Seg2Dgel
Class Sg2glb

java.lang.Object
  extended by Seg2Dgel.Sg2glb
Direct Known Subclasses:
Seg2Dgel, Sg2avg, Sg2bkg, Sg2cc, Sg2data, Sg2dbug, Sg2draw, Sg2fbl, Sg2fnd, Sg2hash, Sg2ini, Sg2ngh, Sg2notch, Sg2rest, Sg2sat, Sg2split, Sg2wrk

public class Sg2glb
extends java.lang.Object

Class Sg2glb is the base class that specifies global variables used by all of the other Seg2Dgel 2D gel segmenter classes.

This code was derived and refactored from GELLAB-II sg2gii C language files.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.

Version:
$Date: 2005/12/22 00:41:56 $ $Revision: 1.32 $
Author:
P. Lemkin, NCI-Frederick, Frederick, MD, 21702
See Also:
Open2Dprot Home

Field Summary
static DbAccession acc
           
static java.lang.String accDatabaseFile
          Full path Accession database file if exists which is xmlDir+accFile
static boolean accDatabaseSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String accFile
          Accession database file if exists
static int accFormatMode
          Accession file input file format mode set by the command line switch -accessionDB:accession.txt or -accessionDB:accession.xml This then gets mapped to either FileIO.IO_FORMAT_XML or IO_FORMAT_TAB_DELIMITED.
static boolean allowTouchingEdgesSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String applicationName
          name of the application
static java.lang.String[] argsV
          Total command list arg list originally set fro main(args)
static boolean averageODSwitch
          The parsed of Command line + gel.rc state switches
static Sg2avg avg
           
static java.lang.String avgPixFile
          tmp/average image file
static java.lang.String banner
          The full version data banner with todays date
static java.lang.String bannerTitle
          The short version data banner for popup titles
static java.lang.String baseImageFileName
          Base file name is the original gel input image file without the directory and WITHOUT the file extension.
static long baseStatusTime
          base starting time in epoch msec time for the status reports
static java.lang.String batchDir
          Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/
static int[] bfav
          Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[] bfavm
          Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[] bfavm1
          Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[] bfavp
          Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[] bfavp1
          Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
static int[] bfog
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogm
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogm1
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogm2
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogm3
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogm4
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogm5
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogp
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogp1
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogp2
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogp3
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogp4
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static int[] bfogp5
          Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
static Sg2bkg bkg
           
static int BKGRD_CODE
          pixel code for the CC background pixel
static boolean bkgrdCorrectionSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String bkgrdPixFile
          tmp/notch filter background image file
static boolean bkgrdSizeFlag
          The parsed of Command line + gel.rc state switches
static int BLACK
          Pixel color for black
static boolean boundaryInSSFSwitch
          The parsed of Command line + gel.rc state switches
static int[] bufbkg
          Background buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
static int[] bufcc
          Rest-of buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
static int[] bufmag
          Magnitude buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
static int[] bufrest
          Rest-of buffered image - unsigned 16-bit line buffer [0:pixWidth-1]
static int c11
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c12
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c13
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c14
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c15
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c16
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c17
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c18
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c19
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c1h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c21
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c22
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c23
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c24
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c25
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c26
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c27
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c28
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c29
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c2h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c31
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c32
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c33
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c34
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c35
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c36
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c37
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c38
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c39
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c3h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c41
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c42
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c43
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c44
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c45
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c46
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c47
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c48
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c49
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c4h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c51
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c52
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c53
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c54
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c55
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c56
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c57
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c58
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c59
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c5h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c61
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c62
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c63
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c64
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c65
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c66
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c67
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c68
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c69
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c6h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c71
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c72
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c73
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c74
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c75
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c76
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c77
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c78
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c79
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c7h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c81
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c82
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c83
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c84
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c85
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c86
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c87
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c88
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c89
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c8h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c91
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c92
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c93
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c94
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c95
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c96
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c97
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c98
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c99
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9a
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9b
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9c
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9d
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9e
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9f
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9g
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int c9h
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca1
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca2
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca3
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca4
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca5
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca6
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca7
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca8
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ca9
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int caa
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cab
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cac
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static java.lang.String cacheDir
          Cache database directory {projDir}/cache/
static int cad
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cae
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int caf
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cag
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cah
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static CalibrateOD cal
           
static int[] cal2gray
          map pixel gray values to calibration value (e.g., OD) by scaling it as: OD*1000 to gray Size [0:maxGrayPixel]
static java.lang.String calFile
          [DEPRICATE] cal/<.cal calibration file>
static int cb1
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb2
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb3
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb4
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb5
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb6
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb7
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb8
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cb9
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cba
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbb
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbc
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbd
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbe
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbf
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbg
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cbh
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static Sg2cc cc
           
static int cc1
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc2
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc3
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc4
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc5
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc6
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc7
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc8
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cc9
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cca
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ccb
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ccc
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ccd
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cce
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ccf
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ccg
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cch
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int ccMinSize
          Parameter threshold min # pixels/CC spot
static boolean ccMinSizeSwitch
          The parsed of Command line + gel.rc state switches
static int ccNum
          initial central core spot number
static java.lang.String ccPixFile
          tmp/central core image file
static int cd1
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd2
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd3
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd4
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd5
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd6
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd7
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd8
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cd9
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cda
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cdb
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cdc
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cdd
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cde
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cdf
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cdg
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static int cdh
          Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood
static boolean computingWindowSwitch
          The parsed of Command line + gel.rc state switches
static char coneOfSilenceMode
          The filter type set by the command line switch -laplacian:B,{P|C}, switch where type is either 'C' or 'P'.
static boolean CONSOLE_FLAG
           
static boolean ctlCorePixSwitch
          The parsed of Command line + gel.rc state switches
static int cwx1
          ULHC X computing window for entire input gel image
static int cwx2
          LRHC X computing window for entire input gel image
static int cwy1
          ULHC Y computing window for entire input gel image
static int cwy2
          LRHC Y computing window for entire input gel image
static Sg2data data
           
static java.lang.String DATE
          CVS Version date
static DbSample dbSample
          Current sample being analyzed
static DbSpot dbSpot
          Current spot being analyzed
static Sg2dbug dbug
           
static int DBUG_ADD_INTERIOR_CC_PIXELS
          Trace inner loop of addInteriorCCpixels() to
static int DBUG_BND_ANALYSIS
          Trace findBoundary(), pushXYboundary(), resetBnd()
static int DBUG_CALC_FEATURES
          Trace calcFeatures() where compute spot values from the images & FBL
static int DBUG_CHAIN_CODE_RLM_ANALYSIS
          Trace pairChainCodeNotches(), findMinMaxPeaksInRLM()and findPairedNotches_in_RLM()
(package private) static boolean DBUG_CONSOLE
          Debugging console text flag
static int DBUG_CVT_BND_TO_CHAINCODE
          Trace cvtBoundaryToChainCode(), cvtChainCode_to_nextXY()
static int DBUG_DRAW_NOTCH_PAIR_LINE
          Trace drawLineBetweenNotchPair() to
static int DBUG_DRAW_SAT_SPOT_BND
          Trace draw boundary of saturated spot CC
static int DBUG_DUMP_CC_PPX
          Trace dump CC images at key points if enabled in code
static int DBUG_FILL_CORNERS
          Trace fillCorners() to fill corners in the current PCC
static int DBUG_FILL_HOLES_IN_PCC_CONCAVITIES
          Trace fillHolesInPCCconcavities() to filler corners in PCC concavities
static int DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE
          Trace findNotches_in_chainCode() to
static int DBUG_FIND_SPOT_LIST
          Trace findSpotList() to find spots
static int DBUG_INNER_LOOP_FIND_SPOT
          Trace inner loop of findSpot() to
static int DBUG_MAX_PROPAGATE
          Trace maxPropagate() to expand from the CC to the PCC
static int DBUG_NBR_COMPONENTS
          Trace numberComponents() to number components in the central core
static int DBUG_PIX_DBCODE
          Trace dbugPixDBcode() to print small NxN pixel windows that match the [dbx1:dbx2, dby1:dby2] window.
static int DBUG_PRINT_GRAY2CAL_MAP
          Trace print gray2cal[] to print the gray2cal[] map
static int DBUG_PROP_SAT_SPOTS
          Trace propSaturatedSpot() to
static int DBUG_PROP_SPOT_TO_2ND_MAXIMA
          Trace propSpotTo2ndDrivMaxima() to prop CC to 2nd maxima to make PCC
static int DBUG_PUSH_XY_INTO_FBL
          Trace pushXYintoFBL() to
static int DBUG_RMV_CONCAVITIES
          Trace rmvConcavities() to remove concavities in the central core
static int DBUG_RMV_INTERIOR_CC_PIXELS
          Trace inner loop of rmvInteriorCCpixels() to
static int DBUG_ROUND_CORNERS
          Trace roundCorners() to round corners of the PCC
static int DBUG_SPLIT_CHECK_SPOT
          Trace splitCheckSpot() to check and split a spot if it is needed
static int DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS
          Trace splitPixByFBLboundaryAnal() to
static boolean DBUG_SWITCHES
          Debugging switches
static int dbugBits
          Parameter threshold -DEBUG:bits
static java.lang.String dbugBitsHelpStr
          Debug bit options help for error messages
static boolean dbugBitsPixFlag
          Special test for DBUG_PIX_NXN bit to to print windows that match the [dbx1:dbx2, dby1:dby2] window.
static int dbx1
          Debugging window for -debug: window
static int dbx2
          Debugging window for -debug: window
static int dby1
          Debugging window for -debug: window
static int dby2
          Debugging window for -debug: window
static boolean debugSwitch
          The parsed of Command line + gel.rc state switches
static boolean defaultSwitch
          The parsed of Command line + gel.rc state switches
static int defaultTypeCode
          Default type for -default: The code is from the list: DFT_2D_GEL, DFT_2D_LC_MS, etc.
static boolean deleteIsolatedPixelsSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String[] demoFileList
          List of demo/ files downloadable from the server
static boolean demoSwitch
          The parsed of Command line + gel.rc state switches
static int DFT_2D_GEL
          Default data type 2D-gel
static int DFT_2D_LC_MS
          Default data type 2D-LC-MS
static int DFT_NO_DB
          Default data type No-database
static boolean didPropSaturatedSpots
          For debugging - to avoid re-propagating split spots
static boolean didSplitSpotFlag
          For debugging - to abort seg and dump intermediate images.
static boolean diffODSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String[] docFileList
          List of documentation files downloadable from the server
static boolean dotsSwitch
          The parsed of Command line + gel.rc state switches
static int dpx1
          Debugging window for -pixdump: window
static int dpx2
          Debugging window for -pixdump: window
static int dpy1
          Debugging window for -pixdump: window
static int dpy2
          Debugging window for -pixdump: window
static Sg2draw draw
           
static char drawBoundaryOverlayType
          The drawing overlay type is set by the command line switch -drawBoundaryt:{O | Z}
static boolean drawBoundarySwitch
          The parsed of Command line + gel.rc state switches
static char drawDotOverlayType
          The drawing overlay type is set by the command line switch -drawDot:{O | Z}
static char drawMEROverlayType
          The drawing overlay type is set by the command line switch -drawMinEnclRect:{O | Z}
static boolean drawMERSwitch
          The parsed of Command line + gel.rc state switches
static char drawPlusOverlayType
          The drawing overlay type is set by the command line switch -drawPlus:{O | Z}
static boolean drawPlusSwitch
          The parsed of Command line + gel.rc state switches
static boolean drawSxSyEllipseSwitch
          The parsed of Command line + gel.rc state switches
static char drawSxSyOverlayType
          The drawing overlay type is set by the command line switch -drawSxSyEllipse:{O | Z}
static boolean drawTitleSwitch
          The parsed of Command line + gel.rc state switches
static boolean dtdSwitch
          The parsed of Command line + gel.rc state switches
(package private) static boolean ENABLE_DEVELOPER_DEBUGGING
          Enable developer debugging when do initial startup.
(package private) static boolean ENABLE_SATURATED_SPOTS
          Enable debugging -saturatedSpots analysis
(package private) static boolean ENABLE_SPOT_SPLITTING
          Enable debugging -splitSpots analysis
static Sg2fbl fbl
           
static java.lang.String fileSeparator
          File separator: Property("file.separator")
static FileIO fio
           
static Sg2fnd fnd
           
static float fourSqrtPi
          Constant 4*sqrt(PI) constant used in computing spot volume
static int[] gHist
          Histogram of pix4 AVERAGE Size [0:maxGrayPixel+1]
static float glbPercentThr
          Parameters and thresholds
static int[] gray2cal
           
static int gridSize
          Parameter threshold grid size i.e.
static Sg2hash hashFBL
          Hash table for FBL used to quickly determine if an (x,y) coord is in the FBL.
static int HASHFBLPRIME
          Initial prime #size of Final Blob List (FBL) hash table.
static Sg2hash hashWS
          Hash table for WS used to quickly determine if an (x,y) coord is in the Working Stack (WS).
static float histThreshold
          Parameters and thresholds
static int i0R
          Extended 5x5 neighborhood for 3x3 'Busse' filter
static int i10
          Gray scale intensity 3X3 neighborhood
static int i11
          Gray scale intensity 3X3 neighborhood
static int i12
          Gray scale intensity 3X3 neighborhood
static int i13
          Gray scale intensity 3X3 neighborhood
static int i14
          Gray scale intensity 3X3 neighborhood
static int i15
          Gray scale intensity 3X3 neighborhood
static int i16
          Gray scale intensity 3X3 neighborhood
static int i17
          Gray scale intensity 3X3 neighborhood
static int i18
          Gray scale intensity 3X3 neighborhood
static int i2U
          Extended 5x5 neighborhood for 3x3 'Busse' filter
static int i4L
          Extended 5x5 neighborhood for 3x3 'Busse' filter
static int i6D
          Extended 5x5 neighborhood for 3x3 'Busse' filter
static Sg2ini ini
           
static java.lang.String inPixFile
          original gel input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions.
static int ISOLATED_PIXEL_CODE
          pixel code for guard region splitting previously merged spots
static int j11
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j12
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j13
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j14
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j15
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j16
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j17
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j18
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j19
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j1h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j21
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j22
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j23
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j24
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j25
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j26
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j27
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j28
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j29
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j2h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j31
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j32
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j33
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j34
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j35
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j36
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j37
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j38
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j39
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j3h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j41
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j42
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j43
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j44
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j45
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j46
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j47
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j48
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j49
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j4h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j51
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j52
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j53
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j54
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j55
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j56
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j57
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j58
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j59
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j5h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j61
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j62
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j63
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j64
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j65
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j66
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j67
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j68
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j69
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j6h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j71
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j72
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j73
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j74
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j75
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j76
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j77
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j78
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j79
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j7h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j81
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j82
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j83
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j84
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j85
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j86
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j87
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j88
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j89
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j8h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j91
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j92
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j93
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j94
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j95
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j96
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j97
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j98
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j99
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9a
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9b
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9c
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9d
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9e
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9f
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9g
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int j9h
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja1
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja2
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja3
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja4
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja5
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja6
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja7
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja8
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int ja9
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jaa
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jab
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jac
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jad
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jae
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jaf
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jag
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jah
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static java.lang.String[] jarFileList
          List of .jar files downloadable from the server
static java.lang.String[] jarLibrFileList
          List of library .jar files downloadable from the server
static int jb1
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb2
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb3
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb4
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb5
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb6
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb7
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb8
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jb9
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jba
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbb
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbc
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbd
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbe
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbf
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbg
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jbh
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc1
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc2
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc3
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc4
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc5
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc6
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc7
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc8
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jc9
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jca
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jcb
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jcc
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jcd
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jce
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jcf
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jcg
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jch
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd1
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd2
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd3
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd4
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd5
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd6
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd7
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd8
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jd9
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jda
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jdb
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jdc
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jdd
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jde
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jdf
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jdg
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static int jdh
          Grayscale intensity data for other filters for up to a 13x17 neighborhood
static boolean keepInputImageSwitch
          The parsed of Command line + gel.rc state switches
static int KILL_SPOT_CODE
          pixel code for deleted spot in central core if NEQ sizing (0 if -noDelete)
static int killSpotColor
          Spot color used for deleted spots.
static boolean laplacianSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String[] legalImageFileExtens
          List of legal gel image file extensions
static int lineLaplacianHeight
          Height for -laplacian:L,, line laplacian filter.
static int lineLaplacianWidth
          Width for -laplacian:{H|V},, line laplacian filter.
static int lowPassSize
          The low pass filter width (3x3, 5x5, 7x7, 13x17(13)) -lowpassFilter:
static boolean lowpassSwitch
          The parsed of Command line + gel.rc state switches
static boolean lp13xZZSwitch
          The parsed of Command line + gel.rc state switches
static boolean lp3x3Switch
          The parsed of Command line + gel.rc state switches
static boolean lp5x5Switch
          The parsed of Command line + gel.rc state switches
static boolean lp7x7Switch
          The parsed of Command line + gel.rc state switches
static java.lang.String mag2ndPixFile
          tmp/magnitude of 2nd directive image file
static int MAX_BUFFERED_SPOTS
          max # spots to buffer in memory when converting the list of spots to string representations.
static int MAX_CC_CODE
          pixel code for maximum labeled central core (CC) pixel
static int MAX_INTERIOR_FBL_SIZE
          Max interior of spot size.
static int MAX_PCC_CODE
          pixel code for maximum labeled propagated central core (PCC) pixel
static int maxColsToPrint
          Parameter threshold max # cols width to print winDump
static int maxGhist
          Histogram statistics [for use in FUTURE]
static int maxGrayPixel
          max Gray Pixel value in the image is (1<
static int MAXSUBSPOTS
          max # subspots a spot can split into
static int meanGhist
          Histogram statistics [for use in FUTURE]
static int merx1
          The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]
static int merx2
          The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]
static int merxp1
          Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.
static int merxp2
          Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.
static int mery1
          The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]
static int mery2
          The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]
static int meryp1
          Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.
static int meryp2
          Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.
static int MHISTSIZE
          Size of histogram for splitting algorithm
static int MIN_CC_CODE
          pixel code for minimum labeled central core (CC) pixel
static int MIN_PCC_CODE
          pixel code for minimum labeled propagated central core (PCC) pixel
static int MINBLOBAREA
          used in findAllSpots()
static int minGhist
          Histogram statistics [for use in FUTURE]
static int MINSPLITSPOTSIZE
          Minimum spot CC size of spot for it to be allowed to be a candidate for spot splitting.
static int nBitsPerPixel
          # of bits/pixel in the image
static int nBkgrdSize
          Parameter threshold -background:32, Size of sq.
static int nBytesPerPixel
          # of bytes/pixel in the image
static boolean NEVER
          NEVER and CONSOLE_FLAG - debugging variables - must not be final!
static Sg2ngh ngh
           
static Sg2notch notch
           
static int nPixels
          total # of pixels in image = pixWidth*pixHeight
static int nStatusName
          # of Report status names saved when do util.showReportStatus(name) calls.
static int nSwitches
          the number of Command line + gel.rc state switches
static boolean optimizeInteriorFBLSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String osName
          name of this operating system: Property("os.name")
static ParamHash paramH
           
static int PCC_BASE_CODE
          pixel code for guard region splitting previously merged spots
static PixReader pix
           
static char[] pix1
          original gel image 16-bit unsigned char in int[], or nBitsPerPixel scaled to 16-bits.
static char[] pix2
          magnitude Laplacian image with mag2ndPixFile.
static char[] pix3
          central core image with ccPixFile.
static char[] pix4
          Averaged gel image after gaussian smoothing with avgPixFile.
static char[] pix5
          Segmented spots output Z image with no background with segPixFile.
static char[] pix6
          Background OD image with bkgrdPixFile.
static char[] pix7
          Rest-of output image with restOfPixFile.
static java.lang.String pixDir
          Original image directory used in picking off project diredctory.
static boolean pixDumpSwitch
          The parsed of Command line + gel.rc state switches
static float pixelSizeMicrons
          Pixel resolution in the gel image in microns/pixel
static java.lang.String pixFileExtn
          Output images are either ".gif" or ".jpg" [TODO] change this to .jpg with JPEG writer.
static int pixHeight
          Input gel image size: height
static int pixWidth
          Input gel image size: width
static java.lang.String ppxDir
          Original sample images directory {projDir}/ppx/
static Sg2reportPopup pra
          generic popup report
static java.lang.String projDir
          Project directory that is either userDir, specified by -projDir:{path}, or extracted from the input file path it the image is in a "/ppx/" subdirectory.
static boolean projDirSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String propertiesFile
          Current startup properties file containing default switches if it exists.
static boolean propertiesFileSwitch
          The parsed of Command line + gel.rc state switches
static int pTileGhist
          Histogram statistics [for use in FUTURE]
(package private) static boolean PUBLISH
          NOTE: overide the following debugging options if publishing on net.
static boolean quickEstimateSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String rdbmsDir
          RDBMS database directory {projDir}/rdbms/
static Sg2rest rest
           
static java.lang.String restOfPixFile
          tmp/central core image file
static boolean restOfPixSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String REVISION
          CVS Revision
static java.lang.String rlmCWfile
          tmp/RML CW file
static boolean rmvDprimeSizingSwitch
          The parsed of Command line + gel.rc state switches
static boolean sampleSwitch
          The parsed of Command line + gel.rc state switches
static Sg2sat sat
           
static boolean saturatedSpotSwitch
          The parsed of Command line + gel.rc state switches
static int scaledMaxOD
          This is the max value index for cal2gray[] it is computed as cal2gray.length-1
static java.lang.String seg2dgelURL
          Hardwired Open2Dprot server connection Switch to S.F.
static java.lang.String segPixFile
          tmp/segmented image image file
static boolean segPixSwitch
          The parsed of Command line + gel.rc state switches
static Seg2Dgel sg2
           
static java.lang.String simpleFileName
          Simple file name is the original gel input image file without the directory and WITH the file extension.
static float sizeFractionGaussianWidth
          Parameters and thresholds
static Sort sort
           
static Sg2split split
           
static boolean splitLargeCCfblByBndAnalSwitch
          The parsed of Command line + gel.rc state switches
static boolean splitLargeCCfblByRLManalSwitch
          The parsed of Command line + gel.rc state switches
static boolean splitLargeCCfblByThreshAnalSwitch
          The parsed of Command line + gel.rc state switches
static int splitMinCCsize
          Parameter threshold lower |CC| bound for splitting spots
static boolean splitSpotSwitch
          The parsed of Command line + gel.rc state switches
static int spotNumber
          initial spot number
static int ssfFormatMode
          SSF output file format mode set by the command line switch ssfFormat:<{F|L|T|X}> where mode is either 'F', 'L', 'T' or 'X'.
static boolean ssfFormatSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String ssfOutputEpilogueFile
          full tab-delim EPILOGUE xml/ Sample Spot-list File full path
static java.lang.String ssfOutputFile
          xml/ Sample Spot-list File full path
static java.lang.String ssfOutputPrefaceFile
          full tab-delim PREFACE xml/ Sample Spot-list File full path
static long startTime
          starting time in epoch msec time
static long[] statusMemoryFree
          Report status memory Free.
static long[] statusMemoryTot
          Report status memory Total.
static java.lang.String[] statusName
          Report status names saved when do util.showReportStatus(name) calls.
static long[] statusStartTime
          Report status starting times entries in epoch msec time Saved when do util.showReportStatus(name) calls.
static java.lang.String[] sw
          Command line + Seg2Dgel.properties state switches
(package private) static boolean[] switchOptCBvalue
          The switchOptcCBvalue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions.
(package private) static java.lang.String[] switchOptData
          The switchOptData[0:(2*nData)-1] is used by the Report Popup that in turn may call PopupOptions.
(package private) static java.lang.String[] switchOptValue
          The switchOptValue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions.
static float t1Area
          Parameter: Lower spot area sizing threshold -thrArea:a1,-
static float t1Density
          Parameter: Lower spot integrated density sizing threshold -thrDensity:d1,-
static float t1Range
          Parameter: Lower spot max-min density sizing threshold -thrRange:d1,-
static float t1SxSyRatio
          Parameter: Lower spot Sx/Sy sizing threshold -thrSxSyRatio:s1,-
static float t2Area
          Parameter: Upper spot area sizing threshold -thrArea:-,a2
static float t2Density
          Parameter: Upper spot integrated density sizing threshold -thrDensity:-,d2
static float t2Range
          Parameter: Upper spot max-min density sizing threshold -thrRange:-,d2
static float t2SxSyRatio
          Parameter: Upper spot mSx/Sy sizing threshold -thrSxSyRatio:-,s2
static int TEST_LARGE_IMAGE
          Temporary debugging flag for debugging specific large saturated images in findSpot() if this value is >0.
static boolean thrAreaSwitch
          The parsed of Command line + gel.rc state switches
static boolean thrDensitySwitch
          The parsed of Command line + gel.rc state switches
static boolean thrRangeSwitch
          The parsed of Command line + gel.rc state switches
static boolean thrSxSyRatioSwitch
          The parsed of Command line + gel.rc state switches
static boolean timerSwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String tmpDir
          Tmp images directory {projDir}/tmp/
static int UNLABELED_CC_CODE
          pixel code for unlabeled central core (CC)pixel
static boolean updateSwitch
          The parsed of Command line + gel.rc state switches
static boolean usageSwitch
          The parsed of Command line + gel.rc state switches
static boolean USE_13X13
          Use 13x17 or 13x13 filters - BUT NOT BOTH !!!!!
static boolean USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND
          Define background as a pixel as either BKGRD_CODE or ISOLATED_PIXEL_CODE otherwise it is just BKGRD_CODE.
(package private) static boolean USE_DEMO_DATA
          Use the demo data by enabling the -demo flag and data.
(package private) static boolean USE_DOM_XML_SSF
          Use DOM/JDOM/...
static boolean use3x3laplacianSwitch
          The parsed of Command line + gel.rc state switches
static boolean use5x5laplacianSwitch
          The parsed of Command line + gel.rc state switches
static boolean useBkgdAndIsolatedPixelFlag
          Define background as a pixel as either BKGRD_CODE or ISOLATED_PIXEL_CODE otherwise it is just BKGRD_CODE.
static boolean useBusseLaplacianSwitch
          The parsed of Command line + gel.rc state switches
static boolean useCopyOfPix1ForPix5Switch
          The parsed of Command line + gel.rc state switches
static boolean useHistGUISwitch
          The parsed of Command line + gel.rc state switches
static boolean useHorizLineLaplacianSwitch
          The parsed of Command line + gel.rc state switches
static boolean usePopupGUISwitch
          The parsed of Command line + gel.rc state switches
static java.lang.String userDir
          current User directory: getProperty("user.dir")+fileSeparator
static boolean useVertLineLaplacianSwitch
          The parsed of Command line + gel.rc state switches
static Util util
           
static java.lang.String VERSION
          Manually define Version number
static int WHITE
          Pixel color for white
static int widthWindmp
          Parameter threshold windmp window size
static int windmpStepSize
          Parameter threshold windmp sampling size.
static Sg2wrk wrk
           
static int wXsize
          Width offset for threshold Gaussian filter size.
static int wYsize
          Height offset for threshold Gaussian filter size.
static int xDbug
          current spot being analyzed w/debug
static java.lang.String xmlDir
          Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.
static int[] xPentrance
           
static int[] xPexit
           
static int yDbug
          current spot being analyzed w/debug
static int[] yPentrance
           
static int[] yPexit
           
static int yTitle
           
 
Constructor Summary
Sg2glb()
           
 
Method Summary
static int get2D(char[] pix, int x, int y)
          get2D() - get the pixel at pix(x,y) computed at (y+pixelWidth+x)
static int get2D(int[] pix, int x, int y)
          get2D() - get the pixel at pix(x,y) computed at (y+pixelWidth+x)
static int[] getPixLineBuf(int[] lineBuf, char[] pix, int y)
          getPixLineBuf() - get the line y from int[] pix into lineBuf[].
static int[] getPixLineBuf(int[] lineBuf, int[] pix, int y)
          getPixLineBuf() - get the line y from int[] pix into lineBuf[].
static void initGlb()
          initGlb() - intialize any resources that must be set upon startup [TODO] Could move some of the above static defs here...
static boolean isDBwindow()
          isDBwindow() - test if (xDbug,yDbug) is inside the debug window.
static boolean isDBwindow(int x, int y)
          isDBwindow() - test if (x,y) is inside the debug window.
static int put2Dbuf(int[] buf, int x, int g)
          put2Dbuf() - save pixel value g at buf[x]
static void resetGlb()
          resetGlb() - reset any resources that must be reset for the next run of the segmenter.
static int set2D(char[] pix, int x, int y, int g)
          set2D() - save the pixel value g at pix(x,y) computed at (y+pixelWidth+x)
static int set2D(int[] pix, int x, int y, int g)
          set2D() - save the pixel value g at pix(x,y) computed at (y+pixelWidth+x)
static boolean setPixLineBuf(int[] lineBuf, char[] pix, int y)
          setPixLineBuf() - save the line y from int[] pix from lineBuf[]
static boolean setPixLineBuf(int[] lineBuf, int[] pix, int y)
          setPixLineBuf() - save the line y from int[] pix from lineBuf[]
static void showReportStatus(java.lang.String opr)
          showReportStatus() - display the msg in popup report line display And update the timer for the opr
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

applicationName

public static final java.lang.String applicationName
name of the application

See Also:
Constant Field Values

PUBLISH

static boolean PUBLISH
NOTE: overide the following debugging options if publishing on net.


USE_DEMO_DATA

static boolean USE_DEMO_DATA
Use the demo data by enabling the -demo flag and data.


ENABLE_DEVELOPER_DEBUGGING

static boolean ENABLE_DEVELOPER_DEBUGGING
Enable developer debugging when do initial startup.


ENABLE_SPOT_SPLITTING

static boolean ENABLE_SPOT_SPLITTING
Enable debugging -splitSpots analysis


ENABLE_SATURATED_SPOTS

static boolean ENABLE_SATURATED_SPOTS
Enable debugging -saturatedSpots analysis


USE_DOM_XML_SSF

static boolean USE_DOM_XML_SSF
Use DOM/JDOM/... XML SSF output writer instead of print statements


TEST_LARGE_IMAGE

public static int TEST_LARGE_IMAGE
Temporary debugging flag for debugging specific large saturated images in findSpot() if this value is >0. Use 0 for NO large images demo/ppx/testGel-2Kx2K.ssf (2) or (-2 noDbug) demo/ppx/testGel-3Kx3K.ssf (3) or (-3 noDbug)


DBUG_SWITCHES

public static boolean DBUG_SWITCHES
Debugging switches


DBUG_CONSOLE

static final boolean DBUG_CONSOLE
Debugging console text flag

See Also:
Constant Field Values

DATE

public static java.lang.String DATE
CVS Version date


REVISION

public static java.lang.String REVISION
CVS Revision


VERSION

public static java.lang.String VERSION
Manually define Version number


NEVER

public static boolean NEVER
NEVER and CONSOLE_FLAG - debugging variables - must not be final!


CONSOLE_FLAG

public static boolean CONSOLE_FLAG

seg2dgelURL

public static final java.lang.String seg2dgelURL
Hardwired Open2Dprot server connection Switch to S.F. when released on S.F.

See Also:
Constant Field Values

jarFileList

public static java.lang.String[] jarFileList
List of .jar files downloadable from the server


jarLibrFileList

public static java.lang.String[] jarLibrFileList
List of library .jar files downloadable from the server


docFileList

public static java.lang.String[] docFileList
List of documentation files downloadable from the server


demoFileList

public static java.lang.String[] demoFileList
List of demo/ files downloadable from the server


MAX_BUFFERED_SPOTS

public static final int MAX_BUFFERED_SPOTS
max # spots to buffer in memory when converting the list of spots to string representations. If the # of spots is LT this threshold then buffer them, else append the spot string to the file as it is converted.

See Also:
Constant Field Values

MAXSUBSPOTS

public static final int MAXSUBSPOTS
max # subspots a spot can split into

See Also:
Constant Field Values

MAX_INTERIOR_FBL_SIZE

public static final int MAX_INTERIOR_FBL_SIZE
Max interior of spot size. Used if optimizing the FBL for CC's interior to a spot.

See Also:
Constant Field Values

HASHFBLPRIME

public static final int HASHFBLPRIME
Initial prime #size of Final Blob List (FBL) hash table. Old values were 7001, 5003, 2003

See Also:
Constant Field Values

MINSPLITSPOTSIZE

public static final int MINSPLITSPOTSIZE
Minimum spot CC size of spot for it to be allowed to be a candidate for spot splitting.

See Also:
Constant Field Values

MHISTSIZE

public static final int MHISTSIZE
Size of histogram for splitting algorithm

See Also:
Constant Field Values

MINBLOBAREA

public static final int MINBLOBAREA
used in findAllSpots()

See Also:
Constant Field Values

USE_13X13

public static final boolean USE_13X13
Use 13x17 or 13x13 filters - BUT NOT BOTH !!!!!

See Also:
Constant Field Values

WHITE

public static final int WHITE
Pixel color for white

See Also:
Constant Field Values

BLACK

public static final int BLACK
Pixel color for black

See Also:
Constant Field Values

USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND

public static final boolean USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND
Define background as a pixel as either BKGRD_CODE or ISOLATED_PIXEL_CODE otherwise it is just BKGRD_CODE.

See Also:
Constant Field Values

BKGRD_CODE

public static final int BKGRD_CODE
pixel code for the CC background pixel

See Also:
Constant Field Values

UNLABELED_CC_CODE

public static final int UNLABELED_CC_CODE
pixel code for unlabeled central core (CC)pixel

See Also:
Constant Field Values

MIN_CC_CODE

public static final int MIN_CC_CODE
pixel code for minimum labeled central core (CC) pixel

See Also:
Constant Field Values

MAX_CC_CODE

public static final int MAX_CC_CODE
pixel code for maximum labeled central core (CC) pixel

See Also:
Constant Field Values

PCC_BASE_CODE

public static final int PCC_BASE_CODE
pixel code for guard region splitting previously merged spots

See Also:
Constant Field Values

MIN_PCC_CODE

public static final int MIN_PCC_CODE
pixel code for minimum labeled propagated central core (PCC) pixel

See Also:
Constant Field Values

MAX_PCC_CODE

public static final int MAX_PCC_CODE
pixel code for maximum labeled propagated central core (PCC) pixel

See Also:
Constant Field Values

KILL_SPOT_CODE

public static final int KILL_SPOT_CODE
pixel code for deleted spot in central core if NEQ sizing (0 if -noDelete)

See Also:
Constant Field Values

ISOLATED_PIXEL_CODE

public static final int ISOLATED_PIXEL_CODE
pixel code for guard region splitting previously merged spots

See Also:
Constant Field Values

DFT_NO_DB

public static final int DFT_NO_DB
Default data type No-database

See Also:
Constant Field Values

DFT_2D_GEL

public static final int DFT_2D_GEL
Default data type 2D-gel

See Also:
Constant Field Values

DFT_2D_LC_MS

public static final int DFT_2D_LC_MS
Default data type 2D-LC-MS

See Also:
Constant Field Values

DBUG_PIX_DBCODE

public static final int DBUG_PIX_DBCODE
Trace dbugPixDBcode() to print small NxN pixel windows that match the [dbx1:dbx2, dby1:dby2] window. For speed, we map this bit to dbugBitsPixFlag.

See Also:
Constant Field Values

DBUG_FIND_SPOT_LIST

public static final int DBUG_FIND_SPOT_LIST
Trace findSpotList() to find spots

See Also:
Constant Field Values

DBUG_PROP_SAT_SPOTS

public static final int DBUG_PROP_SAT_SPOTS
Trace propSaturatedSpot() to

See Also:
Constant Field Values

DBUG_SPLIT_CHECK_SPOT

public static final int DBUG_SPLIT_CHECK_SPOT
Trace splitCheckSpot() to check and split a spot if it is needed

See Also:
Constant Field Values

DBUG_RMV_CONCAVITIES

public static final int DBUG_RMV_CONCAVITIES
Trace rmvConcavities() to remove concavities in the central core

See Also:
Constant Field Values

DBUG_NBR_COMPONENTS

public static final int DBUG_NBR_COMPONENTS
Trace numberComponents() to number components in the central core

See Also:
Constant Field Values

DBUG_MAX_PROPAGATE

public static final int DBUG_MAX_PROPAGATE
Trace maxPropagate() to expand from the CC to the PCC

See Also:
Constant Field Values

DBUG_FILL_CORNERS

public static final int DBUG_FILL_CORNERS
Trace fillCorners() to fill corners in the current PCC

See Also:
Constant Field Values

DBUG_FILL_HOLES_IN_PCC_CONCAVITIES

public static final int DBUG_FILL_HOLES_IN_PCC_CONCAVITIES
Trace fillHolesInPCCconcavities() to filler corners in PCC concavities

See Also:
Constant Field Values

DBUG_ROUND_CORNERS

public static final int DBUG_ROUND_CORNERS
Trace roundCorners() to round corners of the PCC

See Also:
Constant Field Values

DBUG_PROP_SPOT_TO_2ND_MAXIMA

public static final int DBUG_PROP_SPOT_TO_2ND_MAXIMA
Trace propSpotTo2ndDrivMaxima() to prop CC to 2nd maxima to make PCC

See Also:
Constant Field Values

DBUG_PRINT_GRAY2CAL_MAP

public static final int DBUG_PRINT_GRAY2CAL_MAP
Trace print gray2cal[] to print the gray2cal[] map

See Also:
Constant Field Values

DBUG_RMV_INTERIOR_CC_PIXELS

public static final int DBUG_RMV_INTERIOR_CC_PIXELS
Trace inner loop of rmvInteriorCCpixels() to

See Also:
Constant Field Values

DBUG_CALC_FEATURES

public static final int DBUG_CALC_FEATURES
Trace calcFeatures() where compute spot values from the images & FBL

See Also:
Constant Field Values

DBUG_ADD_INTERIOR_CC_PIXELS

public static final int DBUG_ADD_INTERIOR_CC_PIXELS
Trace inner loop of addInteriorCCpixels() to

See Also:
Constant Field Values

DBUG_INNER_LOOP_FIND_SPOT

public static final int DBUG_INNER_LOOP_FIND_SPOT
Trace inner loop of findSpot() to

See Also:
Constant Field Values

DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS

public static final int DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS
Trace splitPixByFBLboundaryAnal() to

See Also:
Constant Field Values

DBUG_BND_ANALYSIS

public static final int DBUG_BND_ANALYSIS
Trace findBoundary(), pushXYboundary(), resetBnd()

See Also:
Constant Field Values

DBUG_CVT_BND_TO_CHAINCODE

public static final int DBUG_CVT_BND_TO_CHAINCODE
Trace cvtBoundaryToChainCode(), cvtChainCode_to_nextXY()

See Also:
Constant Field Values

DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE

public static final int DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE
Trace findNotches_in_chainCode() to

See Also:
Constant Field Values

DBUG_CHAIN_CODE_RLM_ANALYSIS

public static final int DBUG_CHAIN_CODE_RLM_ANALYSIS
Trace pairChainCodeNotches(), findMinMaxPeaksInRLM()and findPairedNotches_in_RLM()

See Also:
Constant Field Values

DBUG_DRAW_NOTCH_PAIR_LINE

public static final int DBUG_DRAW_NOTCH_PAIR_LINE
Trace drawLineBetweenNotchPair() to

See Also:
Constant Field Values

DBUG_PUSH_XY_INTO_FBL

public static final int DBUG_PUSH_XY_INTO_FBL
Trace pushXYintoFBL() to

See Also:
Constant Field Values

DBUG_DRAW_SAT_SPOT_BND

public static final int DBUG_DRAW_SAT_SPOT_BND
Trace draw boundary of saturated spot CC

See Also:
Constant Field Values

DBUG_DUMP_CC_PPX

public static final int DBUG_DUMP_CC_PPX
Trace dump CC images at key points if enabled in code

See Also:
Constant Field Values

dbugBitsHelpStr

public static final java.lang.String dbugBitsHelpStr
Debug bit options help for error messages

See Also:
Constant Field Values

sg2

public static Seg2Dgel sg2

avg

public static Sg2avg avg

bkg

public static Sg2bkg bkg

cc

public static Sg2cc cc

data

public static Sg2data data

dbug

public static Sg2dbug dbug

draw

public static Sg2draw draw

fbl

public static Sg2fbl fbl

fnd

public static Sg2fnd fnd

ini

public static Sg2ini ini

ngh

public static Sg2ngh ngh

notch

public static Sg2notch notch

rest

public static Sg2rest rest

sat

public static Sg2sat sat

split

public static Sg2split split

wrk

public static Sg2wrk wrk

cal

public static CalibrateOD cal

acc

public static DbAccession acc

dbSample

public static DbSample dbSample
Current sample being analyzed


dbSpot

public static DbSpot dbSpot
Current spot being analyzed


fio

public static FileIO fio

paramH

public static ParamHash paramH

pix

public static PixReader pix

sort

public static Sort sort

util

public static Util util

pra

public static Sg2reportPopup pra
generic popup report


bannerTitle

public static java.lang.String bannerTitle
The short version data banner for popup titles


banner

public static java.lang.String banner
The full version data banner with todays date


legalImageFileExtens

public static final java.lang.String[] legalImageFileExtens
List of legal gel image file extensions


accFile

public static java.lang.String accFile
Accession database file if exists


accDatabaseFile

public static java.lang.String accDatabaseFile
Full path Accession database file if exists which is xmlDir+accFile


propertiesFile

public static java.lang.String propertiesFile
Current startup properties file containing default switches if it exists. Set by -propertiesFile:< new file >


pixFileExtn

public static java.lang.String pixFileExtn
Output images are either ".gif" or ".jpg" [TODO] change this to .jpg with JPEG writer.


inPixFile

public static java.lang.String inPixFile
original gel input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions.


simpleFileName

public static java.lang.String simpleFileName
Simple file name is the original gel input image file without the directory and WITH the file extension. Derived from inPixFile or accession database lookup.


baseImageFileName

public static java.lang.String baseImageFileName
Base file name is the original gel input image file without the directory and WITHOUT the file extension. Derived from inPixFile or accession database lookup.


avgPixFile

public static java.lang.String avgPixFile
tmp/average image file


calFile

public static java.lang.String calFile
[DEPRICATE] cal/<.cal calibration file>


ccPixFile

public static java.lang.String ccPixFile
tmp/central core image file


mag2ndPixFile

public static java.lang.String mag2ndPixFile
tmp/magnitude of 2nd directive image file


bkgrdPixFile

public static java.lang.String bkgrdPixFile
tmp/notch filter background image file


segPixFile

public static java.lang.String segPixFile
tmp/segmented image image file


restOfPixFile

public static java.lang.String restOfPixFile
tmp/central core image file


ssfOutputFile

public static java.lang.String ssfOutputFile
xml/ Sample Spot-list File full path


ssfOutputPrefaceFile

public static java.lang.String ssfOutputPrefaceFile
full tab-delim PREFACE xml/ Sample Spot-list File full path


ssfOutputEpilogueFile

public static java.lang.String ssfOutputEpilogueFile
full tab-delim EPILOGUE xml/ Sample Spot-list File full path


rlmCWfile

public static java.lang.String rlmCWfile
tmp/RML CW file


osName

public static java.lang.String osName
name of this operating system: Property("os.name")


fileSeparator

public static java.lang.String fileSeparator
File separator: Property("file.separator")


userDir

public static java.lang.String userDir
current User directory: getProperty("user.dir")+fileSeparator


projDir

public static java.lang.String projDir
Project directory that is either userDir, specified by -projDir:{path}, or extracted from the input file path it the image is in a "/ppx/" subdirectory.


pixDir

public static java.lang.String pixDir
Original image directory used in picking off project diredctory. May or may not be same as ppxDir


batchDir

public static java.lang.String batchDir
Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/


cacheDir

public static java.lang.String cacheDir
Cache database directory {projDir}/cache/


ppxDir

public static java.lang.String ppxDir
Original sample images directory {projDir}/ppx/


rdbmsDir

public static java.lang.String rdbmsDir
RDBMS database directory {projDir}/rdbms/


tmpDir

public static java.lang.String tmpDir
Tmp images directory {projDir}/tmp/


xmlDir

public static java.lang.String xmlDir
Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.


argsV

public static java.lang.String[] argsV
Total command list arg list originally set fro main(args)


sw

public static java.lang.String[] sw
Command line + Seg2Dgel.properties state switches


nSwitches

public static int nSwitches
the number of Command line + gel.rc state switches


accDatabaseSwitch

public static boolean accDatabaseSwitch
The parsed of Command line + gel.rc state switches


allowTouchingEdgesSwitch

public static boolean allowTouchingEdgesSwitch
The parsed of Command line + gel.rc state switches


averageODSwitch

public static boolean averageODSwitch
The parsed of Command line + gel.rc state switches


bkgrdSizeFlag

public static boolean bkgrdSizeFlag
The parsed of Command line + gel.rc state switches


bkgrdCorrectionSwitch

public static boolean bkgrdCorrectionSwitch
The parsed of Command line + gel.rc state switches


boundaryInSSFSwitch

public static boolean boundaryInSSFSwitch
The parsed of Command line + gel.rc state switches


ccMinSizeSwitch

public static boolean ccMinSizeSwitch
The parsed of Command line + gel.rc state switches


ctlCorePixSwitch

public static boolean ctlCorePixSwitch
The parsed of Command line + gel.rc state switches


computingWindowSwitch

public static boolean computingWindowSwitch
The parsed of Command line + gel.rc state switches


debugSwitch

public static boolean debugSwitch
The parsed of Command line + gel.rc state switches


defaultSwitch

public static boolean defaultSwitch
The parsed of Command line + gel.rc state switches


demoSwitch

public static boolean demoSwitch
The parsed of Command line + gel.rc state switches


drawTitleSwitch

public static boolean drawTitleSwitch
The parsed of Command line + gel.rc state switches


diffODSwitch

public static boolean diffODSwitch
The parsed of Command line + gel.rc state switches


deleteIsolatedPixelsSwitch

public static boolean deleteIsolatedPixelsSwitch
The parsed of Command line + gel.rc state switches


dotsSwitch

public static boolean dotsSwitch
The parsed of Command line + gel.rc state switches


drawPlusSwitch

public static boolean drawPlusSwitch
The parsed of Command line + gel.rc state switches


drawBoundarySwitch

public static boolean drawBoundarySwitch
The parsed of Command line + gel.rc state switches


drawMERSwitch

public static boolean drawMERSwitch
The parsed of Command line + gel.rc state switches


drawSxSyEllipseSwitch

public static boolean drawSxSyEllipseSwitch
The parsed of Command line + gel.rc state switches


ssfFormatSwitch

public static boolean ssfFormatSwitch
The parsed of Command line + gel.rc state switches


dtdSwitch

public static boolean dtdSwitch
The parsed of Command line + gel.rc state switches


keepInputImageSwitch

public static boolean keepInputImageSwitch
The parsed of Command line + gel.rc state switches


laplacianSwitch

public static boolean laplacianSwitch
The parsed of Command line + gel.rc state switches


lowpassSwitch

public static boolean lowpassSwitch
The parsed of Command line + gel.rc state switches


lp3x3Switch

public static boolean lp3x3Switch
The parsed of Command line + gel.rc state switches


lp5x5Switch

public static boolean lp5x5Switch
The parsed of Command line + gel.rc state switches


lp7x7Switch

public static boolean lp7x7Switch
The parsed of Command line + gel.rc state switches


lp13xZZSwitch

public static boolean lp13xZZSwitch
The parsed of Command line + gel.rc state switches


pixDumpSwitch

public static boolean pixDumpSwitch
The parsed of Command line + gel.rc state switches


projDirSwitch

public static boolean projDirSwitch
The parsed of Command line + gel.rc state switches


propertiesFileSwitch

public static boolean propertiesFileSwitch
The parsed of Command line + gel.rc state switches


optimizeInteriorFBLSwitch

public static boolean optimizeInteriorFBLSwitch
The parsed of Command line + gel.rc state switches


restOfPixSwitch

public static boolean restOfPixSwitch
The parsed of Command line + gel.rc state switches


rmvDprimeSizingSwitch

public static boolean rmvDprimeSizingSwitch
The parsed of Command line + gel.rc state switches


quickEstimateSwitch

public static boolean quickEstimateSwitch
The parsed of Command line + gel.rc state switches


sampleSwitch

public static boolean sampleSwitch
The parsed of Command line + gel.rc state switches


saturatedSpotSwitch

public static boolean saturatedSpotSwitch
The parsed of Command line + gel.rc state switches


segPixSwitch

public static boolean segPixSwitch
The parsed of Command line + gel.rc state switches


splitSpotSwitch

public static boolean splitSpotSwitch
The parsed of Command line + gel.rc state switches


splitLargeCCfblByBndAnalSwitch

public static boolean splitLargeCCfblByBndAnalSwitch
The parsed of Command line + gel.rc state switches


splitLargeCCfblByRLManalSwitch

public static boolean splitLargeCCfblByRLManalSwitch
The parsed of Command line + gel.rc state switches


splitLargeCCfblByThreshAnalSwitch

public static boolean splitLargeCCfblByThreshAnalSwitch
The parsed of Command line + gel.rc state switches


thrAreaSwitch

public static boolean thrAreaSwitch
The parsed of Command line + gel.rc state switches


thrDensitySwitch

public static boolean thrDensitySwitch
The parsed of Command line + gel.rc state switches


thrRangeSwitch

public static boolean thrRangeSwitch
The parsed of Command line + gel.rc state switches


thrSxSyRatioSwitch

public static boolean thrSxSyRatioSwitch
The parsed of Command line + gel.rc state switches


timerSwitch

public static boolean timerSwitch
The parsed of Command line + gel.rc state switches


updateSwitch

public static boolean updateSwitch
The parsed of Command line + gel.rc state switches


usePopupGUISwitch

public static boolean usePopupGUISwitch
The parsed of Command line + gel.rc state switches


useHistGUISwitch

public static boolean useHistGUISwitch
The parsed of Command line + gel.rc state switches


useCopyOfPix1ForPix5Switch

public static boolean useCopyOfPix1ForPix5Switch
The parsed of Command line + gel.rc state switches


use3x3laplacianSwitch

public static boolean use3x3laplacianSwitch
The parsed of Command line + gel.rc state switches


use5x5laplacianSwitch

public static boolean use5x5laplacianSwitch
The parsed of Command line + gel.rc state switches


useBusseLaplacianSwitch

public static boolean useBusseLaplacianSwitch
The parsed of Command line + gel.rc state switches


useHorizLineLaplacianSwitch

public static boolean useHorizLineLaplacianSwitch
The parsed of Command line + gel.rc state switches


useVertLineLaplacianSwitch

public static boolean useVertLineLaplacianSwitch
The parsed of Command line + gel.rc state switches


usageSwitch

public static boolean usageSwitch
The parsed of Command line + gel.rc state switches


coneOfSilenceMode

public static char coneOfSilenceMode
The filter type set by the command line switch -laplacian:B,{P|C}, switch where type is either 'C' or 'P'.


drawDotOverlayType

public static char drawDotOverlayType
The drawing overlay type is set by the command line switch -drawDot:{O | Z}


drawPlusOverlayType

public static char drawPlusOverlayType
The drawing overlay type is set by the command line switch -drawPlus:{O | Z}


drawBoundaryOverlayType

public static char drawBoundaryOverlayType
The drawing overlay type is set by the command line switch -drawBoundaryt:{O | Z}


drawMEROverlayType

public static char drawMEROverlayType
The drawing overlay type is set by the command line switch -drawMinEnclRect:{O | Z}


drawSxSyOverlayType

public static char drawSxSyOverlayType
The drawing overlay type is set by the command line switch -drawSxSyEllipse:{O | Z}


defaultTypeCode

public static int defaultTypeCode
Default type for -default: The code is from the list: DFT_2D_GEL, DFT_2D_LC_MS, etc.


lowPassSize

public static int lowPassSize
The low pass filter width (3x3, 5x5, 7x7, 13x17(13)) -lowpassFilter:


accFormatMode

public static int accFormatMode
Accession file input file format mode set by the command line switch -accessionDB:accession.txt or -accessionDB:accession.xml This then gets mapped to either FileIO.IO_FORMAT_XML or IO_FORMAT_TAB_DELIMITED.


ssfFormatMode

public static int ssfFormatMode
SSF output file format mode set by the command line switch ssfFormat:<{F|L|T|X}> where mode is either 'F', 'L', 'T' or 'X'. This is one of the FileIO.IO_FORMAT_xxxx constants and is used in various output switch statements.


didSplitSpotFlag

public static boolean didSplitSpotFlag
For debugging - to abort seg and dump intermediate images.


didPropSaturatedSpots

public static boolean didPropSaturatedSpots
For debugging - to avoid re-propagating split spots


useBkgdAndIsolatedPixelFlag

public static boolean useBkgdAndIsolatedPixelFlag
Define background as a pixel as either BKGRD_CODE or ISOLATED_PIXEL_CODE otherwise it is just BKGRD_CODE.


dbugBitsPixFlag

public static boolean dbugBitsPixFlag
Special test for DBUG_PIX_NXN bit to to print windows that match the [dbx1:dbx2, dby1:dby2] window. For speed, we map this bit to dbugBitsPixFlag.


fourSqrtPi

public static float fourSqrtPi
Constant 4*sqrt(PI) constant used in computing spot volume


ccMinSize

public static int ccMinSize
Parameter threshold min # pixels/CC spot


gridSize

public static int gridSize
Parameter threshold grid size i.e. (n/2) for the -laplacian:B,{P|C},


dbugBits

public static int dbugBits
Parameter threshold -DEBUG:bits


splitMinCCsize

public static int splitMinCCsize
Parameter threshold lower |CC| bound for splitting spots


nBkgrdSize

public static int nBkgrdSize
Parameter threshold -background:32, Size of sq. bkgd avg window


widthWindmp

public static int widthWindmp
Parameter threshold windmp window size


maxColsToPrint

public static int maxColsToPrint
Parameter threshold max # cols width to print winDump


windmpStepSize

public static int windmpStepSize
Parameter threshold windmp sampling size. default: sample 1:1


wXsize

public static int wXsize
Width offset for threshold Gaussian filter size. This is reset by -lowpassFilter:


wYsize

public static int wYsize
Height offset for threshold Gaussian filter size. This is reset by -lowpassFilter:


lineLaplacianWidth

public static int lineLaplacianWidth
Width for -laplacian:{H|V},, line laplacian filter.


lineLaplacianHeight

public static int lineLaplacianHeight
Height for -laplacian:L,, line laplacian filter.


glbPercentThr

public static float glbPercentThr
Parameters and thresholds


sizeFractionGaussianWidth

public static float sizeFractionGaussianWidth
Parameters and thresholds


histThreshold

public static float histThreshold
Parameters and thresholds


t1Area

public static float t1Area
Parameter: Lower spot area sizing threshold -thrArea:a1,-


t2Area

public static float t2Area
Parameter: Upper spot area sizing threshold -thrArea:-,a2


t1Density

public static float t1Density
Parameter: Lower spot integrated density sizing threshold -thrDensity:d1,-


t2Density

public static float t2Density
Parameter: Upper spot integrated density sizing threshold -thrDensity:-,d2


t1Range

public static float t1Range
Parameter: Lower spot max-min density sizing threshold -thrRange:d1,-


t2Range

public static float t2Range
Parameter: Upper spot max-min density sizing threshold -thrRange:-,d2


t1SxSyRatio

public static float t1SxSyRatio
Parameter: Lower spot Sx/Sy sizing threshold -thrSxSyRatio:s1,-


t2SxSyRatio

public static float t2SxSyRatio
Parameter: Upper spot mSx/Sy sizing threshold -thrSxSyRatio:-,s2


ccNum

public static int ccNum
initial central core spot number


spotNumber

public static int spotNumber
initial spot number


yTitle

public static int yTitle

hashFBL

public static Sg2hash hashFBL
Hash table for FBL used to quickly determine if an (x,y) coord is in the FBL.


hashWS

public static Sg2hash hashWS
Hash table for WS used to quickly determine if an (x,y) coord is in the Working Stack (WS).


startTime

public static long startTime
starting time in epoch msec time


statusStartTime

public static long[] statusStartTime
Report status starting times entries in epoch msec time Saved when do util.showReportStatus(name) calls. Ignore "Line# ..." names. Size [0:MAX_STATUS_TIMES-1]


statusMemoryTot

public static long[] statusMemoryTot
Report status memory Total. Saved when do util.showReportStatus(name) calls. Ignore "Line# ..." names. Size [0:MAX_STATUS_TIMES-1]


statusMemoryFree

public static long[] statusMemoryFree
Report status memory Free. Saved when do util.showReportStatus(name) calls. Ignore "Line# ..." names. Size [0:MAX_STATUS_TIMES-1]


statusName

public static java.lang.String[] statusName
Report status names saved when do util.showReportStatus(name) calls. Ignore "Line# ..." names. Size [0:MAX_STATUS_TIMES-1]


nStatusName

public static int nStatusName
# of Report status names saved when do util.showReportStatus(name) calls. Ignore "Line# ..." names.


baseStatusTime

public static long baseStatusTime
base starting time in epoch msec time for the status reports


killSpotColor

public static int killSpotColor
Spot color used for deleted spots. This is synced with
 -deleteIsolatedPixels  killSpotColor
 ---------------------  -------------
    true                KILL_SPOT_CODE
    false               BKGRD_CODE


cwx1

public static int cwx1
ULHC X computing window for entire input gel image


cwx2

public static int cwx2
LRHC X computing window for entire input gel image


cwy1

public static int cwy1
ULHC Y computing window for entire input gel image


cwy2

public static int cwy2
LRHC Y computing window for entire input gel image


merx1

public static int merx1
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]


merx2

public static int merx2
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]


mery1

public static int mery1
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]


mery2

public static int mery2
The final spot minimum enclosing rectangle captured when computeFeatures() when it copies the mer[xy]p[12] data that is then copied to the mer[xy][12]


meryp1

public static int meryp1
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.


meryp2

public static int meryp2
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.


merxp1

public static int merxp1
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.


merxp2

public static int merxp2
Working minimum enclosing rectangle created as we do saveFPL() or pushFBL() calls.


dpx1

public static int dpx1
Debugging window for -pixdump: window


dpx2

public static int dpx2
Debugging window for -pixdump: window


dpy1

public static int dpy1
Debugging window for -pixdump: window


dpy2

public static int dpy2
Debugging window for -pixdump: window


dbx1

public static int dbx1
Debugging window for -debug: window


dbx2

public static int dbx2
Debugging window for -debug: window


dby1

public static int dby1
Debugging window for -debug: window


dby2

public static int dby2
Debugging window for -debug: window


xDbug

public static int xDbug
current spot being analyzed w/debug


yDbug

public static int yDbug
current spot being analyzed w/debug


xPentrance

public static int[] xPentrance

xPexit

public static int[] xPexit

yPentrance

public static int[] yPentrance

yPexit

public static int[] yPexit

pixelSizeMicrons

public static float pixelSizeMicrons
Pixel resolution in the gel image in microns/pixel


pixWidth

public static int pixWidth
Input gel image size: width


pixHeight

public static int pixHeight
Input gel image size: height


nPixels

public static int nPixels
total # of pixels in image = pixWidth*pixHeight


nBytesPerPixel

public static int nBytesPerPixel
# of bytes/pixel in the image


nBitsPerPixel

public static int nBitsPerPixel
# of bits/pixel in the image


maxGrayPixel

public static int maxGrayPixel
max Gray Pixel value in the image is (1<

gray2cal

public static int[] gray2cal

cal2gray

public static int[] cal2gray
map pixel gray values to calibration value (e.g., OD) by scaling it as: OD*1000 to gray Size [0:maxGrayPixel]


scaledMaxOD

public static int scaledMaxOD
This is the max value index for cal2gray[] it is computed as cal2gray.length-1


gHist

public static int[] gHist
Histogram of pix4 AVERAGE Size [0:maxGrayPixel+1]


minGhist

public static int minGhist
Histogram statistics [for use in FUTURE]


maxGhist

public static int maxGhist
Histogram statistics [for use in FUTURE]


meanGhist

public static int meanGhist
Histogram statistics [for use in FUTURE]


pTileGhist

public static int pTileGhist
Histogram statistics [for use in FUTURE]


pix1

public static char[] pix1
original gel image 16-bit unsigned char in int[], or nBitsPerPixel scaled to 16-bits.


pix2

public static char[] pix2
magnitude Laplacian image with mag2ndPixFile. It is 16-bit unsigned char in int[].


pix3

public static char[] pix3
central core image with ccPixFile. It is 16-bit unsigned char in int[]


pix4

public static char[] pix4
Averaged gel image after gaussian smoothing with avgPixFile. It is 16-bit unsigned char in int[].


pix5

public static char[] pix5
Segmented spots output Z image with no background with segPixFile. It is 16-bit unsigned char in int[].


pix6

public static char[] pix6
Background OD image with bkgrdPixFile. It is 16-bit unsigned char[].


pix7

public static char[] pix7
Rest-of output image with restOfPixFile. It is 16-bit unsigned char in int[].


bfogm5

public static int[] bfogm5
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogm4

public static int[] bfogm4
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogm3

public static int[] bfogm3
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogm2

public static int[] bfogm2
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogm1

public static int[] bfogm1
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogm

public static int[] bfogm
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfog

public static int[] bfog
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogp

public static int[] bfogp
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogp1

public static int[] bfogp1
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogp2

public static int[] bfogp2
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogp3

public static int[] bfogp3
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogp4

public static int[] bfogp4
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfogp5

public static int[] bfogp5
Input image - 16-bit unsigned char in int[] line buffers for buffered images [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  m5        y-5
  m4        y-4
  m3        y-3
  m2        y-2
  m1        y-1
  -         y
  p1        y+1
  p2        y+2
  p3        y+3
  p4        y+4
  p5        y+5


bfavm1

public static int[] bfavm1
Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  avm1       y-2
  avm        y-1
  av         y
  avp        y+1
  av1        y+2


bfavm

public static int[] bfavm
Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  avm1       y-2
  avm        y-1
  av         y
  avp        y+1
  av1        y+2


bfav

public static int[] bfav
Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  avm1       y-2
  avm        y-1
  av         y
  avp        y+1
  av1        y+2


bfavp

public static int[] bfavp
Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  avm1       y-2
  avm        y-1
  av         y
  avp        y+1
  av1        y+2


bfavp1

public static int[] bfavp1
Average buffered images - unsigned 16-bit line buffers [0:pixWidth-1]
  postfix   line relative to y
  -------   ------------------
  avm1       y-2
  avm        y-1
  av         y
  avp        y+1
  av1        y+2


bufbkg

public static int[] bufbkg
Background buffered image - unsigned 16-bit line buffer [0:pixWidth-1]


bufmag

public static int[] bufmag
Magnitude buffered image - unsigned 16-bit line buffer [0:pixWidth-1]


bufrest

public static int[] bufrest
Rest-of buffered image - unsigned 16-bit line buffer [0:pixWidth-1]


bufcc

public static int[] bufcc
Rest-of buffered image - unsigned 16-bit line buffer [0:pixWidth-1]


i10

public static int i10
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i11

public static int i11
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i12

public static int i12
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i13

public static int i13
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i14

public static int i14
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i15

public static int i15
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i16

public static int i16
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i17

public static int i17
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i18

public static int i18
Gray scale intensity 3X3 neighborhood
 i13 i12 i11
 i14 i18 i10
 i15 i16 i17


i4L

public static int i4L
Extended 5x5 neighborhood for 3x3 'Busse' filter
         i2U
     i13 i12 i11
 i4L i14 i18 i10 i0R
     i15 i16 i17
         i6D


i0R

public static int i0R
Extended 5x5 neighborhood for 3x3 'Busse' filter
         i2U
     i13 i12 i11
 i4L i14 i18 i10 i0R
     i15 i16 i17
         i6D


i2U

public static int i2U
Extended 5x5 neighborhood for 3x3 'Busse' filter
         i2U
     i13 i12 i11
 i4L i14 i18 i10 i0R
     i15 i16 i17
         i6D


i6D

public static int i6D
Extended 5x5 neighborhood for 3x3 'Busse' filter
         i2U
     i13 i12 i11
 i4L i14 i18 i10 i0R
     i15 i16 i17
         i6D


c11

public static int c11
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c12

public static int c12
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c13

public static int c13
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c14

public static int c14
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c15

public static int c15
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c16

public static int c16
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c17

public static int c17
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c18

public static int c18
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c19

public static int c19
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1a

public static int c1a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1b

public static int c1b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1c

public static int c1c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1d

public static int c1d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1e

public static int c1e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1f

public static int c1f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1g

public static int c1g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c1h

public static int c1h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c21

public static int c21
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c22

public static int c22
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c23

public static int c23
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c24

public static int c24
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c25

public static int c25
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c26

public static int c26
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c27

public static int c27
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c28

public static int c28
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c29

public static int c29
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2a

public static int c2a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2b

public static int c2b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2c

public static int c2c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2d

public static int c2d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2e

public static int c2e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2f

public static int c2f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2g

public static int c2g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c2h

public static int c2h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c31

public static int c31
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c32

public static int c32
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c33

public static int c33
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c34

public static int c34
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c35

public static int c35
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c36

public static int c36
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c37

public static int c37
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c38

public static int c38
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c39

public static int c39
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3a

public static int c3a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3b

public static int c3b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3c

public static int c3c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3d

public static int c3d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3e

public static int c3e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3f

public static int c3f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3g

public static int c3g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c3h

public static int c3h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c41

public static int c41
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c42

public static int c42
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c43

public static int c43
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c44

public static int c44
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c45

public static int c45
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c46

public static int c46
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c47

public static int c47
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c48

public static int c48
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c49

public static int c49
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4a

public static int c4a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4b

public static int c4b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4c

public static int c4c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4d

public static int c4d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4e

public static int c4e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4f

public static int c4f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4g

public static int c4g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c4h

public static int c4h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c51

public static int c51
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c52

public static int c52
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c53

public static int c53
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c54

public static int c54
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c55

public static int c55
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c56

public static int c56
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c57

public static int c57
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c58

public static int c58
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c59

public static int c59
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5a

public static int c5a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5b

public static int c5b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5c

public static int c5c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5d

public static int c5d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5e

public static int c5e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5f

public static int c5f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5g

public static int c5g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c5h

public static int c5h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c61

public static int c61
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c62

public static int c62
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c63

public static int c63
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c64

public static int c64
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c65

public static int c65
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c66

public static int c66
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c67

public static int c67
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c68

public static int c68
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c69

public static int c69
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6a

public static int c6a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6b

public static int c6b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6c

public static int c6c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6d

public static int c6d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6e

public static int c6e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6f

public static int c6f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6g

public static int c6g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c6h

public static int c6h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c71

public static int c71
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c72

public static int c72
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c73

public static int c73
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c74

public static int c74
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c75

public static int c75
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c76

public static int c76
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c77

public static int c77
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c78

public static int c78
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c79

public static int c79
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7a

public static int c7a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7b

public static int c7b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7c

public static int c7c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7d

public static int c7d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7e

public static int c7e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7f

public static int c7f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7g

public static int c7g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c7h

public static int c7h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c81

public static int c81
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c82

public static int c82
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c83

public static int c83
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c84

public static int c84
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c85

public static int c85
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c86

public static int c86
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c87

public static int c87
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c88

public static int c88
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c89

public static int c89
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8a

public static int c8a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8b

public static int c8b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8c

public static int c8c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8d

public static int c8d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8e

public static int c8e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8f

public static int c8f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8g

public static int c8g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c8h

public static int c8h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c91

public static int c91
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c92

public static int c92
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c93

public static int c93
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c94

public static int c94
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c95

public static int c95
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c96

public static int c96
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c97

public static int c97
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c98

public static int c98
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c99

public static int c99
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9a

public static int c9a
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9b

public static int c9b
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9c

public static int c9c
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9d

public static int c9d
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9e

public static int c9e
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9f

public static int c9f
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9g

public static int c9g
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


c9h

public static int c9h
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca1

public static int ca1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca2

public static int ca2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca3

public static int ca3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca4

public static int ca4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca5

public static int ca5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca6

public static int ca6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca7

public static int ca7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca8

public static int ca8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ca9

public static int ca9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


caa

public static int caa
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cab

public static int cab
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cac

public static int cac
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cad

public static int cad
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cae

public static int cae
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


caf

public static int caf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cag

public static int cag
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cah

public static int cah
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb1

public static int cb1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb2

public static int cb2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb3

public static int cb3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb4

public static int cb4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb5

public static int cb5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb6

public static int cb6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb7

public static int cb7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb8

public static int cb8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cb9

public static int cb9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cba

public static int cba
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbb

public static int cbb
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbc

public static int cbc
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbd

public static int cbd
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbe

public static int cbe
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbf

public static int cbf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbg

public static int cbg
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cbh

public static int cbh
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc1

public static int cc1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc2

public static int cc2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc3

public static int cc3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc4

public static int cc4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc5

public static int cc5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc6

public static int cc6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc7

public static int cc7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc8

public static int cc8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cc9

public static int cc9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cca

public static int cca
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ccb

public static int ccb
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ccc

public static int ccc
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ccd

public static int ccd
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cce

public static int cce
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ccf

public static int ccf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


ccg

public static int ccg
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cch

public static int cch
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd1

public static int cd1
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd2

public static int cd2
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd3

public static int cd3
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd4

public static int cd4
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd5

public static int cd5
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd6

public static int cd6
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd7

public static int cd7
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd8

public static int cd8
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cd9

public static int cd9
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cda

public static int cda
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cdb

public static int cdb
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cdc

public static int cdc
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cdd

public static int cdd
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cde

public static int cde
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cdf

public static int cdf
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cdg

public static int cdg
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


cdh

public static int cdh
Central core convolution gaussian filter data and for other filters up to a 13x17 neighborhood


j11

public static int j11
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j12

public static int j12
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j13

public static int j13
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j14

public static int j14
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j15

public static int j15
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j16

public static int j16
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j17

public static int j17
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j18

public static int j18
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j19

public static int j19
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1a

public static int j1a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1b

public static int j1b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1c

public static int j1c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1d

public static int j1d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1e

public static int j1e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1f

public static int j1f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1g

public static int j1g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j1h

public static int j1h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j21

public static int j21
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j22

public static int j22
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j23

public static int j23
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j24

public static int j24
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j25

public static int j25
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j26

public static int j26
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j27

public static int j27
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j28

public static int j28
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j29

public static int j29
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2a

public static int j2a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2b

public static int j2b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2c

public static int j2c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2d

public static int j2d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2e

public static int j2e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2f

public static int j2f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2g

public static int j2g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j2h

public static int j2h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j31

public static int j31
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j32

public static int j32
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j33

public static int j33
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j34

public static int j34
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j35

public static int j35
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j36

public static int j36
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j37

public static int j37
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j38

public static int j38
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j39

public static int j39
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3a

public static int j3a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3b

public static int j3b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3c

public static int j3c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3d

public static int j3d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3e

public static int j3e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3f

public static int j3f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3g

public static int j3g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j3h

public static int j3h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j41

public static int j41
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j42

public static int j42
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j43

public static int j43
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j44

public static int j44
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j45

public static int j45
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j46

public static int j46
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j47

public static int j47
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j48

public static int j48
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j49

public static int j49
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4a

public static int j4a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4b

public static int j4b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4c

public static int j4c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4d

public static int j4d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4e

public static int j4e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4f

public static int j4f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4g

public static int j4g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j4h

public static int j4h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j51

public static int j51
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j52

public static int j52
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j53

public static int j53
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j54

public static int j54
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j55

public static int j55
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j56

public static int j56
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j57

public static int j57
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j58

public static int j58
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j59

public static int j59
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5a

public static int j5a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5b

public static int j5b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5c

public static int j5c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5d

public static int j5d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5e

public static int j5e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5f

public static int j5f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5g

public static int j5g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j5h

public static int j5h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j61

public static int j61
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j62

public static int j62
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j63

public static int j63
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j64

public static int j64
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j65

public static int j65
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j66

public static int j66
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j67

public static int j67
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j68

public static int j68
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j69

public static int j69
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6a

public static int j6a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6b

public static int j6b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6c

public static int j6c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6d

public static int j6d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6e

public static int j6e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6f

public static int j6f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6g

public static int j6g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j6h

public static int j6h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j71

public static int j71
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j72

public static int j72
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j73

public static int j73
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j74

public static int j74
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j75

public static int j75
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j76

public static int j76
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j77

public static int j77
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j78

public static int j78
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j79

public static int j79
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7a

public static int j7a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7b

public static int j7b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7c

public static int j7c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7d

public static int j7d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7e

public static int j7e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7f

public static int j7f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7g

public static int j7g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j7h

public static int j7h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j81

public static int j81
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j82

public static int j82
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j83

public static int j83
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j84

public static int j84
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j85

public static int j85
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j86

public static int j86
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j87

public static int j87
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j88

public static int j88
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j89

public static int j89
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8a

public static int j8a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8b

public static int j8b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8c

public static int j8c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8d

public static int j8d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8e

public static int j8e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8f

public static int j8f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8g

public static int j8g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j8h

public static int j8h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j91

public static int j91
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j92

public static int j92
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j93

public static int j93
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j94

public static int j94
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j95

public static int j95
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j96

public static int j96
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j97

public static int j97
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j98

public static int j98
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j99

public static int j99
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9a

public static int j9a
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9b

public static int j9b
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9c

public static int j9c
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9d

public static int j9d
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9e

public static int j9e
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9f

public static int j9f
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9g

public static int j9g
Grayscale intensity data for other filters for up to a 13x17 neighborhood


j9h

public static int j9h
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja1

public static int ja1
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja2

public static int ja2
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja3

public static int ja3
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja4

public static int ja4
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja5

public static int ja5
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja6

public static int ja6
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja7

public static int ja7
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja8

public static int ja8
Grayscale intensity data for other filters for up to a 13x17 neighborhood


ja9

public static int ja9
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jaa

public static int jaa
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jab

public static int jab
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jac

public static int jac
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jad

public static int jad
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jae

public static int jae
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jaf

public static int jaf
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jag

public static int jag
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jah

public static int jah
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb1

public static int jb1
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb2

public static int jb2
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb3

public static int jb3
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb4

public static int jb4
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb5

public static int jb5
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb6

public static int jb6
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb7

public static int jb7
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb8

public static int jb8
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jb9

public static int jb9
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jba

public static int jba
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbb

public static int jbb
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbc

public static int jbc
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbd

public static int jbd
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbe

public static int jbe
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbf

public static int jbf
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbg

public static int jbg
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jbh

public static int jbh
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc1

public static int jc1
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc2

public static int jc2
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc3

public static int jc3
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc4

public static int jc4
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc5

public static int jc5
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc6

public static int jc6
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc7

public static int jc7
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc8

public static int jc8
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jc9

public static int jc9
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jca

public static int jca
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jcb

public static int jcb
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jcc

public static int jcc
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jcd

public static int jcd
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jce

public static int jce
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jcf

public static int jcf
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jcg

public static int jcg
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jch

public static int jch
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd1

public static int jd1
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd2

public static int jd2
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd3

public static int jd3
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd4

public static int jd4
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd5

public static int jd5
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd6

public static int jd6
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd7

public static int jd7
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd8

public static int jd8
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jd9

public static int jd9
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jda

public static int jda
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jdb

public static int jdb
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jdc

public static int jdc
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jdd

public static int jdd
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jde

public static int jde
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jdf

public static int jdf
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jdg

public static int jdg
Grayscale intensity data for other filters for up to a 13x17 neighborhood


jdh

public static int jdh
Grayscale intensity data for other filters for up to a 13x17 neighborhood


switchOptData

static java.lang.String[] switchOptData
The switchOptData[0:(2*nData)-1] is used by the Report Popup that in turn may call PopupOptions. It contains pairs of (prompt, helpStr) data. If the prompt data has a "-", then make a CheckBox (switchOptCBvalue), else it is a Label with the prompt data. If the user data is not null, then make a TextField with this user (switchOptValue) data on the right else make an empty Label.


switchOptCBvalue

static boolean[] switchOptCBvalue
The switchOptcCBvalue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions. It contains boolean values of switch data use for Checkboxes.


switchOptValue

static java.lang.String[] switchOptValue
The switchOptValue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions. It contains String values of associated switch data.

Constructor Detail

Sg2glb

public Sg2glb()
Method Detail

initGlb

public static void initGlb()
initGlb() - intialize any resources that must be set upon startup [TODO] Could move some of the above static defs here...


resetGlb

public static void resetGlb()
resetGlb() - reset any resources that must be reset for the next run of the segmenter. [TODO] Could move a subset of the above static defs here...


getPixLineBuf

public static final int[] getPixLineBuf(int[] lineBuf,
                                        int[] pix,
                                        int y)
getPixLineBuf() - get the line y from int[] pix into lineBuf[].

Parameters:
lineBuf - array predefined of [pixWidth].
pix - is the image buffer
y - is the line to use
Returns:
lineBuf[] with the data, else zero-filled array if problem

getPixLineBuf

public static final int[] getPixLineBuf(int[] lineBuf,
                                        char[] pix,
                                        int y)
getPixLineBuf() - get the line y from int[] pix into lineBuf[].

Parameters:
lineBuf - array predefined of [pixWidth].
pix - is the image buffer
y - is the line to use
Returns:
lineBuf[] with the data, else zero-filled array if problem

setPixLineBuf

public static final boolean setPixLineBuf(int[] lineBuf,
                                          int[] pix,
                                          int y)
setPixLineBuf() - save the line y from int[] pix from lineBuf[]

Parameters:
lineBuf - array predefined of [pixWidth]
pix - is the image buffer
y - is the line to use
Returns:
true if succeed

setPixLineBuf

public static final boolean setPixLineBuf(int[] lineBuf,
                                          char[] pix,
                                          int y)
setPixLineBuf() - save the line y from int[] pix from lineBuf[]

Parameters:
lineBuf - array predefined of [pixWidth]
pix - is the image buffer
y - is the line to use
Returns:
true if succeed

get2D

public static final int get2D(int[] pix,
                              int x,
                              int y)
get2D() - get the pixel at pix(x,y) computed at (y+pixelWidth+x)

Parameters:
pix - is the image buffer
x - of pixel
y - of pixel
Returns:
true if succeed

get2D

public static final int get2D(char[] pix,
                              int x,
                              int y)
get2D() - get the pixel at pix(x,y) computed at (y+pixelWidth+x)

Parameters:
pix - is the image buffer
x - of pixel
y - of pixel
Returns:
true if succeed

set2D

public static final int set2D(int[] pix,
                              int x,
                              int y,
                              int g)
set2D() - save the pixel value g at pix(x,y) computed at (y+pixelWidth+x)

Parameters:
pix - is the image buffer
x - of pixel
y - of pixel
g - is new int value to save
Returns:
g

set2D

public static final int set2D(char[] pix,
                              int x,
                              int y,
                              int g)
set2D() - save the pixel value g at pix(x,y) computed at (y+pixelWidth+x)

Parameters:
pix - is the image buffer
x - of pixel
y - of pixel
g - is new int value to save
Returns:
g

put2Dbuf

public static final int put2Dbuf(int[] buf,
                                 int x,
                                 int g)
put2Dbuf() - save pixel value g at buf[x]

Parameters:
pix - is the image buffer
x - of pixel
g - is new int value to save
Returns:
g

isDBwindow

public static final boolean isDBwindow()
isDBwindow() - test if (xDbug,yDbug) is inside the debug window. i.e., (xDbug>=dbx1 && xDbug<=dbx2 && yDbug>=dby1 && yDbug<=dby2))

Returns:
true if inside debug window

isDBwindow

public static final boolean isDBwindow(int x,
                                       int y)
isDBwindow() - test if (x,y) is inside the debug window. i.e., (xDbug>=dbx1 && xDbug<=dbx2 && yDbug>=dby1 && yDbug<=dby2))

Parameters:
x - is value to test
y - is value to test
Returns:
true if inside debug window

showReportStatus

public static void showReportStatus(java.lang.String opr)
showReportStatus() - display the msg in popup report line display And update the timer for the opr

Parameters:
opr - to display