Class Sg2ini

  extended by Seg2Dgel.Sg2glb
      extended by Seg2Dgel.Sg2ini

public class Sg2ini
extends Sg2glb

Class sg2ini initializes data structures for the 2D Gel Spot Segmenter

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

$Date: 2005/12/22 00:37:50 $ $Revision: 1.34 $
P. Lemkin, NCI-Frederick, Frederick, MD, 21702
See Also:
Open2Dprot Home

Field Summary
Fields inherited from class Seg2Dgel.Sg2glb
acc, accDatabaseFile, accDatabaseSwitch, accFile, accFormatMode, allowTouchingEdgesSwitch, applicationName, argsV, averageODSwitch, avg, avgPixFile, banner, bannerTitle, baseImageFileName, baseStatusTime, batchDir, bfav, bfavm, bfavm1, bfavp, bfavp1, bfog, bfogm, bfogm1, bfogm2, bfogm3, bfogm4, bfogm5, bfogp, bfogp1, bfogp2, bfogp3, bfogp4, bfogp5, bkg, BKGRD_CODE, bkgrdCorrectionSwitch, bkgrdPixFile, bkgrdSizeFlag, BLACK, boundaryInSSFSwitch, bufbkg, bufcc, bufmag, bufrest, c11, c12, c13, c14, c15, c16, c17, c18, c19, c1a, c1b, c1c, c1d, c1e, c1f, c1g, c1h, c21, c22, c23, c24, c25, c26, c27, c28, c29, c2a, c2b, c2c, c2d, c2e, c2f, c2g, c2h, c31, c32, c33, c34, c35, c36, c37, c38, c39, c3a, c3b, c3c, c3d, c3e, c3f, c3g, c3h, c41, c42, c43, c44, c45, c46, c47, c48, c49, c4a, c4b, c4c, c4d, c4e, c4f, c4g, c4h, c51, c52, c53, c54, c55, c56, c57, c58, c59, c5a, c5b, c5c, c5d, c5e, c5f, c5g, c5h, c61, c62, c63, c64, c65, c66, c67, c68, c69, c6a, c6b, c6c, c6d, c6e, c6f, c6g, c6h, c71, c72, c73, c74, c75, c76, c77, c78, c79, c7a, c7b, c7c, c7d, c7e, c7f, c7g, c7h, c81, c82, c83, c84, c85, c86, c87, c88, c89, c8a, c8b, c8c, c8d, c8e, c8f, c8g, c8h, c91, c92, c93, c94, c95, c96, c97, c98, c99, c9a, c9b, c9c, c9d, c9e, c9f, c9g, c9h, ca1, ca2, ca3, ca4, ca5, ca6, ca7, ca8, ca9, caa, cab, cac, cacheDir, cad, cae, caf, cag, cah, cal, cal2gray, calFile, cb1, cb2, cb3, cb4, cb5, cb6, cb7, cb8, cb9, cba, cbb, cbc, cbd, cbe, cbf, cbg, cbh, cc, cc1, cc2, cc3, cc4, cc5, cc6, cc7, cc8, cc9, cca, ccb, ccc, ccd, cce, ccf, ccg, cch, ccMinSize, ccMinSizeSwitch, ccNum, ccPixFile, cd1, cd2, cd3, cd4, cd5, cd6, cd7, cd8, cd9, cda, cdb, cdc, cdd, cde, cdf, cdg, cdh, computingWindowSwitch, coneOfSilenceMode, CONSOLE_FLAG, ctlCorePixSwitch, cwx1, cwx2, cwy1, cwy2, data, DATE, dbSample, dbSpot, dbug, DBUG_ADD_INTERIOR_CC_PIXELS, DBUG_BND_ANALYSIS, DBUG_CALC_FEATURES, DBUG_CHAIN_CODE_RLM_ANALYSIS, DBUG_CONSOLE, DBUG_CVT_BND_TO_CHAINCODE, DBUG_DRAW_NOTCH_PAIR_LINE, DBUG_DRAW_SAT_SPOT_BND, DBUG_DUMP_CC_PPX, DBUG_FILL_CORNERS, DBUG_FILL_HOLES_IN_PCC_CONCAVITIES, DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE, DBUG_FIND_SPOT_LIST, DBUG_INNER_LOOP_FIND_SPOT, DBUG_MAX_PROPAGATE, DBUG_NBR_COMPONENTS, DBUG_PIX_DBCODE, DBUG_PRINT_GRAY2CAL_MAP, DBUG_PROP_SAT_SPOTS, DBUG_PROP_SPOT_TO_2ND_MAXIMA, DBUG_PUSH_XY_INTO_FBL, DBUG_RMV_CONCAVITIES, DBUG_RMV_INTERIOR_CC_PIXELS, DBUG_ROUND_CORNERS, DBUG_SPLIT_CHECK_SPOT, DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS, DBUG_SWITCHES, dbugBits, dbugBitsHelpStr, dbugBitsPixFlag, dbx1, dbx2, dby1, dby2, debugSwitch, defaultSwitch, defaultTypeCode, deleteIsolatedPixelsSwitch, demoFileList, demoSwitch, DFT_2D_GEL, DFT_2D_LC_MS, DFT_NO_DB, didPropSaturatedSpots, didSplitSpotFlag, diffODSwitch, docFileList, dotsSwitch, dpx1, dpx2, dpy1, dpy2, draw, drawBoundaryOverlayType, drawBoundarySwitch, drawDotOverlayType, drawMEROverlayType, drawMERSwitch, drawPlusOverlayType, drawPlusSwitch, drawSxSyEllipseSwitch, drawSxSyOverlayType, drawTitleSwitch, dtdSwitch, ENABLE_DEVELOPER_DEBUGGING, ENABLE_SATURATED_SPOTS, ENABLE_SPOT_SPLITTING, fbl, fileSeparator, fio, fnd, fourSqrtPi, gHist, glbPercentThr, gray2cal, gridSize, hashFBL, HASHFBLPRIME, hashWS, histThreshold, i0R, i10, i11, i12, i13, i14, i15, i16, i17, i18, i2U, i4L, i6D, ini, inPixFile, ISOLATED_PIXEL_CODE, j11, j12, j13, j14, j15, j16, j17, j18, j19, j1a, j1b, j1c, j1d, j1e, j1f, j1g, j1h, j21, j22, j23, j24, j25, j26, j27, j28, j29, j2a, j2b, j2c, j2d, j2e, j2f, j2g, j2h, j31, j32, j33, j34, j35, j36, j37, j38, j39, j3a, j3b, j3c, j3d, j3e, j3f, j3g, j3h, j41, j42, j43, j44, j45, j46, j47, j48, j49, j4a, j4b, j4c, j4d, j4e, j4f, j4g, j4h, j51, j52, j53, j54, j55, j56, j57, j58, j59, j5a, j5b, j5c, j5d, j5e, j5f, j5g, j5h, j61, j62, j63, j64, j65, j66, j67, j68, j69, j6a, j6b, j6c, j6d, j6e, j6f, j6g, j6h, j71, j72, j73, j74, j75, j76, j77, j78, j79, j7a, j7b, j7c, j7d, j7e, j7f, j7g, j7h, j81, j82, j83, j84, j85, j86, j87, j88, j89, j8a, j8b, j8c, j8d, j8e, j8f, j8g, j8h, j91, j92, j93, j94, j95, j96, j97, j98, j99, j9a, j9b, j9c, j9d, j9e, j9f, j9g, j9h, ja1, ja2, ja3, ja4, ja5, ja6, ja7, ja8, ja9, jaa, jab, jac, jad, jae, jaf, jag, jah, jarFileList, jarLibrFileList, jb1, jb2, jb3, jb4, jb5, jb6, jb7, jb8, jb9, jba, jbb, jbc, jbd, jbe, jbf, jbg, jbh, jc1, jc2, jc3, jc4, jc5, jc6, jc7, jc8, jc9, jca, jcb, jcc, jcd, jce, jcf, jcg, jch, jd1, jd2, jd3, jd4, jd5, jd6, jd7, jd8, jd9, jda, jdb, jdc, jdd, jde, jdf, jdg, jdh, keepInputImageSwitch, KILL_SPOT_CODE, killSpotColor, laplacianSwitch, legalImageFileExtens, lineLaplacianHeight, lineLaplacianWidth, lowPassSize, lowpassSwitch, lp13xZZSwitch, lp3x3Switch, lp5x5Switch, lp7x7Switch, mag2ndPixFile, MAX_BUFFERED_SPOTS, MAX_CC_CODE, MAX_INTERIOR_FBL_SIZE, MAX_PCC_CODE, maxColsToPrint, maxGhist, maxGrayPixel, MAXSUBSPOTS, meanGhist, merx1, merx2, merxp1, merxp2, mery1, mery2, meryp1, meryp2, MHISTSIZE, MIN_CC_CODE, MIN_PCC_CODE, MINBLOBAREA, minGhist, MINSPLITSPOTSIZE, nBitsPerPixel, nBkgrdSize, nBytesPerPixel, NEVER, ngh, notch, nPixels, nStatusName, nSwitches, optimizeInteriorFBLSwitch, osName, paramH, PCC_BASE_CODE, pix, pix1, pix2, pix3, pix4, pix5, pix6, pix7, pixDir, pixDumpSwitch, pixelSizeMicrons, pixFileExtn, pixHeight, pixWidth, ppxDir, pra, projDir, projDirSwitch, propertiesFile, propertiesFileSwitch, pTileGhist, PUBLISH, quickEstimateSwitch, rdbmsDir, rest, restOfPixFile, restOfPixSwitch, REVISION, rlmCWfile, rmvDprimeSizingSwitch, sampleSwitch, sat, saturatedSpotSwitch, scaledMaxOD, seg2dgelURL, segPixFile, segPixSwitch, sg2, simpleFileName, sizeFractionGaussianWidth, sort, split, splitLargeCCfblByBndAnalSwitch, splitLargeCCfblByRLManalSwitch, splitLargeCCfblByThreshAnalSwitch, splitMinCCsize, splitSpotSwitch, spotNumber, ssfFormatMode, ssfFormatSwitch, ssfOutputEpilogueFile, ssfOutputFile, ssfOutputPrefaceFile, startTime, statusMemoryFree, statusMemoryTot, statusName, statusStartTime, sw, switchOptCBvalue, switchOptData, switchOptValue, t1Area, t1Density, t1Range, t1SxSyRatio, t2Area, t2Density, t2Range, t2SxSyRatio, TEST_LARGE_IMAGE, thrAreaSwitch, thrDensitySwitch, thrRangeSwitch, thrSxSyRatioSwitch, timerSwitch, tmpDir, UNLABELED_CC_CODE, updateSwitch, usageSwitch, USE_13X13, USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND, USE_DEMO_DATA, USE_DOM_XML_SSF, use3x3laplacianSwitch, use5x5laplacianSwitch, useBkgdAndIsolatedPixelFlag, useBusseLaplacianSwitch, useCopyOfPix1ForPix5Switch, useHistGUISwitch, useHorizLineLaplacianSwitch, usePopupGUISwitch, userDir, useVertLineLaplacianSwitch, util, VERSION, WHITE, widthWindmp, windmpStepSize, wrk, wXsize, wYsize, xDbug, xmlDir, xPentrance, xPexit, yDbug, yPentrance, yPexit, yTitle
Constructor Summary
          Sg2ini() - Constructor
Method Summary
static void additionalInit()
          additionalInit() - initialize other parameters now that we have the computing window, image size, bits/pixel, OD calibration, etc.
static void createLineBuffers()
          createLineBuffers() - create line buffers
static int cvtDefaultType(java.lang.String defType)
          cvtDefaultType() - remap default type to standard string
static void initCW()
          initCW() - initialize the main and debugging computing windows and adjust edges based on gaussian -lowpass filter size (wXsize,wYsize).
static int initSwitchOptionsData()
          initSwitchOptionsData() - init the switchOptionsData[0:(3*nData)-1] data is used by the Sg2reportPopup that in turn may call Sg2optionsPopup.
 boolean switchAnalysis(java.lang.String[] argv)
          switchAnalysis() - Analyze the command line.
Methods inherited from class Seg2Dgel.Sg2glb
get2D, get2D, getPixLineBuf, getPixLineBuf, initGlb, isDBwindow, isDBwindow, put2Dbuf, resetGlb, set2D, set2D, setPixLineBuf, setPixLineBuf, showReportStatus
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail


public Sg2ini()
Sg2ini() - Constructor

Method Detail


public boolean switchAnalysis(java.lang.String[] argv)
switchAnalysis() - Analyze the command line. Then set corresponding switches, lookup the accession file and get the picture name. Then check it it is there. Do misc. stuff.

argv - is the list of command line args.
truue if not problems parsing switches


public static void additionalInit()
additionalInit() - initialize other parameters now that we have the computing window, image size, bits/pixel, OD calibration, etc.


public static void initCW()
initCW() - initialize the main and debugging computing windows and adjust edges based on gaussian -lowpass filter size (wXsize,wYsize). Also set up the lpNxNSwitch options. If there is no computing window, then set the computing window to the image size.


public static int cvtDefaultType(java.lang.String defType)
cvtDefaultType() - remap default type to standard string

defType - default type
standard type name code DFT_2D_GEL, DFT_2D_LC_MS)


public static void createLineBuffers()
createLineBuffers() - create line buffers


public static int initSwitchOptionsData()
initSwitchOptionsData() - init the switchOptionsData[0:(3*nData)-1] data is used by the Sg2reportPopup that in turn may call Sg2optionsPopup. The following is passed to Sg2optionsPopup() and contains data triples of (optionPrompt, guiBuilderSpec, helpStr) . If the optionPrompt data has a "-", then make a CheckBox, else it is a Label with the optionPrompt data.
 If the guiBuilderSpec has a "#", then it is a file browser.
 If the guiBuilderSpec has a "$", then it is a directory browser.
 If the guiBuilderSpec has a
    then it is set of Sliders implemented on the right as Scrollbars
 If the guiBuilderSpec has a "{A|B|C...Z}1,{A|B|C...Z}2,...", 
    then it is set of Choices (i.e., between the {...} 
 If  guiBuilderSpec has a "*1,*2,..." entries in the list, 
    then get that data from the comma separated text area.
 If the user data is not null, then make a TextField with this
 user data on the right else make an empty Label.

 guiBuilderSpec syntax  to specify one or more in the command options
 1. sliders 
  guiBuilderSpec is "@1Minimum area[10,2000,1.0,0],@2Maximum area[10,2000,1.0,0]"

 2. popup file browser
      "#Gel image file"
   guiBuilderSpec is "#"

 3. popup directory browser
      "@Project directory" 
   guiBuilderSpec is "@Project directory" 
      -projDir:$Project directory$

 4. choice.
      -lowpassFilter:{3 | 5 | B}1,gridSize,{P | C}2
   guiBuilderSpec is "{3|5|B}1,-,{P|C}3",

size of the switch arrays