Serialized Form

Package <Unnamed>

Class BuildGUI extends javax.swing.JFrame implements Serializable

serialVersionUID: 0L

Serialized Fields

flk

Flicker flk

Flicker instance

util

Util util

Util instance

title

java.lang.String title

title for frame

mbar

java.awt.MenuBar mbar

menu bar

pdq

PopupDialogQuery pdq

generic popup dialog

pra

ShowReportPopup pra

generic popup report

pImages

javax.swing.JPanel pImages

+++++++ Gui stuff +++++++

selectedComponent

java.awt.Component selectedComponent

from Mouse Adapters

fileMenu

java.awt.Menu fileMenu

"File" pull down Menu list

editMenu

java.awt.Menu editMenu

"Edit" pull down Menu list

viewMenu

java.awt.Menu viewMenu

"View" pull down Menu list

lmsMenu

java.awt.Menu lmsMenu

"Landmark" pull down Menu list

xformMenu

java.awt.Menu xformMenu

"Transform" pull down Menu list

quantMenu

java.awt.Menu quantMenu

"Quantify" pull down Menu list

pluginMenu

java.awt.Menu pluginMenu

"Plugins" pull down Menu list

helpMenu

java.awt.Menu helpMenu

"Help" pull down Menu list

fDemoMenuStub

java.awt.Menu fDemoMenuStub

last fDemo menu tree stub for use if rebuild it

fMapMenuStub

java.awt.Menu fMapMenuStub

last fMap menu tree stub for use if rebuild it

fRecentMenuStub

java.awt.Menu fRecentMenuStub

last fRecent menu tree stub for use if rebuild it

fUserMenuStub

java.awt.Menu fUserMenuStub

last fUser menu tree stub for use if rebuild it

sUserPairTreeMnu

java.awt.Menu sUserPairTreeMnu

Add directories for paired user images tree

sUserSingleTreeMnu

java.awt.Menu sUserSingleTreeMnu

Add directories for single user images tree

mi_flickerCB

java.awt.CheckboxMenuItem mi_flickerCB

View menu checkbox item linked with flickerCheckbox

mi_ViewLmsCB

java.awt.CheckboxMenuItem mi_ViewLmsCB

View landmarks menu item checkbox

mi_ViewTargetCB

java.awt.CheckboxMenuItem mi_ViewTargetCB

View target menu item checkbox

mi_ViewTrialObjCB

java.awt.CheckboxMenuItem mi_ViewTrialObjCB

View trial object menu item checkbox

mi_ViewBoundaryCB

java.awt.CheckboxMenuItem mi_ViewBoundaryCB

View boundaries menu item checkbox

mi_ViewRoiCB

java.awt.CheckboxMenuItem mi_ViewRoiCB

View ROI rectangle menu item checkbox

mi_ViewMeasCircleCB

java.awt.CheckboxMenuItem mi_ViewMeasCircleCB

View measurement circles menu item checkbox

mi_ViewLastMeasSpotAsCircleCB

java.awt.CheckboxMenuItem mi_ViewLastMeasSpotAsCircleCB

[FUTURE] View last measured spot location as "circle"{ann} menu item checkbox

mi_ViewLastMeasSpotAsPlusCB

java.awt.CheckboxMenuItem mi_ViewLastMeasSpotAsPlusCB

View last measured spot location as "+"{ann} menu item checkbox

mi_ViewMeasSpotLocAsCircleCB

java.awt.CheckboxMenuItem mi_ViewMeasSpotLocAsCircleCB

View measured spot location as "circle"{ann} menu item checkbox. Radio button with mi_ViewMeasSpotLocAsPlusCB

mi_ViewMeasSpotLocAsPlusCB

java.awt.CheckboxMenuItem mi_ViewMeasSpotLocAsPlusCB

View measured spot location as "+"{ann} menu item checkbox. Radio button with mi_ViewMeasSpotLocAsCircleCB

mi_ViewAnnSpotNbrCB

java.awt.CheckboxMenuItem mi_ViewAnnSpotNbrCB

View measured spot annotation {ann} as "spot.nbr" menu item checkbox

mi_ViewAnnSpotIdCB

java.awt.CheckboxMenuItem mi_ViewAnnSpotIdCB

View measured spot annotation {ann} as "spot.id" menu item checkbox

mi_MultPopupsCB

java.awt.CheckboxMenuItem mi_MultPopupsCB

View multiple browser popups menu item checkbox

mi_GangScrollImgsCB

java.awt.CheckboxMenuItem mi_GangScrollImgsCB

View gang scrolling menu item checkbox

mi_GangZoomImgsCB

java.awt.CheckboxMenuItem mi_GangZoomImgsCB

View gang scrolling menu item checkbox

mi_GangBCImgsCB

java.awt.CheckboxMenuItem mi_GangBCImgsCB

View gang brightness/contrast menu item checkbox

mi_useGuardImgsCB

java.awt.CheckboxMenuItem mi_useGuardImgsCB

mi_DispGrayValsCB

java.awt.CheckboxMenuItem mi_DispGrayValsCB

View display gray level in image title menu item checkbox

mi_showReportPopupCB

java.awt.CheckboxMenuItem mi_showReportPopupCB

View Report Popup item checkbox

mi_useNTSCrgbTograyCvtCB

java.awt.CheckboxMenuItem mi_useNTSCrgbTograyCvtCB

Convert RGB image to grayscale using NTSC transform if needed checkbox.

mi_autoMeasProtLookupPopupCB

java.awt.CheckboxMenuItem mi_autoMeasProtLookupPopupCB

Auto measure, protein lookup in active server and Web page popup

mi_useSwiss2DpageServerCB

java.awt.CheckboxMenuItem mi_useSwiss2DpageServerCB

Use Swiss-2DPAGE DB (SWISS-2DPAGE) access checkbox.

mi_usePIRUniprotServerCB

java.awt.CheckboxMenuItem mi_usePIRUniprotServerCB

Use PIR UniProt DB (UNIPROT) access checkbox.

mi_usePIRiProClassServerCB

java.awt.CheckboxMenuItem mi_usePIRiProClassServerCB

Use PIR iProClass DB (IPROCLASS) access checkbox.

mi_usePIRiProLinkServerCB

java.awt.CheckboxMenuItem mi_usePIRiProLinkServerCB

Use PIR uProLink DB (IPROLINK) access checkbox.

mi_dbugCB

java.awt.CheckboxMenuItem mi_dbugCB

View DEBUGGING menu item checkbox

mi_Quant_UseLeukemiaDemoCalibCB

java.awt.CheckboxMenuItem mi_Quant_UseLeukemiaDemoCalibCB

Use demo leukemia gels ND wedge calibration preloads item checkbox

mi_QuantTotDensityCB

java.awt.CheckboxMenuItem mi_QuantTotDensityCB

Quant menu to compute total integrated density for spot else the mean item checkbox

mi_QuantSpotListModeCB

java.awt.CheckboxMenuItem mi_QuantSpotListModeCB

mi_MeasCtrCB

java.awt.CheckboxMenuItem mi_MeasCtrCB

Use measurement counters checkbox

mi_thresholdInsideCB

java.awt.CheckboxMenuItem mi_thresholdInsideCB

Quant threshold Inside menu item checkbox

mi_WinDmpSize5x5CB

java.awt.CheckboxMenuItem mi_WinDmpSize5x5CB

Quant menu WinDmp size 5x5 checkbox

mi_WinDmpSize10x10CB

java.awt.CheckboxMenuItem mi_WinDmpSize10x10CB

Quant menu WinDmp size 10x10 checkbox

mi_WinDmpSize15x15CB

java.awt.CheckboxMenuItem mi_WinDmpSize15x15CB

Quant menu WinDmp size 15x15 checkbox

mi_WinDmpSize20x20CB

java.awt.CheckboxMenuItem mi_WinDmpSize20x20CB

Quant menu WinDmp size 20x20 checkbox

mi_WinDmpSize25x25CB

java.awt.CheckboxMenuItem mi_WinDmpSize25x25CB

Quant menu WinDmp size 25x25 checkbox

mi_WinDmpSize30x30CB

java.awt.CheckboxMenuItem mi_WinDmpSize30x30CB

Quant menu WinDmp size 30x30 checkbox

mi_WinDmpSize35x35CB

java.awt.CheckboxMenuItem mi_WinDmpSize35x35CB

Quant menu WinDmp size 35x35 checkbox

mi_WinDmpSize40x40CB

java.awt.CheckboxMenuItem mi_WinDmpSize40x40CB

Quant menu WinDmp size 40x40 checkbox

mi_WinDmpRadixDecCB

java.awt.CheckboxMenuItem mi_WinDmpRadixDecCB

Quant menu WinDmp radix decimal mode checkbox

mi_WinDmpRadixOctCB

java.awt.CheckboxMenuItem mi_WinDmpRadixOctCB

Quant menu WinDmp radix octal mode checkbox

mi_WinDmpRadixHexCB

java.awt.CheckboxMenuItem mi_WinDmpRadixHexCB

Quant menu WinDmp radix hex mode checkbox

mi_WinDmpRadixODCB

java.awt.CheckboxMenuItem mi_WinDmpRadixODCB

Quant menu WinDmp radix optical density mode checkbox

mi_useLogTIFFfilesCB

java.awt.CheckboxMenuItem mi_useLogTIFFfilesCB

Use log of TIFF file else scale to 8-bit data

mi_saveOimagesWhenSaveStateCB

java.awt.CheckboxMenuItem mi_saveOimagesWhenSaveStateCB

mi_useProteinDBbrowserCB

java.awt.CheckboxMenuItem mi_useProteinDBbrowserCB

flickerCheckbox

javax.swing.JCheckBox flickerCheckbox

Toggle flicker on/off

clickableCheckbox

javax.swing.JCheckBox clickableCheckbox

enable clickable images

allowXformsCheckbox

javax.swing.JCheckBox allowXformsCheckbox

Allow transforms, so that there is no oImg.

composeXformCheckbox

javax.swing.JCheckBox composeXformCheckbox

xform previous oImg Image

textMsgLabel1

javax.swing.JLabel textMsgLabel1

GUI text 1 msg line

textMsgLabel2

javax.swing.JLabel textMsgLabel2

GUI text 2 msg line

maxMsgSize

int maxMsgSize

max text length that can be put into msg1 or msg2

zoomLabel

javax.swing.JLabel zoomLabel

GUI label for zoom scroll (AWT zoom)

zoomMagLabel

javax.swing.JLabel zoomMagLabel

GUI label for zoom scroll de_zoom transform over 1/N to NX zoom (-N to +N))

angleLabel

javax.swing.JLabel angleLabel

GUI label for angle scroll

eScaleLabel

javax.swing.JLabel eScaleLabel

GUI label for eScale scroll

zScaleLabel

javax.swing.JLabel zScaleLabel

GUI label for zScale scroll

contrastLabel

javax.swing.JLabel contrastLabel

GUI label for contrast scroll

brightnessLabel

javax.swing.JLabel brightnessLabel

GUI label for brightness scroll

threshold2Label

javax.swing.JLabel threshold2Label

GUI label for threshold 2 scroll

threshold1Label

javax.swing.JLabel threshold1Label

GUI label for threshold 1 scroll

measCircleRadiusLabel

javax.swing.JLabel measCircleRadiusLabel

GUI label for measCircleRadius scroll

canvasSizeLabel

javax.swing.JLabel canvasSizeLabel

GUI label for "Canvas size: xxxx"

zoomBar

java.awt.Scrollbar zoomBar

scroll bar for (AWT display zoom)

zoomMagBar

java.awt.Scrollbar zoomMagBar

scroll bar for zoom (de_zoom transform over 1/N to NX zoom (-N to +N))

angleBar

java.awt.Scrollbar angleBar

scroll bar for angle

eScaleBar

java.awt.Scrollbar eScaleBar

scroll bar for eScale

zScaleBar

java.awt.Scrollbar zScaleBar

scroll bar for zScale

contrastBar

java.awt.Scrollbar contrastBar

scroll bar for contasrt

brightnessBar

java.awt.Scrollbar brightnessBar

scroll bar for brightness

threshold2Bar

java.awt.Scrollbar threshold2Bar

scroll bar for threshold2

threshold1Bar

java.awt.Scrollbar threshold1Bar

scroll bar for threshold1

measCircleRadiusBar

java.awt.Scrollbar measCircleRadiusBar

scroll bar for measCircleRadius

Class Flicker extends javax.swing.JFrame implements Serializable

Serialized Fields

NOT_AVAIL_YET

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

boolean USE_GUARD

Enable guard region in the menu

USE_PLUGINS

boolean USE_PLUGINS

Enable plugins in the menu

USE_GANG_BC

boolean USE_GANG_BC

DEBUGGING Enable using "View Gang Brightness/Contrast"

DBUG_NTSC_RGB2GRAY

boolean DBUG_NTSC_RGB2GRAY

DEBUGGING convert color RGB image to grayscale using NTSC algor.

USE_AWT_ZOOM

boolean USE_AWT_ZOOM

Enable using AWT implemented zoom only does positive integer zoom

USE_DE_ZOOM

boolean USE_DE_ZOOM

Enable using de_zoom transform over 1/N to NX zoom (-N to +N)

GC_MEMORY_DBUG

boolean GC_MEMORY_DBUG

Enable pretty-printing GC Memory debugging

DEF_CIRCLE_MASK_RADIUS

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.

aff

Affine aff

Affine instance

bGui

BuildGUI bGui

BuildGUI instance of user interface

cal

CalibrateOD cal

Calibrate OD instance

ekb

EventKbd ekb

get kbd event handler

evs

EventScroller evs

instance of event scroller handler

evMu

EventMenu evMu

fio

FileIO fio

FileIO utilities

fDemo

FlkDemo fDemo

FlkDemo database

fUser

FlkUser fUser

FlkUser database

fm

FlkMap fm

FlkMap database

fRecent

FlkRecent fRecent

FlkRecent database

imgIO

ImageIO imgIO

Flicker image I/O and conversion functions

ix

ImageXform ix

image transform

info

Info info

Info status region

lms

Landmark lms

list of landmarks

piMgr

PluginMgr piMgr

Plugin manager

sxf

SpatialXform sxf

poly warp spatial transform

spt

Spot spt

Spot structures

tr

TiffLoader tr

Tiff image reader

util

Util util

misc utility methods

windmp

Windump windmp

Window digital data dump

lastIS

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

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

ImageScroller i1IS

scrollable image 1 scrollable image (left)

i2IS

ImageScroller i2IS

scrollable image 2 scrollable image (right)

iData1

ImageData iData1

image 1 picture data associated with ImageScroller i1IS (left)

iData2

ImageData iData2

image 2 picture data associated with ImageScroller i2IS (right)

imgXform

ImageXform imgXform

current image transform if any

ixf1

ImageXform ixf1

image transform for image 1 if any

ixf2

ImageXform ixf2

image transform for image 2 if any

runT

java.lang.Thread runT

Flicker thread

notDoneFlag

boolean notDoneFlag

Set to kill the run loop

args

java.lang.String[] args

flkStateFile

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

java.lang.String lastISName

last IS that was clicked on

startupDate

java.util.Date startupDate

title

java.lang.String title

Title of program

activeImage

java.lang.String activeImage

active image "left", "right", "both" === was both

sWorking

java.lang.String sWorking

incremental loading message

errStr

java.lang.String errStr

error string if not ""

colorMode

int colorMode

method to use when filter RBG in ImageScroller

alertColor

java.awt.Color alertColor

Color to use for background of alert messages

lastMsgColor

java.awt.Color lastMsgColor

save last message color state

lastMsgStr

java.lang.String lastMsgStr

save last message state

popupWindowName

java.lang.String popupWindowName

default name of popup window

imageFile1

java.lang.String imageFile1

full path of image 1 (left) file or URL

imageFile2

java.lang.String imageFile2

full path of image 2 (right) file or URL

xformName

java.lang.String xformName

current transform

imageFont

java.awt.Font imageFont

image font for overlay

textFont

java.awt.Font textFont

text font for messages

showI1flag

boolean showI1flag

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

finished1

boolean finished1

flag that finished transform 1

finished2

boolean finished2

finished transform 2

xformThreadCtr

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

boolean validAffineFlag

set when do valid affine xform

errorLoadingImageFlag

boolean errorLoadingImageFlag

set by ImageObserver imageUpdate()

displayInfoFlag

boolean displayInfoFlag

if TRUE then display enter/exit info

doingXformFlag

boolean doingXformFlag

doing the transform

isSuspendedFlag

boolean isSuspendedFlag

Threads were suspended by stop()

readyFlag

boolean readyFlag

finished reading images.

imageLoadErrorFlag

boolean imageLoadErrorFlag

true if image loading error

abortFlag

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

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

boolean viewLMSflag

view landmarks overlay

viewTargetFlag

boolean viewTargetFlag

view target overlay

viewTrialObjFlag

boolean viewTrialObjFlag

view trial objects overlay

viewBoundaryFlag

boolean viewBoundaryFlag

view boundary overlay

viewRoiFlag

boolean viewRoiFlag

view ROI overlay

viewMeasCircleFlag

boolean viewMeasCircleFlag

view measurement circle overlay

viewDrawSpotLocCircleFlag

boolean viewDrawSpotLocCircleFlag

view measurement location as 'circle'{annotation} overlay

viewDrawSpotLocPlusFlag

boolean viewDrawSpotLocPlusFlag

view measurement location as '+'{annotation} overlay

viewDrawSpotAnnNbrFlag

boolean viewDrawSpotAnnNbrFlag

view measurement annotation as 'spot nbr' overlay

viewDrawSpotAnnIdFlag

boolean viewDrawSpotAnnIdFlag

view measurement annotation as 'spot nbr' overlay

viewMultPopups

boolean viewMultPopups

view multiple popups

viewGangScrollFlag

boolean viewGangScrollFlag

gang scroll both images

viewGangZoomFlag

boolean viewGangZoomFlag

gang zoom both images

viewGangBCFlag

boolean viewGangBCFlag

gang brightnessContrast both images

viewDispGrayValuesFlag

boolean viewDispGrayValuesFlag

view display image RGB as gray values

firstTimeThruFlag

boolean firstTimeThruFlag

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

viewNormalizedColorFlag

boolean viewNormalizedColorFlag

view normalized color

viewPseudoColorFlag

boolean viewPseudoColorFlag

view pseudo color display

viewRGB2GrayFlag

boolean viewRGB2GrayFlag

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

viewReportPopupFlag

boolean viewReportPopupFlag

view Report popup window

useGuardRegionImageFlag

boolean useGuardRegionImageFlag

useNTSCrgbTograyCvtFlag

boolean useNTSCrgbTograyCvtFlag

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

doMeasureProtIDlookupAndPopupFlag

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

boolean useSwiss2DpageServerFlag

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

usePIRUniprotServerFlag

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

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

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

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

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

boolean useThresholdInsideFlag

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

saveOimagesWhenSaveStateflag

boolean saveOimagesWhenSaveStateflag

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

useProteinDBbrowserFlag

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

boolean userClickableImageDBflag

User enabled image as clickable DB checkbox to get DB entry

allowXformFlag

boolean allowXformFlag

transforms are allowed

composeXformFlag

boolean composeXformFlag

Replace(Preserve) orig imgs w/ xforms

dbugFlag

boolean dbugFlag

true if debug printout, set by GUI

prevFlickerFlag

boolean prevFlickerFlag

previous state of flickerFlag saved when start ain ImageXform

flickerFlag

boolean flickerFlag

enable flickering, set by GUI also from if set

clickableCGIbaseURL1

java.lang.String clickableCGIbaseURL1

is clickable to get DB entry

clickableCGIbaseURL2

java.lang.String clickableCGIbaseURL2

is clickable to get DB entry

clickableCGIbaseURL1pix

java.lang.String clickableCGIbaseURL1pix

is clickable to get DB entry

clickableCGIbaseURL2pix

java.lang.String clickableCGIbaseURL2pix

is clickable to get DB entry

isClickableDBflag

boolean isClickableDBflag

flag set if currently selected image is clickable

curState

SliderState curState

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

defaultFlickerDelay

int defaultFlickerDelay

default delay if not flickering

flkCanvasSize

int flkCanvasSize

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

canvasSize

int canvasSize

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

frameWidth

int frameWidth

main frame width

frameHeight

int frameHeight

main frame height

scrWidth

int scrWidth

min (FRAME_WIDTH, screenWidth)

scrHeight

int scrHeight

min (FRAME_HEIGHT, screenHeight)

resizeFrameFlag

boolean resizeFrameFlag

allow dragging the frame to cause it to resize

winDumpRadix

int winDumpRadix

WinDump data printing radix

maxColsToPrint

int maxColsToPrint

WinDump window size in pixels

useLogInputFlag

boolean useLogInputFlag

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

useTotDensityFlag

boolean useTotDensityFlag

"Use sum density else mean" in measurements

useMeasCtrFlag

boolean useMeasCtrFlag

"Use measurement counters" in measurements

spotsListModeFlag

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

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

int measCircleRadius

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

circleMask

int[][] circleMask

"measurement" circle mask of size nCirMask X nCirMask

nCirMask

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

java.awt.Point imgPos

position of the image for flickering

objPos

java.awt.Point objPos

position of the object for flickering

imagesToProcess

int imagesToProcess

CountDown to determine if finished. 1 or 2 transforms

nbrUniqueAFT

int nbrUniqueAFT

set to # of unique non-colinear affine transform

thrColinearity

float thrColinearity

co-linearity threshold for testing LMS

minLSQcolinearity1

float minLSQcolinearity1

for image 1 w.r.t landmarks

minLSQcolinearity2

float minLSQcolinearity2

for image 2 w.r.t landmarks

roiColor

java.awt.Color roiColor

trialObjColor

java.awt.Color trialObjColor

Adjustable trial object color

lmsColor

java.awt.Color lmsColor

Adjustable landmark color

bkgrdCircleColor

java.awt.Color bkgrdCircleColor

Adjustable measurement circle color

measCircleColor

java.awt.Color measCircleColor

Adjustable measurement circle color

guardRegionColor

java.awt.Color guardRegionColor

Adjustable guard region color

efName

java.lang.String[] efName

name of command

efMnuName

java.lang.String[] efMnuName

what appears in menu

efNbr

int[] efNbr

function number 1 to MAX_EXTERN_FCTS

repaintLockFlag

boolean repaintLockFlag

xForm sync

Class ImageScroller extends java.awt.Panel implements Serializable

Serialized Fields

flk

Flicker flk

util

Util util

iData

ImageData iData

Image data for mapGraytoOD[] that will be set later...

isWidth

int isWidth

width of image from iData.iWidth or zoomed data

isHeight

int isHeight

height of image from iData.iHeight or zoomed data

state

SliderState state

SliderState threshold parameters associated with the image

siCanvas

ScrollableImageCanvas siCanvas

pointer to the associated image canvas

southPanel

java.awt.Panel southPanel

opt. holds vs & Delay scroll box SOUTH

dPanel

java.awt.Panel dPanel

opt. holds Delay scroll label & bar

delayLabel

javax.swing.JLabel delayLabel

opt. label for image delay

delayBar

java.awt.Scrollbar delayBar

opt. scroll bar for image delay

txtField

java.awt.TextField txtField

image title placed above canvas

preferredWidth

int preferredWidth

preferred width of canvas

preferredHeight

int preferredHeight

preferred height of canvas

steps

int steps

prewired scroller steps

pagestep

int pagestep

thickness of scroller

img_selectedFlag

boolean img_selectedFlag

set if xObj,yObj is set

useScrollBarsFlag

boolean useScrollBarsFlag

create and use scrollers flag

repackFlag

boolean repackFlag

oGifFileName

java.lang.String oGifFileName

Name of GIF file used in "SaveAs" of oImg to local GIF file

name

java.lang.String name

obj name "left", "right" or "both".

title

java.lang.String title

current title for image scroller associated with iData

sp

java.awt.ScrollPane sp

scroller for the canvas, siCanvas

aH

java.awt.Adjustable aH

deals with scroller events

aV

java.awt.Adjustable aV

deals with scroller events

scrollPos

java.awt.Point scrollPos

keep track of ScrollPostions

oldIWidth

int oldIWidth

calc ScrollPostions

oldIHeight

int oldIHeight

calc ScrollPostions

bcImgF

BrightnessContrastFilter bcImgF

Instance of Brightness/Contrast Filter. It is reused across images for this image scroller.

xObj

int xObj

X cursor position mapped to image

yObj

int yObj

Y cursor position mapped to image

guardRegionFlag

boolean guardRegionFlag

guard region flag

guardWidth

int guardWidth

size of right & left guard region

guardHeight

int guardHeight

size of top & bottom guard region

guardImgWidth

int guardImgWidth

size of img with guard region

guardImgHeight

int guardImgHeight

size of img with guard region

Class Popup extends java.awt.Frame implements Serializable

Serialized Fields

flk

Flicker flk

util

Util util

fileDialog

java.awt.FileDialog fileDialog

for use in popup FileDialog

Class PopupTextFieldDialog extends java.awt.Dialog implements Serializable

Serialized Fields

flk

Flicker flk

util

Util util

f

java.awt.Frame f

Frame where dialog box is added

msg

java.lang.String msg

Message to display

answer

java.lang.String answer

Returned value from text field

okFlag

boolean okFlag

Returned true if pressed DONE

tf

java.awt.TextField tf

text field

Class PopupYesNoDialogBox extends java.awt.Dialog implements Serializable

Serialized Fields

f

java.awt.Frame f

Frame where dialog box is added

msg

java.lang.String msg

Message for dialog box

yesMsg

java.lang.String yesMsg

Yes label for dialog box

noMsg

java.lang.String noMsg

No label for dialog box

cancelMsg

java.lang.String cancelMsg

Cancel label for dialog box

bgColor

java.awt.Color bgColor

background color

okFlag

boolean okFlag

flag set by the yes button (no or cancel button set to false)

cancelFlag

boolean cancelFlag

flag set by cancel button