Serialized Form
serialVersionUID: 0L
ssi
Sg2showImage ssi
sg2
Seg2Dgel sg2
- link to global instance
preferredWidth
int preferredWidth
- preferred size of canvas
preferredHeight
int preferredHeight
- preferred size of canvas
mediumFont
java.awt.Font mediumFont
- medium font used for labeling
largeFont
java.awt.Font largeFont
- medium font used for labeling
optBkgrdColor
java.awt.Color optBkgrdColor
histColor
java.awt.Color histColor
histTopColor
java.awt.Color histTopColor
activeBinColor
java.awt.Color activeBinColor
- Active bin peak on histogram color
meanValueBinColor
java.awt.Color meanValueBinColor
- Mean value bin peak on histogram color
modeValueBinColor
java.awt.Color modeValueBinColor
- Mode value bin peak on histogram color
medianValueBinColor
java.awt.Color medianValueBinColor
- Median value bin peak on histogram color
labelColor
java.awt.Color labelColor
frameSize
java.awt.Dimension frameSize
- size of frame
cWidth
int cWidth
- working canvas width
cHeight
int cHeight
- working canvas height
dataName
java.lang.String dataName
- name of the data used in histogram
dataUnits
java.lang.String dataUnits
- data units abbreviation
sHist
int[] sHist
- local SCALED histogram [0:nShist-1]data
nShist
int nShist
- size of input unscaled histogram[] data
sHistDisp
int[] sHistDisp
- local SCALED histogram [0:nShist-1] scaled to
max data value of nShist
xPainted
int[] xPainted
- local SCALED histogram X position
activeBin
int activeBin
- active bin idx of SCALED sHist[0:nHist-1] else -1
activeBinValue
float activeBinValue
- active bin data value corresponding to activeBinidx of SCALED
sHist[0:nHist-1]. Only valid if activeBin is NEQ -1
xULHC
int xULHC
- upper X left hand corner of hist. graph
yULHC
int yULHC
- upper Y left hand corner of hist. graph
xLRHC
int xLRHC
- lower Y right hand corner of hist. graph
yLRHC
int yLRHC
- lower Y right hand corner of hist. graph
minShistIdx
int minShistIdx
- min non-zero bin of sHist to be displayed
maxShistIdx
int maxShistIdx
- max non-zero bin of sHist to be displayed
meanShistIdx
int meanShistIdx
- mean non-zero bin of sHist to be displayed
medianShistIdx
int medianShistIdx
- median non-zero bin of sHist to be displayed
modeShistIdx
int modeShistIdx
- mode non-zero bin of sHist to be displayed
minShistFreq
int minShistFreq
- min sHist Frequency in sHist value to be displayed
maxShistFreq
int maxShistFreq
- max sHist Frequency in sHist value to be displayed
minHistFreqValue
int minHistFreqValue
- The minimum frequency value in hist[]
maxHistFreqValue
int maxHistFreqValue
- The maximum frequency in hist[]
meanDataValue
float meanDataValue
- mean non-zero data value of sHist to be displayed
medianDataValue
float medianDataValue
- median non-zero data value of sHist to be displayed
modeDataValue
float modeDataValue
- mode non-zero data value of sHist to be displayed
meanDataGrayValue
int meanDataGrayValue
- mean non-zero data gray value of sHist to display for Image density
medianDataGrayValue
int medianDataGrayValue
- median non-zero data gray value of sHist to display for Image density
modeDataGrayValue
int modeDataGrayValue
- mode non-zero data gray value of sHist to display for Image density
minDataValue
float minDataValue
- The minimum data value at hist[0]
maxDataValue
float maxDataValue
- The maximum data value at hist[max index]
binScale
float binScale
- sHist[] Bin width sampling or averaging distance computed
as floating (nHist/nShist) to map hist[] to a sHist[] bin.
scaleFreq
float scaleFreq
- sHist[] frequency scale factor computed as
floating (maxHistFreq/nShist)
changeGuiFlag
boolean changeGuiFlag
- flag to indicating that the GUI may have changed and that it should
be rebuilt.
hasHistGUIflag
boolean hasHistGUIflag
- flag to indicate that the GUI contains the Histogram sub-GUI
useHistGUIflag
boolean useHistGUIflag
- flag to use simple ImageViewer w/o histogram or full GUI
with the histogram
roiX1
int roiX1
- ROI ULHC X
roiY1
int roiY1
- ROI ULHC Y
roiX2
int roiX2
- ROI LRHC X
roiY2
int roiY2
- ROI LRHC Y
dispName
java.lang.String dispName
- Name of image to display after a segmentation
dispPixI
int[] dispPixI
- Picture buffer int[] of image to display after a segmentation.
Note this is read either from the pix? variable or from
the file if the pix? variable is null.
dispPixC
char[] dispPixC
- Picture buffer char[] of image to display after a segmentation.
Note this is read either from the pix? variable or from
the file if the pix? variable is null.
dispPixFile
java.lang.String dispPixFile
- File of image to display after a segmentation. Used if dispPixI/C is
null.
histType
int histType
- type of data to use with the histogram
useFilterByBinFlag
boolean useFilterByBinFlag
- menu CB item to filter spots by testing if the histogram active bin
is selected and histogram spot feature meets the active bin test
nbrPassedFilter
int nbrPassedFilter
- # of spots passing filter
hasHistFlag
boolean hasHistFlag
- Histogram exists and should be drawn. This is cleared if we
decide to blank out the histogram.
serialVersionUID: 0L
sg2
Seg2Dgel sg2
- instance of the main class
useHistGUIflag
boolean useHistGUIflag
- flag to use simple ImageViewer w/o histogram or full GUI
with the histogram
baseImageFile
java.lang.String baseImageFile
- base name of the image for use in the title
changeGuiFlag
boolean changeGuiFlag
- flag to indicating that the GUI may have changed and that it should
be rebuilt.
hasHistGUIflag
boolean hasHistGUIflag
- flag to indicate that the GUI contains the Histogram sub-GUI
VIEW_WIDTH_NO_HIST
int VIEW_WIDTH_NO_HIST
- Width of the frame without histogram
VIEW_WIDTH_WITH_HIST
int VIEW_WIDTH_WITH_HIST
- Width of the frame with histogram
VIEW_HEIGHT
int VIEW_HEIGHT
- Height of the frame with and without histogram
ROI_NONE
int ROI_NONE
- No ROI code
ROI_CW
int ROI_CW
- Computing Window ROI code
ROI_ND
int ROI_ND
- Step Wedge ROI code
ROI_DBUG
int ROI_DBUG
- Debugging region ROI code
ROI_PIXDUMP
int ROI_PIXDUMP
- Picture dump region ROI code
ROI_WORKING
int ROI_WORKING
- Working ROI code. This ROI may then be copied to the CW, DBUG or
PIXDUMP ROIs
mbar
java.awt.MenuBar mbar
- menu bar for the frame
fileMenu
java.awt.Menu fileMenu
- "File" pull down Menu list
roiMenu
java.awt.Menu roiMenu
- "RegionOfInterest" pull down Menu list
viewMenu
java.awt.Menu viewMenu
- "View" pull down Menu list
histMenu
java.awt.Menu histMenu
- "Histogram" pull down Menu list
histChoice
java.awt.Choice histChoice
- "Histogram" Choice list
zoomChoice
java.awt.Choice zoomChoice
- "Zoom" Choice list
controlPanel
javax.swing.JPanel controlPanel
- Control panel for the main frame
ms
MenuSupport ms
- Menu support functions using Hashtables to tack what is active
sg2Vi
Sg2viewImage sg2Vi
- Sg2ViewImage to hold the image
msgTextArea
java.awt.TextArea msgTextArea
- Text area GUI for message rporting
textAreaFontSize
int textAreaFontSize
- font size
textFontFamily
java.lang.String textFontFamily
- font family for message window
fontFamily
java.lang.String fontFamily
smallFont
java.awt.Font smallFont
mediumFont
java.awt.Font mediumFont
largeFont
java.awt.Font largeFont
dispPixChoice
java.awt.Choice dispPixChoice
- Selector for image to display after a segmentation
pixHeight
int pixHeight
- The height of the image
pixWidth
int pixWidth
- The width of the image
radixChoice
java.awt.Choice radixChoice
- Selector for windmp radix
radixName
java.lang.String radixName
- Name winDump radix
radix
int radix
- Code for winDump radix
windmpSizeChoice
java.awt.Choice windmpSizeChoice
- Selector for winDump size
windmpSizeName
java.lang.String windmpSizeName
- Name windump size
windmpSize
int windmpSize
- Code for winDump size
roiChoice
java.awt.Choice roiChoice
- Selector for show ROI CW overlay
roiName
java.lang.String roiName
- name for show ROI CW overlay
roiCode
int roiCode
- code for show ROI CW overlay
roiWORKING
Roi roiWORKING
- Internal "WORKING",ROI_WORKING instance that can be used to
set the CW, DBUG or PIXDUMP (not the ND) Rois
roiCW
Roi roiCW
roiND
Roi roiND
- ""ND",ROI_ND instance
roiDBUG
Roi roiDBUG
- "DBUG",ROI_DBUG instance
roiPIXDUMP
Roi roiPIXDUMP
- "PIXDUMP",ROI_PIXDUMP instance
allSpotsCB
java.awt.Checkbox allSpotsCB
- the "All spots" Checkbox
allSpotsFlag
boolean allSpotsFlag
- set from "All spots" checkbox
showSpotNbrsFlag
boolean showSpotNbrsFlag
- set from "View spot numbers" checkbox
isVisibleFlag
boolean isVisibleFlag
- Set true if window is visible
drawHorizSliceFlag
boolean drawHorizSliceFlag
- menu CB item to display horizontal slice
drawVertSliceFlag
boolean drawVertSliceFlag
- menu CB item to display vertical slice
filterGEQactiveBinFlag
boolean filterGEQactiveBinFlag
- menu CB item to test spots for GEQ activeBin value, else
LEQ activeBin value fromt the selected histogram bin for
the histogram histType spot data.
useFilterByBinFlag
boolean useFilterByBinFlag
- menu CB item to filter spots by testing if the histogram active bin
is selected and histogram spot feature meets the active bin test
nbrPassedFilter
int nbrPassedFilter
- # of spots passing filter
useDragCB
java.awt.Checkbox useDragCB
- the "Use drag" checkbox
useDragFlag
boolean useDragFlag
- set from "Use drag" checkbox
logReportCB
java.awt.Checkbox logReportCB
- the "Log report" checkbox
logReportFlag
boolean logReportFlag
- set from "Log report" checkbox
viewWidth
int viewWidth
viewHeight
int viewHeight
zoomVal
int zoomVal
showCWflag
boolean showCWflag
showNDCWflag
boolean showNDCWflag
showDbugCWflag
boolean showDbugCWflag
showPixdumpCWflag
boolean showPixdumpCWflag
hCanvas
Sg2drawHistogram hCanvas
- Histogram Canvas to hold the image
hist
int[] hist
- full input unscaled histogram data [0:nHist-1]
nHist
int nHist
- size of input unscaled histogram[] data
histType
int histType
- type of data to use with the histogram
dataUnits
java.lang.String dataUnits
- Data type as fct of histogram data type
minDataValue
float minDataValue
- Minimum value expected for current hist[] data
maxDataValue
float maxDataValue
- Maximum value expected for current hist[] data
maxGrayPixel
int maxGrayPixel
- Maximum gray value for pixel
dispPixC
char[] dispPixC
- Picture buffer char[] of image to display after a segmentation.
Note this is read either from the pix? variable or from
the file if the pix? variable is null.
dispName
java.lang.String dispName
- Name of image to display after a segmentation
nPixels
int nPixels
- The pixWidth*pixHeight
dispPixFile
java.lang.String dispPixFile
- File of image to display after a segmentation.
Used if dispPixC is null.
dispPixWorking
char[] dispPixWorking
- Picture buffer char[] of image to display after a segmentation.
Note this is read either from the pix? variable or from
the file if the pix? variable is null.
selImgIdx
int selImgIdx
- image index
nPixList
int nPixList
pixNameList
java.lang.String[] pixNameList
- list of display picture names for choices
pixMenuList
java.lang.String[] pixMenuList
- list of display picture menu commands for choices
pixFileList
java.lang.String[] pixFileList
pixClist
char[][] pixClist
- List of display pix associate char[] images
pixGrayBits
int[] pixGrayBits
- list of max gray pixel sizes of pixClist pixels
pImg
java.awt.Image pImg
- Image to display
preferedCanvasSize
java.awt.Dimension preferedCanvasSize
splitPanelFlag
boolean splitPanelFlag
- to use spiltPane or not
serialVersionUID: 0L
ROI_NONE
int ROI_NONE
ROI_CW
int ROI_CW
ROI_ND
int ROI_ND
ROI_DBUG
int ROI_DBUG
ROI_PIXDUMP
int ROI_PIXDUMP
MAX_ROI
int MAX_ROI
- max roi
VIEW_HEIGHT
int VIEW_HEIGHT
- Height of the frame with and without histogram
cwRoi
Roi cwRoi
- ROI for computing window
roiND
Roi roiND
- ""ND",ROI_ND instance
dbRoi
Roi dbRoi
- Debugging window for -debug: window
dpRoi
Roi dpRoi
- Debugging window for -pixdump: window
roiName
java.lang.String roiName
- name for show ROI CW overlay
roiCode
int roiCode
- code for specific ROI overlays
sg2
Seg2Dgel sg2
- instance of main class
sig
Sg2showImage sig
- popup Image viewer GUI
cal
CalibrateOD cal
- instance of calibrate
dbSample
DbSample dbSample
- instance of current sample
si
ScrollableImage si
- scroller for image display
dol
DrawOverlays dol
- instance of DrawOverlays
viewWidth
int viewWidth
viewHeight
int viewHeight
nPixels
int nPixels
- The pixWidth*pixHeight
cWidth
int cWidth
- canvas width
cHeight
int cHeight
- canvas height
paintCtr
int paintCtr
- for debugging
pixHeight
int pixHeight
- pixel height
pixWidth
int pixWidth
- pixel width
xImg
int xImg
- image address (x,y)+(xBase,yBase)
yImg
int yImg
- image address (x,y)+(xBase,yBase)
roiList
RoiList roiList
- list of ROIs for drawing
maxRoi
int maxRoi