Seg2Dgel
Class Sg2hash

java.lang.Object
  Seg2Dgel.Sg2glb
      Seg2Dgel.Sg2hash

public class Sg2hash
extends Sg2glb

Class Sg2hash specifies the picture hash table used by the 2D gel spot segmenter. There may be more than one hash table used so we make the data dynamic. E.g., hashFBL, hashWS etc.

A hash table (hIdxTbl or hXYtbl)[0:sizeHashPrime] is used to determine if a (x,y) coordinate is in the hash table and where (if its value is non:zero). Formerly a linear search of the FBL or WS was performed, but the hash function take its place and is much faster. Prime number hashing is used. The hash table will grow if required. When the hash table is "released", we merely need to clear the entires. This may be faster than just reallocating the memory, although for larger hash tables, it may just be faster to reallocate the memory.

The packing format is as follows:

       # bits      24         16
              -----------------------
 hIdxTbl[]    | free | index to FBL |
              -----------------------

       # bits     16     16
              --------------
  hXYtbl[]    |   X  |  Y  |
              --------------

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: 2005/10/23 12:44:55 $ $Revision: 1.5 $

Author:

P. Lemkin, NCI-Frederick, Frederick, MD, 21702

See Also:

Open2Dprot Home

Field Summary

private Sg2fbl	fblHash instance of Final Blob List (FBL) associated with the hash
private int[]	hIdxTbl hash table index to FBL or WS stack data which is the associated hash table value.
private int[]	hXYtbl hash table packed XY (x<<16 | y) data used as the key.
(package private) int[]	pixBitMap [FUTURE] alternate hashing schem using a pix bitmap to lookup pixel membership.
int	sizeHashPrime current hash table prime number size
int	sizeHashPrimeDefault default hash table prime number size
private Sg2wrk	wrkHash instance of Working Stack (WS) associated with the hash

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

Sg2hash()
Sg2hash() - initialize the hash table data structures to empty.

Method Summary

void	clearHash() clearHash() - clear the pix hash table by writing zero into the table.
int	getHash(int x, int y) getHash() - get the FBL or WS stack index value if (x,y) is in the XY point picture hash table.
int	getHashSize() getHashSize() - get the size of the current picture hash table
int	growHashFBL(Sg2fbl fbl, int newHashSizeMax) growHashFBL() - grow the FBL hash tables to at least the newSize by finding a prime number GEQ the specified newSize.
int	growHashWS(Sg2wrk wrk, int newSize) growHashWS() - grow the WS hash tables to at least the newSize by finding a prime number GEQ the specified newSize.
void	putHashFBL(int stackIdx, int x, int y) putHashFBL() - put (x,y) into the XY point picture FBL hash table hXYtbl[] and also save the corresponding FBL stack index value in hIdxTbl[].
void	putHashWS(int stackIdx, int x, int y) putHashWS() - put (x,y) into the XY point picture WS hash table hXYtbl[] and also save the corresponding WS stack index value in hIdxTbl[].
int	unpackHashX(int hashValue) unpackHashX() - extract the X value from the hash XY packed value
int	unpackHashY(int hashValue) unpackHashY() - extract the Y value from the hash XY packed value

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

sizeHashPrimeDefault

public int sizeHashPrimeDefault

default hash table prime number size

sizeHashPrime

public int sizeHashPrime

current hash table prime number size

hXYtbl

private int[] hXYtbl

hash table packed XY (x<<16 | y) data used as the key.

hIdxTbl

private int[] hIdxTbl

hash table index to FBL or WS stack data which is the associated hash table value.

fblHash

private Sg2fbl fblHash

instance of Final Blob List (FBL) associated with the hash

wrkHash

private Sg2wrk wrkHash

instance of Working Stack (WS) associated with the hash

pixBitMap

int[] pixBitMap

[FUTURE] alternate hashing schem using a pix bitmap to lookup pixel membership. This is of size [((pixWidth*pixHeight)/32+1]. Clear the list by deleting FBL or WS pixels BEFORE doing a fbl.clearFBL() or wrk.clearWS().

Constructor Detail

Sg2hash

public Sg2hash()

Sg2hash() - initialize the hash table data structures to empty.

Method Detail

growHashFBL

public final int growHashFBL(Sg2fbl fbl,
                             int newHashSizeMax)

growHashFBL() - grow the FBL hash tables to at least the newSize by finding a prime number GEQ the specified newSize. If the current sizeHashPrime is GEQ newSize, just return sizeHashPrime. If it exists already, then copy the previous hash table data to the new hash table.

Parameters:

Sg2fbl - instance of FBL associated with hash table

newSize - is the minimum size of the hash table.

Returns:

current size of hash table which may be larger if regrown

growHashWS

public final int growHashWS(Sg2wrk wrk,
                            int newSize)

growHashWS() - grow the WS hash tables to at least the newSize by finding a prime number GEQ the specified newSize. If the current sizeHashPrime is GEQ newSize, just return sizeHashPrime. If it exists already, then copy the previous hash table data to the new hash table.

Parameters:

Sg2wrk - instance of WS associated with hash table

newSize - is the minimum size of the hash table.

Returns:

current size of hash table which may be larger if regrown

getHashSize

public final int getHashSize()

getHashSize() - get the size of the current picture hash table

clearHash

public final void clearHash()

clearHash() - clear the pix hash table by writing zero into the table. NOTE: it may be faster to reallocate it for very large hash tables.

putHashFBL

public final void putHashFBL(int stackIdx,
                             int x,
                             int y)

putHashFBL() - put (x,y) into the XY point picture FBL hash table hXYtbl[] and also save the corresponding FBL stack index value in hIdxTbl[].

putHashWS

public final void putHashWS(int stackIdx,
                            int x,
                            int y)

putHashWS() - put (x,y) into the XY point picture WS hash table hXYtbl[] and also save the corresponding WS stack index value in hIdxTbl[].

getHash

public final int getHash(int x,
                         int y)

getHash() - get the FBL or WS stack index value if (x,y) is in the XY point picture hash table.

Returns:

spot stack index value which is >= 0 if found, and is -1 if not found

unpackHashX

public final int unpackHashX(int hashValue)

unpackHashX() - extract the X value from the hash XY packed value

Returns:

unpacked X value

unpackHashY

public final int unpackHashY(int hashValue)

unpackHashY() - extract the Y value from the hash XY packed value

Returns:

unpacked X value