Seg2Dgel
Class Sg2dbug

java.lang.Object
  extended by Seg2Dgel.Sg2glb
      extended by Seg2Dgel.Sg2dbug

public class Sg2dbug
extends Sg2glb

Class Sg2dbug contains debug print methods for image neighbohood, windows, etc. used by the 2D Gel Spot Segmenter Seg2Dgel. This class contains methods for reading and parsing the Seg2Dgel.dbug name/bits file for use in print out the debug bits list if the -debug switch was invoked.

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: 2005/10/21 17:08:03 $ $Revision: 1.19 $
Author:
P. Lemkin, NCI-Frederick, Frederick, MD, 21702
See Also:
Open2Dprot Home

Field Summary
static java.lang.String[] dbugBitName
          Debug bits name from the parsed Seg2Dgel.dbug file
static int[] dbugBitValues
          Debug bits values from the parsed Seg2Dgel.dbug file
 
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
Sg2dbug()
          Sg2dbug() - Constructor
 
Method Summary
static void dbugPixDBcode(char[] pix, int radixMode, java.lang.String title)
          dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2].
static void dbugPixDBcode(char[] pix, java.lang.String title)
          dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2].
static void dbugPixNxNcode(char[] pix, int x, int y, int n, java.lang.String title)
          dbugPixNxNcode() - print window of size (n X n) of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dbx1:dbx2, dby1:dby2] to ssfFD.
static void pixDump(char[] pix, int radixMode, java.lang.String title)
          pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled.
static void pixDump(char[] pix, java.lang.String title)
          pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled.
static void pixNxNalways(char[] pix, int x, int y, int n, java.lang.String title)
          pixNxNalways() - always print window of current char[] picture
static java.lang.String pixNxNtoStr(char[] pix, int x, int y, int n, int radix, java.lang.String title)
          pixNxNtoStr() - convert current char[] picture of size nXn to string.
static java.lang.String pixNxNtoStr(char[] pix, int x, int y, int n, java.lang.String title)
          pixNxNtoStr() - convert current char[] picture of size nXn to string.
private static java.lang.String windmp(char[] pix, int x1, int x2, int y1, int y2, int width, java.lang.String title, int radixMode, int linesize, int maxColsToPrint, int stepSize)
          windmp() - Draw a window from picture 16-bit char[] 'pix' at:
 
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
 

Field Detail

dbugBitValues

public static int[] dbugBitValues
Debug bits values from the parsed Seg2Dgel.dbug file


dbugBitName

public static java.lang.String[] dbugBitName
Debug bits name from the parsed Seg2Dgel.dbug file

Constructor Detail

Sg2dbug

public Sg2dbug()
Sg2dbug() - Constructor

Method Detail

pixDump

public static final void pixDump(char[] pix,
                                 java.lang.String title)
pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled. Displays image in [dpx1:dpx2,dpy1:dpy2] ROI.

Parameters:
pix - is the image to use
title - is the header for the output window

pixDump

public static final void pixDump(char[] pix,
                                 int radixMode,
                                 java.lang.String title)
pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled. Displays image in [dpx1:dpx2,dpy1:dpy2,] ROI.

Parameters:
pix - is the image to use
radixMode - is SHOW_OCTAL, SHOW_DECIMAL, SHOW_HEX or SHOW_OD
title - is the header for the output window

dbugPixDBcode

public static final void dbugPixDBcode(char[] pix,
                                       java.lang.String title)
dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2]. Don't print if outside of the window. Use decimal and the widthWindmp size

Parameters:
pix - is the image to use
title - is the header for the output window

dbugPixDBcode

public static final void dbugPixDBcode(char[] pix,
                                       int radixMode,
                                       java.lang.String title)
dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2]. Don't print if outside of the window. Use decimal and the widthWindmp size

Parameters:
pix - is the image to use
radixMode - is Util.SHOW_OCTAL, SHOW_DECIMAL, SHOW_HEX or SHOW_OD
title - is the header for the output window

dbugPixNxNcode

public static final void dbugPixNxNcode(char[] pix,
                                        int x,
                                        int y,
                                        int n,
                                        java.lang.String title)
dbugPixNxNcode() - print window of size (n X n) of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dbx1:dbx2, dby1:dby2] to ssfFD. Don't print if outside of the window.

Parameters:
pix - is the image to use
x - is the center X of the neighborhood
y - is the center Y of the neighborhood
n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)
title - is the header for the output window

pixNxNalways

public static final void pixNxNalways(char[] pix,
                                      int x,
                                      int y,
                                      int n,
                                      java.lang.String title)
pixNxNalways() - always print window of current char[] picture

Parameters:
pix - is the image to use
x - is the center X of the neighborhood
y - is the center Y of the neighborhood
n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)
title - is the header for the output window

pixNxNtoStr

public static final java.lang.String pixNxNtoStr(char[] pix,
                                                 int x,
                                                 int y,
                                                 int n,
                                                 java.lang.String title)
pixNxNtoStr() - convert current char[] picture of size nXn to string.

Parameters:
pix - is the image to use
x - is the center X of the neighborhood
y - is the center Y of the neighborhood
n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)
title - is the header for the output window

pixNxNtoStr

public static final java.lang.String pixNxNtoStr(char[] pix,
                                                 int x,
                                                 int y,
                                                 int n,
                                                 int radix,
                                                 java.lang.String title)
pixNxNtoStr() - convert current char[] picture of size nXn to string.

Parameters:
pix - is the image to use
x - is the center X of the neighborhood
y - is the center Y of the neighborhood
n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)
title - is the header for the output window

windmp

private static final java.lang.String windmp(char[] pix,
                                             int x1,
                                             int x2,
                                             int y1,
                                             int y2,
                                             int width,
                                             java.lang.String title,
                                             int radixMode,
                                             int linesize,
                                             int maxColsToPrint,
                                             int stepSize)
windmp() - Draw a window from picture 16-bit char[] 'pix' at:
 x1,y1x2,y1
 ...
 x1,y2x2,y2.

Parameters:
pix - is image data
x1 - is left column
x2 - is right column
y1 - is top row
y2 - is bottom row
width - is the size of row
title - is title for printout
radixMode - is 0=OCTAL 1=DECIMAL 2= HEX(byte), 3= HEX(16-bits).
linesize - is Length of a line in image
maxColsToPrint - is the number of columns to print. For 80 column terminal width is 18 and 30 for a 132 column terminal.
stepSize - is pixel step size for sample/average in [1:32], 1 default
Returns:
string of window data