:
either flk.iData1 or flk.iData2, else null if not selected.

paintComponent

public void paintComponent(java.awt.Graphics g)
paintComponent() - paint Flicker

Parameters:
g - is graphics context

windowClosing

public void windowClosing(java.awt.event.WindowEvent windowEvent)
Specified by:
windowClosing in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent windowEvent)
Specified by:
windowClosed in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent windowEvent)
Specified by:
windowActivated in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent windowEvent)
Specified by:
windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent windowEvent)
Specified by:
windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent windowEvent)
Specified by:
windowIconified in interface java.awt.event.WindowListener

windowOpened

public void windowOpened(java.awt.event.WindowEvent windowEvent)
Specified by:
windowOpened in interface java.awt.event.WindowListener

componentHidden

public void componentHidden(java.awt.event.ComponentEvent componentEvent)
Specified by:
componentHidden in interface java.awt.event.ComponentListener

componentMoved

public void componentMoved(java.awt.event.ComponentEvent componentEvent)
Specified by:
componentMoved in interface java.awt.event.ComponentListener

componentShown

public void componentShown(java.awt.event.ComponentEvent componentEvent)
Specified by:
componentShown in interface java.awt.event.ComponentListener

componentResized

public void componentResized(java.awt.event.ComponentEvent componentEvent)
componentResized() - resize canvases to proper sizes when frame is resized. [TODO]:

Specified by:
componentResized in interface java.awt.event.ComponentListener
Parameters:
componentEvent - event