Seg2Dgel
Class Sg2glb

java.lang.Object
  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

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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.

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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.

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Constant Field Values

MAXSUBSPOTS

public static final int MAXSUBSPOTS

max # subspots a spot can split into

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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.

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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

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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.

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Constant Field Values

MHISTSIZE

public static final int MHISTSIZE

Size of histogram for splitting algorithm

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Constant Field Values

MINBLOBAREA

public static final int MINBLOBAREA

used in findAllSpots()

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Constant Field Values

USE_13X13

public static final boolean USE_13X13

Use 13x17 or 13x13 filters - BUT NOT BOTH !!!!!

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Constant Field Values

WHITE

public static final int WHITE

Pixel color for white

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Constant Field Values

BLACK

public static final int BLACK

Pixel color for black

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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.

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Constant Field Values

BKGRD_CODE

public static final int BKGRD_CODE

pixel code for the CC background pixel

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Constant Field Values

UNLABELED_CC_CODE

public static final int UNLABELED_CC_CODE

pixel code for unlabeled central core (CC)pixel

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Constant Field Values

MIN_CC_CODE

public static final int MIN_CC_CODE

pixel code for minimum labeled central core (CC) pixel

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Constant Field Values

MAX_CC_CODE

public static final int MAX_CC_CODE

pixel code for maximum labeled central core (CC) pixel

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Constant Field Values

PCC_BASE_CODE

public static final int PCC_BASE_CODE

pixel code for guard region splitting previously merged spots

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Constant Field Values

MIN_PCC_CODE

public static final int MIN_PCC_CODE

pixel code for minimum labeled propagated central core (PCC) pixel

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Constant Field Values

MAX_PCC_CODE

public static final int MAX_PCC_CODE

pixel code for maximum labeled propagated central core (PCC) pixel

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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)

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Constant Field Values

ISOLATED_PIXEL_CODE

public static final int ISOLATED_PIXEL_CODE

pixel code for guard region splitting previously merged spots

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Constant Field Values

DFT_NO_DB

public static final int DFT_NO_DB

Default data type No-database

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Constant Field Values

DFT_2D_GEL

public static final int DFT_2D_GEL

Default data type 2D-gel

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Constant Field Values

DFT_2D_LC_MS

public static final int DFT_2D_LC_MS

Default data type 2D-LC-MS

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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.

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Constant Field Values

DBUG_FIND_SPOT_LIST

public static final int DBUG_FIND_SPOT_LIST

Trace findSpotList() to find spots

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Constant Field Values

DBUG_PROP_SAT_SPOTS

public static final int DBUG_PROP_SAT_SPOTS

Trace propSaturatedSpot() to

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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

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Constant Field Values

DBUG_RMV_CONCAVITIES

public static final int DBUG_RMV_CONCAVITIES

Trace rmvConcavities() to remove concavities in the central core

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Constant Field Values

DBUG_NBR_COMPONENTS

public static final int DBUG_NBR_COMPONENTS

Trace numberComponents() to number components in the central core

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Constant Field Values

DBUG_MAX_PROPAGATE

public static final int DBUG_MAX_PROPAGATE

Trace maxPropagate() to expand from the CC to the PCC

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Constant Field Values

DBUG_FILL_CORNERS

public static final int DBUG_FILL_CORNERS

Trace fillCorners() to fill corners in the current PCC

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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

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Constant Field Values

DBUG_ROUND_CORNERS

public static final int DBUG_ROUND_CORNERS

Trace roundCorners() to round corners of the PCC

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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

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Constant Field Values

DBUG_PRINT_GRAY2CAL_MAP

public static final int DBUG_PRINT_GRAY2CAL_MAP

Trace print gray2cal[] to print the gray2cal[] map

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Constant Field Values

DBUG_RMV_INTERIOR_CC_PIXELS

public static final int DBUG_RMV_INTERIOR_CC_PIXELS

Trace inner loop of rmvInteriorCCpixels() to

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Constant Field Values

DBUG_CALC_FEATURES

public static final int DBUG_CALC_FEATURES

Trace calcFeatures() where compute spot values from the images & FBL

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Constant Field Values

DBUG_ADD_INTERIOR_CC_PIXELS

public static final int DBUG_ADD_INTERIOR_CC_PIXELS

Trace inner loop of addInteriorCCpixels() to

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Constant Field Values

DBUG_INNER_LOOP_FIND_SPOT

public static final int DBUG_INNER_LOOP_FIND_SPOT

Trace inner loop of findSpot() to

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Constant Field Values

DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS

public static final int DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS

Trace splitPixByFBLboundaryAnal() to

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Constant Field Values

DBUG_BND_ANALYSIS

public static final int DBUG_BND_ANALYSIS

Trace findBoundary(), pushXYboundary(), resetBnd()

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Constant Field Values

DBUG_CVT_BND_TO_CHAINCODE

public static final int DBUG_CVT_BND_TO_CHAINCODE

Trace cvtBoundaryToChainCode(), cvtChainCode_to_nextXY()

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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

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Constant Field Values

DBUG_CHAIN_CODE_RLM_ANALYSIS

public static final int DBUG_CHAIN_CODE_RLM_ANALYSIS

Trace pairChainCodeNotches(), findMinMaxPeaksInRLM()and findPairedNotches_in_RLM()

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Constant Field Values

DBUG_DRAW_NOTCH_PAIR_LINE

public static final int DBUG_DRAW_NOTCH_PAIR_LINE

Trace drawLineBetweenNotchPair() to

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Constant Field Values

DBUG_PUSH_XY_INTO_FBL

public static final int DBUG_PUSH_XY_INTO_FBL

Trace pushXYintoFBL() to

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Constant Field Values

DBUG_DRAW_SAT_SPOT_BND

public static final int DBUG_DRAW_SAT_SPOT_BND

Trace draw boundary of saturated spot CC

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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

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Constant Field Values

dbugBitsHelpStr

public static final java.lang.String dbugBitsHelpStr

Debug bit options help for error messages

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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