teem-commit — gets email notification of all Teem svn commits

[Teem-commit] teem/src/dye methodsDye.c,1.6,1.7

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/dye
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26582/dye

Modified Files:
	methodsDye.c 
Log Message:
killed off AIR_FREE and AIR_FCLOSE macros- they were just way too cute for their own good

Index: methodsDye.c
===================================================================
RCS file: /cvsroot/teem/teem/src/dye/methodsDye.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** methodsDye.c	7 Jan 2004 15:34:28 -0000	1.6
--- methodsDye.c	13 Mar 2004 20:03:09 -0000	1.7
***************
*** 52,58 ****
        }
      }
!     if (dyeSpaceLast == spc)
        spc = dyeSpaceUnknown;
!     AIR_FREE(str);
    }
    return spc;
--- 52,59 ----
        }
      }
!     if (dyeSpaceLast == spc) {
        spc = dyeSpaceUnknown;
!     }
!     str = airFree(str);
    }
    return spc;
***************
*** 141,145 ****
  
    if (col) {
!     AIR_FREE(col);
    }
    return NULL;
--- 142,146 ----
  
    if (col) {
!     col = airFree(col);
    }
    return NULL;
***************
*** 175,179 ****
      biffAdd(DYE, err); return 1;
    }
!   AIR_FREE(str);
  
    dyeColorSet(col, spc, v0, v1, v2);
--- 176,180 ----
      biffAdd(DYE, err); return 1;
    }
!   str = airFree(str);
  
    dyeColorSet(col, spc, v0, v1, v2);

[Teem-commit] teem/src/echo methodsEcho.c,1.13,1.14 objmethods.c,1.8,1.9 renderEcho.c,1.24,1.25

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/echo
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26582/echo

Modified Files:
	methodsEcho.c objmethods.c renderEcho.c 
Log Message:
killed off AIR_FREE and AIR_FCLOSE macros- they were just way too cute for their own good

Index: methodsEcho.c
===================================================================
RCS file: /cvsroot/teem/teem/src/echo/methodsEcho.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** methodsEcho.c	7 Jan 2004 15:34:28 -0000	1.13
--- methodsEcho.c	13 Mar 2004 20:03:09 -0000	1.14
***************
*** 54,58 ****
  echoRTParmNix(echoRTParm *parm) {
  
!   AIR_FREE(parm);
  
    return NULL;
--- 54,58 ----
  echoRTParmNix(echoRTParm *parm) {
  
!   parm = airFree(parm);
  
    return NULL;
***************
*** 74,78 ****
  echoGlobalStateNix(echoGlobalState *state) {
  
!   AIR_FREE(state);
    return NULL;
  }
--- 74,78 ----
  echoGlobalStateNix(echoGlobalState *state) {
  
!   state = airFree(state);
    return NULL;
  }
***************
*** 100,106 ****
      nrrdNuke(state->njitt);
      nrrdNuke(state->nperm);
!     AIR_FREE(state->permBuff);
!     AIR_FREE(state->chanBuff);
!     AIR_FREE(state);
    }
    return NULL;
--- 100,106 ----
      nrrdNuke(state->njitt);
      nrrdNuke(state->nperm);
!     state->permBuff = airFree(state->permBuff);
!     state->chanBuff = airFree(state->chanBuff);
!     state = airFree(state);
    }
    return NULL;
***************
*** 183,187 ****
      airArrayNuke(scene->nrrdArr);
      /* don't touch envmap nrrd */
!     AIR_FREE(scene);
    }
    return NULL;
--- 183,187 ----
      airArrayNuke(scene->nrrdArr);
      /* don't touch envmap nrrd */
!     scene = airFree(scene);
    }
    return NULL;

Index: objmethods.c
===================================================================
RCS file: /cvsroot/teem/teem/src/echo/objmethods.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** objmethods.c	7 Jan 2004 15:34:28 -0000	1.8
--- objmethods.c	13 Mar 2004 20:03:09 -0000	1.9
***************
*** 98,103 ****
  	 )
  NIX_TMPL(TriMesh,
! 	 AIR_FREE(obj->pos);
! 	 AIR_FREE(obj->vert);
  	 )
  
--- 98,103 ----
  	 )
  NIX_TMPL(TriMesh,
! 	 obj->pos = airFree(obj->pos);
! 	 obj->vert = airFree(obj->vert);
  	 )
  

Index: renderEcho.c
===================================================================
RCS file: /cvsroot/teem/teem/src/echo/renderEcho.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** renderEcho.c	7 Jan 2004 15:34:28 -0000	1.24
--- renderEcho.c	13 Mar 2004 20:03:09 -0000	1.25
***************
*** 50,54 ****
  		  "x,y", "jittable", "sample");
  
!   AIR_FREE(tstate->permBuff);
    if (!( tstate->permBuff = (int*)calloc(parm->numSamples, sizeof(int)) )) {
      sprintf(err, "%s: couldn't allocate permutation buffer", me);
--- 50,54 ----
  		  "x,y", "jittable", "sample");
  
!   tstate->permBuff = airFree(tstate->permBuff);
    if (!( tstate->permBuff = (int*)calloc(parm->numSamples, sizeof(int)) )) {
      sprintf(err, "%s: couldn't allocate permutation buffer", me);
***************
*** 56,60 ****
    }
  
!   AIR_FREE(tstate->chanBuff);
    if (!( tstate->chanBuff =
  	 (echoCol_t*)calloc(ECHO_IMG_CHANNELS * parm->numSamples,
--- 56,60 ----
    }
  
!   tstate->chanBuff = airFree(tstate->chanBuff);
    if (!( tstate->chanBuff =
  	 (echoCol_t*)calloc(ECHO_IMG_CHANNELS * parm->numSamples,

[Teem-commit] teem/src/hest methodsHest.c,1.9,1.10 parseHest.c,1.13,1.14

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/hest
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26582/hest

Modified Files:
	methodsHest.c parseHest.c 
Log Message:
killed off AIR_FREE and AIR_FCLOSE macros- they were just way too cute for their own good

Index: methodsHest.c
===================================================================
RCS file: /cvsroot/teem/teem/src/hest/methodsHest.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** methodsHest.c	7 Jan 2004 15:34:29 -0000	1.9
--- methodsHest.c	13 Mar 2004 20:03:09 -0000	1.10
***************
*** 55,59 ****
  hestParmFree(hestParm *parm) {
  
!   AIR_FREE(parm);
    return NULL;
  }
--- 55,59 ----
  hestParmFree(hestParm *parm) {
  
!   parm = airFree(parm);
    return NULL;
  }
***************
*** 149,156 ****
  _hestOptFree(hestOpt *opt) {
    
!   AIR_FREE(opt->flag);
!   AIR_FREE(opt->name);
!   AIR_FREE(opt->dflt);
!   AIR_FREE(opt->info);
    return;
  }
--- 149,156 ----
  _hestOptFree(hestOpt *opt) {
    
!   opt->flag = airFree(opt->flag);
!   opt->name = airFree(opt->name);
!   opt->dflt = airFree(opt->dflt);
!   opt->info = airFree(opt->info);
    return;
  }

Index: parseHest.c
===================================================================
RCS file: /cvsroot/teem/teem/src/hest/parseHest.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** parseHest.c	7 Jan 2004 15:34:29 -0000	1.13
--- parseHest.c	13 Mar 2004 20:03:09 -0000	1.14
***************
*** 441,445 ****
      if (appr[flag]) {
        airMopSub(pmop, prms[flag], airFree);
!       AIR_FREE(prms[flag]);
      }
      prms[flag] = _hestExtract(argcP, argv, a, nprm[flag]);
--- 441,445 ----
      if (appr[flag]) {
        airMopSub(pmop, prms[flag], airFree);
!       prms[flag] = airFree(prms[flag]);
      }
      prms[flag] = _hestExtract(argcP, argv, a, nprm[flag]);
***************
*** 641,645 ****
        tmpS = airStrdup(prms[op]);
        nprm[op] = airStrntok(tmpS, " ");
!       AIR_FREE(tmpS);
        /* printf("!%s: nprm[%d] in default = %d\n", me, op, nprm[op]); */
        if (opt[op].min < _hestMax(opt[op].max)) {
--- 641,645 ----
        tmpS = airStrdup(prms[op]);
        nprm[op] = airStrntok(tmpS, " ");
!       tmpS = airFree(tmpS);
        /* printf("!%s: nprm[%d] in default = %d\n", me, op, nprm[op]); */
        if (opt[op].min < _hestMax(opt[op].max)) {
***************
*** 874,878 ****
  	  if (opt[op].flag && 1 == _hestCase(opt, udflt, nprm, appr, op)) {
  	    /* we just parsed the default, but now we want to "invert" it */
! 	    AIR_FREE(*((char**)vP));
  	    opt[op].alloc = 0;
  	  }
--- 874,878 ----
  	  if (opt[op].flag && 1 == _hestCase(opt, udflt, nprm, appr, op)) {
  	    /* we just parsed the default, but now we want to "invert" it */
! 	    *((char**)vP) = airFree(*((char**)vP));
  	    opt[op].alloc = 0;
  	  }
***************
*** 1192,1196 ****
      case 1:
        if (airTypeOther != opt[op].type) {
! 	AIR_FREE(*vP);
        }
        else {
--- 1192,1196 ----
      case 1:
        if (airTypeOther != opt[op].type) {
! 	*vP = airFree(*vP);
        }
        else {
***************
*** 1202,1206 ****
  	}
  	else {
! 	  AIR_FREE(*vP);
  	}
        }
--- 1202,1206 ----
  	}
  	else {
! 	  *vP = airFree(*vP);
  	}
        }
***************
*** 1209,1213 ****
        if (airTypeString == opt[op].type) {
  	for (i=0; i<=opt[op].min-1; i++) {
! 	  AIR_FREE(str[i]);
  	}
        }
--- 1209,1213 ----
        if (airTypeString == opt[op].type) {
  	for (i=0; i<=opt[op].min-1; i++) {
! 	  str[i] = airFree(str[i]);
  	}
        }
***************
*** 1221,1227 ****
        if (airTypeString == opt[op].type) {
  	for (i=0; i<=*(opt[op].sawP)-1; i++) {
! 	  AIR_FREE((*strP)[i]);
  	}
! 	AIR_FREE(*strP);
        }
        else {
--- 1221,1227 ----
        if (airTypeString == opt[op].type) {
  	for (i=0; i<=*(opt[op].sawP)-1; i++) {
! 	  (*strP)[i] = airFree((*strP)[i]);
  	}
! 	*strP = airFree(*strP);
        }
        else {
***************
*** 1229,1233 ****
  	  (*vAP)[i] = opt[op].CB->destroy((*vAP)[i]);
  	}
! 	AIR_FREE(*vAP);
        }
        break;
--- 1229,1233 ----
  	  (*vAP)[i] = opt[op].CB->destroy((*vAP)[i]);
  	}
! 	*vAP = airFree(*vAP);
        }
        break;

[Teem-commit] teem/src/gage ctx.c,1.12,1.13 miscGage.c,1.10,1.11 pvl.c,1.11,1.12 update.c,1.12,1.13

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26582/gage

Modified Files:
	ctx.c miscGage.c pvl.c update.c 
Log Message:
killed off AIR_FREE and AIR_FCLOSE macros- they were just way too cute for their own good

Index: ctx.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/ctx.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** ctx.c	16 Jan 2004 17:35:12 -0000	1.12
--- ctx.c	13 Mar 2004 20:03:09 -0000	1.13
***************
*** 78,86 ****
      }
      ctx->shape = gageShapeNix(ctx->shape);
!     AIR_FREE(ctx->fw);
!     AIR_FREE(ctx->fsl);
!     AIR_FREE(ctx->off);
    }
!   AIR_FREE(ctx);
    return NULL;
  }
--- 78,86 ----
      }
      ctx->shape = gageShapeNix(ctx->shape);
!     ctx->fw = airFree(ctx->fw);
!     ctx->fsl = airFree(ctx->fsl);
!     ctx->off = airFree(ctx->off);
    }
!   ctx = airFree(ctx);
    return NULL;
  }

Index: miscGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/miscGage.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** miscGage.c	13 Feb 2004 22:56:15 -0000	1.10
--- miscGage.c	13 Mar 2004 20:03:09 -0000	1.11
***************
*** 231,235 ****
  
    if (isp) {
!     AIR_FREE(isp);
    }
    return NULL;
--- 231,235 ----
  
    if (isp) {
!     isp = airFree(isp);
    }
    return NULL;

Index: pvl.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/pvl.c,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** pvl.c	19 Feb 2004 03:50:02 -0000	1.11
--- pvl.c	13 Mar 2004 20:03:09 -0000	1.12
***************
*** 155,167 ****
  gagePerVolumeNix (gagePerVolume *pvl) {
  
!   AIR_FREE(pvl->iv3);
!   AIR_FREE(pvl->iv2);
!   AIR_FREE(pvl->iv1);
    if (!pvl->thisIsACopy && pvl->nixer) {
      pvl->nixer(pvl->npad, pvl->kind, pvl);
    }
!   AIR_FREE(pvl->answer);
!   AIR_FREE(pvl->directAnswer);
!   AIR_FREE(pvl);
    return NULL;
  }
--- 155,167 ----
  gagePerVolumeNix (gagePerVolume *pvl) {
  
!   pvl->iv3 = airFree(pvl->iv3);
!   pvl->iv2 = airFree(pvl->iv2);
!   pvl->iv1 = airFree(pvl->iv1);
    if (!pvl->thisIsACopy && pvl->nixer) {
      pvl->nixer(pvl->npad, pvl->kind, pvl);
    }
!   pvl->answer = airFree(pvl->answer);
!   pvl->directAnswer = airFree(pvl->directAnswer);
!   pvl = airFree(pvl);
    return NULL;
  }

Index: update.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/update.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** update.c	13 Feb 2004 22:56:15 -0000	1.12
--- update.c	13 Mar 2004 20:03:09 -0000	1.13
***************
*** 336,342 ****
    if (ctx->verbose) fprintf(stderr, "%s: hello\n", me);
    fd = GAGE_FD(ctx);
!   AIR_FREE(ctx->fsl);
!   AIR_FREE(ctx->fw);
!   AIR_FREE(ctx->off);
    ctx->fsl = (gage_t *)calloc(fd*3, sizeof(gage_t));
    ctx->fw = (gage_t *)calloc(fd*3*GAGE_KERNEL_NUM, sizeof(gage_t));
--- 336,342 ----
    if (ctx->verbose) fprintf(stderr, "%s: hello\n", me);
    fd = GAGE_FD(ctx);
!   ctx->fsl = airFree(ctx->fsl);
!   ctx->fw = airFree(ctx->fw);
!   ctx->off = airFree(ctx->off);
    ctx->fsl = (gage_t *)calloc(fd*3, sizeof(gage_t));
    ctx->fw = (gage_t *)calloc(fd*3*GAGE_KERNEL_NUM, sizeof(gage_t));
***************
*** 348,354 ****
    for (i=0; i<ctx->numPvl; i++) {
      pvl = ctx->pvl[i];
!     AIR_FREE(pvl->iv3);
!     AIR_FREE(pvl->iv2);
!     AIR_FREE(pvl->iv1);
      pvl->iv3 = (gage_t *)calloc(fd*fd*fd*pvl->kind->valLen, sizeof(gage_t));
      pvl->iv2 = (gage_t *)calloc(fd*fd*pvl->kind->valLen, sizeof(gage_t));
--- 348,354 ----
    for (i=0; i<ctx->numPvl; i++) {
      pvl = ctx->pvl[i];
!     pvl->iv3 = airFree(pvl->iv3);
!     pvl->iv2 = airFree(pvl->iv2);
!     pvl->iv1 = airFree(pvl->iv1);
      pvl->iv3 = (gage_t *)calloc(fd*fd*fd*pvl->kind->valLen, sizeof(gage_t));
      pvl->iv2 = (gage_t *)calloc(fd*fd*pvl->kind->valLen, sizeof(gage_t));

[Teem-commit] teem/src/mite renderMite.c,1.13,1.14 shade.c,1.2,1.3 thread.c,1.13,1.14 user.c,1.17,1.18

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26582/mite

Modified Files:
	renderMite.c shade.c thread.c user.c 
Log Message:
killed off AIR_FREE and AIR_FCLOSE macros- they were just way too cute for their own good

Index: renderMite.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/renderMite.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** renderMite.c	4 Mar 2004 14:04:08 -0000	1.13
--- renderMite.c	13 Mar 2004 20:03:10 -0000	1.14
***************
*** 29,33 ****
      mrr->rmop = airMopNew();
      if (!mrr->rmop) {
!       AIR_FREE(mrr);
        return mrr;
      }
--- 29,33 ----
      mrr->rmop = airMopNew();
      if (!mrr->rmop) {
!       mrr = airFree(mrr);
        return mrr;
      }
***************
*** 55,59 ****
    if (mrr) {
      airMopOkay(mrr->rmop);
!     AIR_FREE(mrr);
    }
    return NULL;
--- 55,59 ----
    if (mrr) {
      airMopOkay(mrr->rmop);
!     mrr = airFree(mrr);
    }
    return NULL;

Index: shade.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/shade.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** shade.c	29 Feb 2004 13:42:41 -0000	1.2
--- shade.c	13 Mar 2004 20:03:10 -0000	1.3
***************
*** 48,52 ****
      shpec->scl0 = gageItemSpecNix(shpec->scl0);
      shpec->scl1 = gageItemSpecNix(shpec->scl1);
!     AIR_FREE(shpec);
    }
    return NULL;
--- 48,52 ----
      shpec->scl0 = gageItemSpecNix(shpec->scl0);
      shpec->scl1 = gageItemSpecNix(shpec->scl1);
!     shpec = airFree(shpec);
    }
    return NULL;

Index: thread.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/thread.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** thread.c	4 Mar 2004 14:04:08 -0000	1.13
--- thread.c	13 Mar 2004 20:03:10 -0000	1.14
***************
*** 69,75 ****
  miteThreadNix(miteThread *mtt) {
  
!   AIR_FREE(mtt->ansMiteVal);
!   AIR_FREE(mtt->directAnsMiteVal);
!   AIR_FREE(mtt);
    return NULL;
  }
--- 69,75 ----
  miteThreadNix(miteThread *mtt) {
  
!   mtt->ansMiteVal = airFree(mtt->ansMiteVal);
!   mtt->directAnsMiteVal = airFree(mtt->directAnsMiteVal);
!   mtt = airFree(mtt);
    return NULL;
  }

Index: user.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/user.c,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** user.c	4 Mar 2004 14:04:08 -0000	1.17
--- user.c	13 Mar 2004 20:03:10 -0000	1.18
***************
*** 69,73 ****
    if (muu) {
      airMopOkay(muu->umop);
!     AIR_FREE(muu);
    }
    return NULL;
--- 69,73 ----
    if (muu) {
      airMopOkay(muu->umop);
!     muu = airFree(muu);
    }
    return NULL;

[Teem-commit] teem/src/nrrd filt.c,1.39,1.40

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1068

Modified Files:
	filt.c 
Log Message:
plugged memory leak

Index: filt.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/filt.c,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** filt.c	7 Jan 2004 15:34:30 -0000	1.39
--- filt.c	8 Mar 2004 14:58:37 -0000	1.40
***************
*** 361,364 ****
--- 361,365 ----
    }
    range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeFalse);
+   airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
    if (!(hist = (float*)calloc(bins, sizeof(float)))) {
      sprintf(err, "%s: couldn't allocate histogram (%d bins)", me, bins);

[Teem-commit] teem/src/ten epireg.c,1.26,1.27 tendEpireg.c,1.14,1.15

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29863

Modified Files:
	epireg.c tendEpireg.c 
Log Message:
NO API CHANGES: attempts at refining registration method, and other inconsequential changes

Index: epireg.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/epireg.c,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** epireg.c	7 Mar 2004 00:49:06 -0000	1.26
--- epireg.c	8 Mar 2004 14:41:24 -0000	1.27
***************
*** 333,336 ****
--- 333,337 ----
         and merge up (to bright) all small dark pieces, where
         (currently) small is big/2 */
+     big = -1;
      if (nrrdCCFind(ncc, &nval, nthr[ni], nrrdTypeDefault, conny)
  	|| nrrdCCSize(nsize, ncc)
***************
*** 338,345 ****
  	|| nrrdCCMerge(ncc, ncc, nval, -1, big-1, 0, conny)
  	|| nrrdCCRevalue(nthr[ni], ncc, nval)) {
!       sprintf(err, "%s: trouble with 3-D processing nthr[%d]", me, ni);
!       biffMove(TEN, err, NRRD); return 1;
      }
      for (z=0; z<sz; z++) {
        if ( nrrdSlice(nslc, nthr[ni], 2, z)
  	   || nrrdCCFind(ncc, &nval, nslc, nrrdTypeDefault, conny)
--- 339,353 ----
  	|| nrrdCCMerge(ncc, ncc, nval, -1, big-1, 0, conny)
  	|| nrrdCCRevalue(nthr[ni], ncc, nval)) {
!       if (big) {
! 	sprintf(err, "%s: trouble with 3-D processing nthr[%d]", me, ni);
! 	biffMove(TEN, err, NRRD); return 1;
!       } else {
! 	sprintf(err, "%s: got size 0 for biggest bright CC of nthr[%d]",
! 		me, ni);
! 	biffAdd(TEN, err); return 1;
!       }
      }
      for (z=0; z<sz; z++) {
+       big = -1;
        if ( nrrdSlice(nslc, nthr[ni], 2, z)
  	   || nrrdCCFind(ncc, &nval, nslc, nrrdTypeDefault, conny)
***************
*** 349,354 ****
  	   || nrrdCCRevalue(nslc, ncc, nval)
  	   || nrrdSplice(nthr[ni], nthr[ni], nslc, 2, z) ) {
! 	sprintf(err, "%s: trouble processing slice %d of nthr[%d]", me, z, ni);
! 	biffMove(TEN, err, NRRD); return 1;
        }
      }
--- 357,368 ----
  	   || nrrdCCRevalue(nslc, ncc, nval)
  	   || nrrdSplice(nthr[ni], nthr[ni], nslc, 2, z) ) {
! 	if (big) {
! 	  sprintf(err, "%s: trouble processing slice %d of nthr[%d]",
! 		  me, z, ni);
! 	  biffMove(TEN, err, NRRD); return 1;
! 	} else {
! 	  /* biggest bright CC on this slice had size 0
! 	     <==> there was no bright CC on this slice, move on */
! 	}
        }
      }
***************
*** 414,422 ****
  	}
        }
-       if (!N) {
- 	sprintf(err, "%s: saw no non-zero pixels in nthresh[%d]; "
- 		"DWI threshold too high?", me, ni);
- 	biffAdd(TEN, err); return 1;
-       }
        if (N == sx*sy) {
  	sprintf(err, "%s: saw only non-zero pixels in nthresh[%d]; "
--- 428,431 ----
***************
*** 424,452 ****
  	biffAdd(TEN, err); return 1;
        }
!       mx /= N;
!       my /= N;
!       cx = sx/2.0;
!       cy = sy/2.0;
!       /* ------ find M02, M11, M20 */
!       M02 = M11 = M20 = 0.0;
!       for (yi=0; yi<sy; yi++) {
! 	for (xi=0; xi<sx; xi++) {
! 	  val = thr[xi + sx*yi];
! 	  x = xi - cx;
! 	  y = yi - cy;
! 	  M02 += y*y*val;
! 	  M11 += x*y*val;
! 	  M20 += x*x*val;
  	}
        }
-       M02 /= N;
-       M11 /= N;
-       M20 /= N;
-       /* ------ set output */
-       mom[MEAN_X] = mx;
-       mom[MEAN_Y] = my;
-       mom[M_02] = M02;
-       mom[M_11] = M11;
-       mom[M_20] = M20;
        thr += sx*sy;
        mom += 5;
--- 433,471 ----
  	biffAdd(TEN, err); return 1;
        }
!       if (N) {
! 	/* there were non-zero pixels */
! 	mx /= N;
! 	my /= N;
! 	cx = sx/2.0;
! 	cy = sy/2.0;
! 	/* ------ find M02, M11, M20 */
! 	M02 = M11 = M20 = 0.0;
! 	for (yi=0; yi<sy; yi++) {
! 	  for (xi=0; xi<sx; xi++) {
! 	    val = thr[xi + sx*yi];
! 	    x = xi - cx;
! 	    y = yi - cy;
! 	    M02 += y*y*val;
! 	    M11 += x*y*val;
! 	    M20 += x*x*val;
! 	  }
  	}
+ 	M02 /= N;
+ 	M11 /= N;
+ 	M20 /= N;
+ 	/* ------ set output */
+ 	mom[MEAN_X] = mx;
+ 	mom[MEAN_Y] = my;
+ 	mom[M_02] = M02;
+ 	mom[M_11] = M11;
+ 	mom[M_20] = M20;
+       } else {
+ 	/* there were no non-zero pixels */
+ 	mom[MEAN_X] = 0;
+ 	mom[MEAN_Y] = 0;
+ 	mom[M_02] = 0;
+ 	mom[M_11] = 0;
+ 	mom[M_20] = 0;
        }
        thr += sx*sy;
        mom += 5;
***************
*** 509,526 ****
  _tenEpiRegEstimHST(Nrrd *nhst, Nrrd *npxfr, int ninLen, Nrrd *ngrad) {
    char me[]="_tenEpiRegEstimHST", err[AIR_STRLEN_MED];
!   double *hst, *grad, *mat1, *vec, *ans, *pxfr, *gA, *gB;
    int z, sz, A, B, npairs, ri;
!   Nrrd *nmat1, *nvec, *ninv, *nans;
    airArray *mop;
  
    mop = airMopNew();
!   airMopAdd(mop, nmat1=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   airMopAdd(mop, ninv=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
    airMopAdd(mop, nvec=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
    airMopAdd(mop, nans=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   npairs = ninLen*(ninLen-1);
!   sz = npxfr->axis[1].size;
!   if (nrrdMaybeAlloc(nhst, nrrdTypeDouble, 2, 9, sz)
!       || nrrdMaybeAlloc(nmat1, nrrdTypeDouble, 2, 3, npairs)
        || nrrdMaybeAlloc(nvec, nrrdTypeDouble, 2, 1, npairs)) {
      sprintf(err, "%s: couldn't allocate HST nrrd", me);
--- 528,560 ----
  _tenEpiRegEstimHST(Nrrd *nhst, Nrrd *npxfr, int ninLen, Nrrd *ngrad) {
    char me[]="_tenEpiRegEstimHST", err[AIR_STRLEN_MED];
!   double *hst, *grad, *mat, *vec, *ans, *pxfr, *gA, *gB;
    int z, sz, A, B, npairs, ri;
!   Nrrd **nmat, *nvec, **ninv, *nans;
    airArray *mop;
+   int order;
+ 
+   order = 1;
+ 
+   sz = npxfr->axis[1].size;
+   npairs = ninLen*(ninLen-1);
  
    mop = airMopNew();
!   nmat = (Nrrd**)calloc(sz, sizeof(Nrrd*));
!   ninv = (Nrrd**)calloc(sz, sizeof(Nrrd*));
!   airMopAdd(mop, nmat, airFree, airMopAlways);
!   airMopAdd(mop, ninv, airFree, airMopAlways);
!   for (z=0; z<sz; z++) {
!     airMopAdd(mop, nmat[z]=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!     if (nrrdMaybeAlloc(nmat[z], nrrdTypeDouble, 2,
! 		       (1 == order ? 3 : 9), npairs)) {
!       sprintf(err, "%s: couldn't allocate fitting matrices", me);
!       biffMove(TEN, err, NRRD); airMopError(mop); return 1;
!     }
!     airMopAdd(mop, ninv[z]=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   }
    airMopAdd(mop, nvec=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
    airMopAdd(mop, nans=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   if (nrrdMaybeAlloc(nhst, nrrdTypeDouble, 2,
! 		     (1 == order ? 9 : 27), sz)
        || nrrdMaybeAlloc(nvec, nrrdTypeDouble, 2, 1, npairs)) {
      sprintf(err, "%s: couldn't allocate HST nrrd", me);
***************
*** 528,539 ****
    }
    nrrdAxisInfoSet(nhst, nrrdAxisInfoLabel,
! 		  "Hx,Hy,Hz,Sx,Sy,Sz,Tx,Ty,Tz", "z");
!   grad = (double *)(ngrad->data);
!   mat1 = (double *)(nmat1->data);
!   vec = (double *)(nvec->data);
  
!   /* ------ find Sx, Sy, Sz per slice */
    for (z=0; z<sz; z++) {
!     hst = (double *)(nhst->data) + 0 + 9*z;
      ri = 0;
      for (A=0; A<ninLen; A++) {
--- 562,574 ----
    }
    nrrdAxisInfoSet(nhst, nrrdAxisInfoLabel,
! 		  (1 == order 
! 		   ? "Hx,Hy,Hz,Sx,Sy,Sz,Tx,Ty,Tz"
! 		   : "HST parms"), "z");
  
!   /* ------ per-slice: compute model fitting matrix and its pseudo-inverse */
!   grad = (double *)(ngrad->data);
    for (z=0; z<sz; z++) {
!     hst = (double *)(nhst->data) + (1 == order ? 9 : 27)*z;
!     mat = (double *)(nmat[z]->data);
      ri = 0;
      for (A=0; A<ninLen; A++) {
***************
*** 543,565 ****
  	gA = grad + 0 + 3*A;
  	gB = grad + 0 + 3*B;
! 	ELL_3V_SET(mat1 + 3*ri,
! 		   pxfr[SCALE]*gA[0] - gB[0],
! 		   pxfr[SCALE]*gA[1] - gB[1],
! 		   pxfr[SCALE]*gA[2] - gB[2]);
! 	vec[ri] = 1 - pxfr[SCALE];
  	ri += 1;
        }
      }
!     ell_Nm_pseudo_inv(ninv, nmat1);
!     ell_Nm_mul(nans, ninv, nvec);
!     ans = (double *)(nans->data);
!     hst[3] = ans[0];
!     hst[4] = ans[1];
!     hst[5] = ans[2];
    }
  
    /* ------ find Hx, Hy, Hz per slice */
    for (z=0; z<sz; z++) {
!     hst = (double *)(nhst->data) + 0 + 9*z;
      ri = 0;
      for (A=0; A<ninLen; A++) {
--- 578,636 ----
  	gA = grad + 0 + 3*A;
  	gB = grad + 0 + 3*B;
! 	if (1 == order) {
! 	  ELL_3V_SET(mat + 3*ri,
! 		     gB[0] - pxfr[SCALE]*gA[0],
! 		     gB[1] - pxfr[SCALE]*gA[1],
! 		     gB[2] - pxfr[SCALE]*gA[2]);
! 	} else {
! 	  ELL_9V_SET(mat + 9*ri,
! 		     gB[0] - pxfr[SCALE]*gA[0],
! 		     gB[1] - pxfr[SCALE]*gA[1],
! 		     gB[2] - pxfr[SCALE]*gA[2],
! 		     gB[0] - pxfr[SCALE]*gA[0],
! 		     gB[1] - pxfr[SCALE]*gA[1],
! 		     gB[2] - pxfr[SCALE]*gA[2],
! 		     gB[0] - pxfr[SCALE]*gA[0],
! 		     gB[1] - pxfr[SCALE]*gA[1],
! 		     gB[2] - pxfr[SCALE]*gA[2]);
! 		     /*
! 		     gB[0]*gB[0] - pxfr[SCALE]*gA[0]*gA[0],
! 		     gB[1]*gB[1] - pxfr[SCALE]*gA[1]*gA[1],
! 		     gB[2]*gB[2] - pxfr[SCALE]*gA[2]*gA[2],
! 		     gB[0]*gB[1] - pxfr[SCALE]*gA[0]*gA[1],
! 		     gB[0]*gB[2] - pxfr[SCALE]*gA[0]*gA[2],
! 		     gB[1]*gB[2] - pxfr[SCALE]*gA[1]*gA[2]);
! 		     */
! 	}
  	ri += 1;
        }
      }
!     if (nrrdHasNonExist(nmat[z])) {
!       /* as happens if there were zero slices in the segmentation output */
!       if (1 == order) {
! 	ELL_3V_SET(hst + 0*3, 0, 0, 0);
! 	ELL_3V_SET(hst + 1*3, 0, 0, 0);
! 	ELL_3V_SET(hst + 2*3, 0, 0, 0);
!       } else {
! 	ELL_9V_SET(hst + 0*9, 0, 0, 0, 0, 0, 0, 0, 0, 0);
! 	ELL_9V_SET(hst + 1*9, 0, 0, 0, 0, 0, 0, 0, 0, 0);
! 	ELL_9V_SET(hst + 2*9, 0, 0, 0, 0, 0, 0, 0, 0, 0);
!       }
!     } else {
!       if (ell_Nm_pseudo_inv(ninv[z], nmat[z])) {
! 	sprintf(err, "%s: trouble estimating model (slice %d)", me, z);
! 	biffMove(TEN, err, ELL); airMopError(mop); return 1;
!       }
!     }
    }
  
    /* ------ find Hx, Hy, Hz per slice */
+   vec = (double *)(nvec->data);
    for (z=0; z<sz; z++) {
!     if (nrrdHasNonExist(nmat[z])) {
!       /* we've already zero-ed out this row in the HST nrrd */
!       continue;
!     }
!     hst = (double *)(nhst->data) + (1 == order ? 9 : 27)*z;
      ri = 0;
      for (A=0; A<ninLen; A++) {
***************
*** 567,591 ****
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
- 	gA = grad + 0 + 3*A;
- 	gB = grad + 0 + 3*B;
- 	ELL_3V_SET(mat1 + 3*ri,
- 		   gB[0] - pxfr[SCALE]*gA[0],
- 		   gB[1] - pxfr[SCALE]*gA[1],
- 		   gB[2] - pxfr[SCALE]*gA[2]);
  	vec[ri] = pxfr[SHEAR];
  	ri += 1;
        }
      }
!     ell_Nm_pseudo_inv(ninv, nmat1);
!     ell_Nm_mul(nans, ninv, nvec);
      ans = (double *)(nans->data);
!     hst[0] = ans[0];
!     hst[1] = ans[1];
!     hst[2] = ans[2];
    }
  
    /* ------ find Tx, Ty, Tz per slice */
    for (z=0; z<sz; z++) {
!     hst = (double *)(nhst->data) + 0 + 9*z;
      ri = 0;
      for (A=0; A<ninLen; A++) {
--- 638,694 ----
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
  	vec[ri] = pxfr[SHEAR];
  	ri += 1;
        }
      }
!     if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Hx, Hy, Hz",
! 	      me, z);
!       biffMove(TEN, err, ELL); airMopError(mop); return 1;
!     }
      ans = (double *)(nans->data);
!     if (1 == order) {
!       ELL_3V_COPY(hst + 0*3, ans);
!     } else {
!       ELL_9V_COPY(hst + 0*9, ans);
!     }
!   }
! 
!   /* ------ find Sx, Sy, Sz per slice */
!   for (z=0; z<sz; z++) {
!     if (nrrdHasNonExist(nmat[z])) {
!       /* we've already zero-ed out this row in the HST nrrd */
!       continue;
!     }
!     hst = (double *)(nhst->data) + (1 == order ? 9 : 27)*z;
!     ri = 0;
!     for (A=0; A<ninLen; A++) {
!       for (B=0; B<ninLen; B++) {
! 	if (A == B) continue;
! 	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
! 	vec[ri] = pxfr[SCALE] - 1;
! 	ri += 1;
!       }
!     }
!     if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Sx, Sy, Sz",
! 	      me, z);
!       biffMove(TEN, err, ELL); airMopError(mop); return 1;
!     }
!     ans = (double *)(nans->data);
!     if (1 == order) {
!       ELL_3V_COPY(hst + 1*3, ans);
!     } else {
!       ELL_9V_COPY(hst + 1*9, ans);
!     }
    }
  
    /* ------ find Tx, Ty, Tz per slice */
    for (z=0; z<sz; z++) {
!     if (nrrdHasNonExist(nmat[z])) {
!       /* we've already zero-ed out this row in the HST nrrd */
!       continue;
!     }
!     hst = (double *)(nhst->data) + (1 == order ? 9 : 27)*z;
      ri = 0;
      for (A=0; A<ninLen; A++) {
***************
*** 593,612 ****
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
- 	gA = grad + 0 + 3*A;
- 	gB = grad + 0 + 3*B;
- 	ELL_3V_SET(mat1 + 3*ri,
- 		   gB[0] - pxfr[SCALE]*gA[0],
- 		   gB[1] - pxfr[SCALE]*gA[1],
- 		   gB[2] - pxfr[SCALE]*gA[2]);
  	vec[ri] = pxfr[TRAN];
  	ri += 1;
        }
      }
!     ell_Nm_pseudo_inv(ninv, nmat1);
!     ell_Nm_mul(nans, ninv, nvec);
      ans = (double *)(nans->data);
!     hst[6] = ans[0];
!     hst[7] = ans[1];
!     hst[8] = ans[2];
    }
  
--- 696,714 ----
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
  	vec[ri] = pxfr[TRAN];
  	ri += 1;
        }
      }
!     if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Tx, Ty, Tz",
! 	      me, z);
!       biffMove(TEN, err, ELL); airMopError(mop); return 1;
!     }
      ans = (double *)(nans->data);
!     if (1 == order) {
!       ELL_3V_COPY(hst + 2*3, ans);
!     } else {
!       ELL_9V_COPY(hst + 2*9, ans);
!     }
    }
  
***************
*** 670,674 ****
    /* initial ordering: messiness, slice index */
    for (zi=0; zi<sz; zi++) {
!     two[0 + 2*zi] = mess[zi];
      two[1 + 2*zi] = zi;
    }
--- 772,778 ----
    /* initial ordering: messiness, slice index */
    for (zi=0; zi<sz; zi++) {
!     two[0 + 2*zi] = (AIR_EXISTS(mess[zi])
! 		     ? mess[zi]
! 		     : 666);  /* don't use empty slices */
      two[1 + 2*zi] = zi;
    }
***************
*** 693,697 ****
    }
  
!   /* perform fitting for each column in hst */
    hst = (double*)(nhst->data);
    sh = nhst->axis[0].size;
--- 797,802 ----
    }
  
!   /* perform fitting for each column in hst (regardless of 
!      whether we're using a 1st or 2nd order model */
    hst = (double*)(nhst->data);
    sh = nhst->axis[0].size;
***************
*** 724,730 ****
  		 int reference, int ni, int zi,
  		 Nrrd *npxfr, Nrrd *nhst, Nrrd *ngrad) {
!   double *xfr, *hst, *grad;
    int sz, ninLen;
  
    /* these could also have been passed to us, but we can also discover them */
    sz = npxfr->axis[1].size;
--- 829,839 ----
  		 int reference, int ni, int zi,
  		 Nrrd *npxfr, Nrrd *nhst, Nrrd *ngrad) {
!   double *xfr, *hst, *_grad, grad[9]; /* big enough for 2nd order */
    int sz, ninLen;
  
+   int order;
+   
+   order = 1;
+ 
    /* these could also have been passed to us, but we can also discover them */
    sz = npxfr->axis[1].size;
***************
*** 734,742 ****
      /* we use the estimated H,S,T vectors to determine distortion
         as a function of gradient direction, and then invert this */
!     hst = (double*)(nhst->data) + 0 + 9*zi;
!     grad = (double*)(ngrad->data) + 0 + 3*ni;
!     *hhP = ELL_3V_DOT(grad, hst + 0*3);
!     *ssP = 1 + ELL_3V_DOT(grad, hst + 1*3);
!     *ttP = ELL_3V_DOT(grad, hst + 2*3);
    } else {
      /* we register against a specific DWI */
--- 843,865 ----
      /* we use the estimated H,S,T vectors to determine distortion
         as a function of gradient direction, and then invert this */
!     _grad = (double*)(ngrad->data) + 0 + 3*ni;
!     if (1 == order) {
!       hst = (double*)(nhst->data) + 0 + 9*zi;
!       *hhP = ELL_3V_DOT(_grad, hst + 0*3);
!       *ssP = 1 + ELL_3V_DOT(_grad, hst + 1*3);
!       *ttP = ELL_3V_DOT(_grad, hst + 2*3);
!     } else {
!       hst = (double*)(nhst->data) + 0 + 27*zi;
!       ELL_9V_SET(grad, _grad[0], _grad[1], _grad[2],
! 		 _grad[0], _grad[1], _grad[2],
! 		 _grad[0], _grad[1], _grad[2]);
! 		 /*
! 		 _grad[0]*_grad[0], _grad[1]*_grad[1], _grad[2]*_grad[2],
! 		 _grad[0]*_grad[1], _grad[0]*_grad[2], _grad[1]*_grad[2]);
! 		 */
!       *hhP = ELL_9V_DOT(grad, hst + 0*9);
!       *ssP = 1 + ELL_9V_DOT(grad, hst + 1*9);
!       *ttP = ELL_9V_DOT(grad, hst + 2*9);
!     }
    } else {
      /* we register against a specific DWI */

Index: tendEpireg.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendEpireg.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** tendEpireg.c	7 Jan 2004 15:34:31 -0000	1.14
--- tendEpireg.c	8 Mar 2004 14:41:24 -0000	1.15
***************
*** 140,144 ****
    if (rret) {
      airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
!     fprintf(stderr, "%s: trouble doing epireg \"%s\":\n%s\n", me, buff, err);
      airMopError(mop); return 1;
    }
--- 140,144 ----
    if (rret) {
      airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
!     fprintf(stderr, "%s: trouble doing epireg:\n%s\n", me, err);
      airMopError(mop); return 1;
    }

[Teem-commit] teem/src/ell ellMacros.h,1.40,1.41

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29468

Modified Files:
	ellMacros.h 
Log Message:
some more macros

Index: ellMacros.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/ellMacros.h,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** ellMacros.h	1 Mar 2004 10:19:44 -0000	1.40
--- ellMacros.h	8 Mar 2004 14:39:48 -0000	1.41
***************
*** 757,760 ****
--- 757,787 ----
     (v2)[6] = (v1)[6])
  
+ #define ELL_9V_SET(v, a, b, c, d, e, f, g, h, i) \
+   ((v)[0]=(a), (v)[1]=(b), (v)[2]=(c), \
+    (v)[3]=(d), (v)[4]=(e), (v)[5]=(f), \
+    (v)[6]=(g), (v)[7]=(h), (v)[8]=(i))
+ 
+ #define ELL_9V_COPY(v2, v1) \
+   ((v2)[0] = (v1)[0],       \
+    (v2)[1] = (v1)[1],       \
+    (v2)[2] = (v1)[2],       \
+    (v2)[3] = (v1)[3],       \
+    (v2)[4] = (v1)[4],       \
+    (v2)[5] = (v1)[5],       \
+    (v2)[6] = (v1)[6],       \
+    (v2)[7] = (v1)[7],       \
+    (v2)[8] = (v1)[8])
+ 
+ #define ELL_9V_DOT(v1, v2) \
+   ((v1)[0]*(v2)[0] +       \
+    (v1)[1]*(v2)[1] +       \
+    (v1)[2]*(v2)[2] +       \
+    (v1)[3]*(v2)[3] +       \
+    (v1)[4]*(v2)[4] +       \
+    (v1)[5]*(v2)[5] +       \
+    (v1)[6]*(v2)[6] +       \
+    (v1)[7]*(v2)[7] +       \
+    (v1)[8]*(v2)[8])
+ 
  #ifdef __cplusplus
     }

[Teem-commit] teem/src/ell genmat.c,1.5,1.6

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29340

Modified Files:
	genmat.c 
Log Message:
clarified error message

Index: genmat.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/genmat.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** genmat.c	1 Mar 2004 10:19:44 -0000	1.5
--- genmat.c	8 Mar 2004 14:39:30 -0000	1.6
***************
*** 130,134 ****
    }
  
!   /* find vv[i]: max of abs of everything in row i */
    for (i=0; i<NN; i++) {
      big = 0.0;
--- 130,134 ----
    }
  
!   /* find vv[i]: max of abs of everything in column i */
    for (i=0; i<NN; i++) {
      big = 0.0;
***************
*** 139,143 ****
      }
      if (!big) {
!       sprintf(err, "%s: singular matrix since row %d all zero", me, i);
        biffAdd(ELL, err); ret = 1; goto seeya;
      }
--- 139,143 ----
      }
      if (!big) {
!       sprintf(err, "%s: singular matrix since column %d all zero", me, i);
        biffAdd(ELL, err); ret = 1; goto seeya;
      }

[Teem-commit] teem/src/ten chan.c,1.30,1.31

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18490

Modified Files:
	chan.c 
Log Message:
tenSimulateOne: 
- fixed basic bug in handling of off-diagonal entries of B-matrix
tenEstimateLinear4D: 
- fixed basic bug in computation of unknown B0 field
- should be able to save out tensor error field with knownB0 either true or false
- changed tweaking heuristic in automatic DWI threshold detection




Index: chan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/chan.c,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** chan.c	27 Feb 2004 10:23:56 -0000	1.30
--- chan.c	7 Mar 2004 00:52:57 -0000	1.31
***************
*** 141,145 ****
  ** output:
  ** ten[0]..ten[6] will be the confidence value followed by the tensor
! ** -------------- !IF knownB0 -------------------------
  ** input:
  ** dwi[0]..dwi[DD-1] are the DD DWI values,
--- 141,145 ----
  ** output:
  ** ten[0]..ten[6] will be the confidence value followed by the tensor
! ** -------------- IF !knownB0 -------------------------
  ** input:
  ** dwi[0]..dwi[DD-1] are the DD DWI values,
***************
*** 160,163 ****
--- 160,167 ----
    
    if (knownB0) {
+     if (B0P) {
+       /* we save this as a courtesy */
+       *B0P = AIR_MAX(dwi[0], 1);
+     }
      logB0 = log(AIR_MAX(dwi[0], 1));
      mean = 0;
***************
*** 197,202 ****
  	ten[j+1] = tmp;
        } else {
  	if (B0P) {
! 	  *B0P = tmp;
  	}
        }
--- 201,207 ----
  	ten[j+1] = tmp;
        } else {
+ 	/* we're on seventh row, for finding B0 */
  	if (B0P) {
! 	  *B0P = exp(b*tmp);
  	}
        }
***************
*** 266,296 ****
  		    float thresh, float soft, float b) {
    char me[]="tenEstimateLinear4D", err[AIR_STRLEN_MED];
!   Nrrd *nemat, *ncrop, *nhist;
    airArray *mop;
!   int E, DD, d, II, sx, sy, sz, cmin[4], cmax[4], amap[4] = {-1,1,2,3};
    float *ten, dwi1[_TEN_MAX_DWI_NUM], *terr=NULL, 
!     *B0=NULL, (*lup)(const void *, size_t);
!   double *emat;
    NrrdRange *range;
- 
-   /*
-   HEY: uncomment with tenSimulate stuff is working for unknown B0 case
-   Nrrd *nbmat;
-   double *bmat;
-   const char *bk;
    float dwi2[_TEN_MAX_DWI_NUM], te, d1, d2;
-   */
  
    if (!(nten && ndwi && _nbmat)) {
!     /* nerrP can be NULL */
      sprintf(err, "%s: got NULL pointer", me);
      biffAdd(TEN, err); return 1;
    }
-   if (!knownB0 && !nB0P) {
-     /* For the time being, this needless restriction helps simplify things */
-     sprintf(err, "%s: sorry, don't know (and hence will estimate) B=0 image, "
- 	    "but didn't get a Nrrd* to put it in", me);
-     biffAdd(TEN, err); return 1;
-   }
    if (!( 4 == ndwi->dim && 7 <= ndwi->axis[0].size )) {
      sprintf(err, "%s: dwi should be 4-D array with axis 0 size >= 7", me);
--- 271,288 ----
  		    float thresh, float soft, float b) {
    char me[]="tenEstimateLinear4D", err[AIR_STRLEN_MED];
!   Nrrd *nemat, *nbmat, *ncrop, *nhist;
    airArray *mop;
!   int E, DD, d, II, sx, sy, sz, cmin[4], cmax[4], amap[4];
    float *ten, dwi1[_TEN_MAX_DWI_NUM], *terr=NULL, 
!     _B0, *B0, (*lup)(const void *, size_t);
!   double *emat, *bmat;
    NrrdRange *range;
    float dwi2[_TEN_MAX_DWI_NUM], te, d1, d2;
  
    if (!(nten && ndwi && _nbmat)) {
!     /* nerrP and _NB0P can be NULL */
      sprintf(err, "%s: got NULL pointer", me);
      biffAdd(TEN, err); return 1;
    }
    if (!( 4 == ndwi->dim && 7 <= ndwi->axis[0].size )) {
      sprintf(err, "%s: dwi should be 4-D array with axis 0 size >= 7", me);
***************
*** 318,326 ****
    
    mop = airMopNew();
!   /* HEY, right now, nbmat is not used for anything (not tenSimulate stuff)
!      because tenSimulate currently can't handle the unknown B0 case */
!   /* airMopAdd(mop, nbmat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways); */
    airMopAdd(mop, nemat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   if (tenEMatrixCalc(nemat, _nbmat, knownB0)) {
      sprintf(err, "%s: trouble computing estimation matrix", me);
      biffAdd(TEN, err); return 1;
--- 310,320 ----
    
    mop = airMopNew();
!   airMopAdd(mop, nbmat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   if (nrrdConvert(nbmat, _nbmat, nrrdTypeDouble)) {
!     sprintf(err, "%s: trouble converting to doubles", me);
!     biffMove(TEN, err, NRRD); return 1;
!   }
    airMopAdd(mop, nemat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
!   if (tenEMatrixCalc(nemat, nbmat, knownB0)) {
      sprintf(err, "%s: trouble computing estimation matrix", me);
      biffAdd(TEN, err); return 1;
***************
*** 347,351 ****
        biffMove(TEN, err, NRRD); airMopError(mop); return 1;
      }
!     if (_tenFindValley(&thresh, nhist, 0.85)) {
        sprintf(err, "%s: problem finding DW histogram valley", me);
        biffAdd(TEN, err); airMopError(mop); return 1;
--- 341,345 ----
        biffMove(TEN, err, NRRD); airMopError(mop); return 1;
      }
!     if (_tenFindValley(&thresh, nhist, 0.75, AIR_FALSE)) {
        sprintf(err, "%s: problem finding DW histogram valley", me);
        biffAdd(TEN, err); airMopError(mop); return 1;
***************
*** 358,367 ****
    }
    if (nterrP) {
- 
-     /* HEY HEY HEY HEY */
-     sprintf(err, "%s: sorry, this functionality currently disabled", me);
-     biffAdd(TEN, err); return 1;
-     /* HEY HEY HEY HEY */
- 
      if (!(*nterrP)) {
        *nterrP = nrrdNew();
--- 352,355 ----
***************
*** 386,391 ****
      airMopAdd(mop, *nB0P, (airMopper)nrrdNuke, airMopOnError);
      B0 = (float*)((*nB0P)->data);
    }
!   /* bmat = (double*)(nbmat->data); */
    emat = (double*)(nemat->data);
    ten = (float*)(nten->data);
--- 374,381 ----
      airMopAdd(mop, *nB0P, (airMopper)nrrdNuke, airMopOnError);
      B0 = (float*)((*nB0P)->data);
+   } else {
+     B0 = NULL;
    }
!   bmat = (double*)(nbmat->data);
    emat = (double*)(nemat->data);
    ten = (float*)(nten->data);
***************
*** 398,421 ****
  	fprintf(stderr, "%s: input dwi1[%d] = %g\n", me, d, dwi1[d]);
      }
!     tenEstimateLinearSingle(ten, B0, dwi1, emat, DD, knownB0, thresh, soft, b);
!     if (tenVerbose) 
        fprintf(stderr, "%s: output ten = (%g) %g,%g,%g  %g,%g  %g\n", me,
  	      ten[0], ten[1], ten[2], ten[3], ten[4], ten[5], ten[6]);
      if (nterrP) {
-       /*
-       tenSimulateOne(dwi2, dwi1[0], ten, bmat, DD, b);
        te = 0;
!       for (d=0; d<DD; d++) {
! 	d1 = AIR_MAX(dwi1[d], 1);
! 	d2 = AIR_MAX(dwi2[d], 1);
! 	te += (d1 - d2)*(d1 - d2);
! 	if (tenVerbose)
! 	  fprintf(stderr, "%s: dwi1,2[%d] = %g,%g --> %g\n",
! 		  me, d, dwi1[d], dwi2[d], te);
        }
        *terr = sqrt(te);
-       */
        terr += 1;
!     }
      ten += 7;
      if (B0) {
--- 388,425 ----
  	fprintf(stderr, "%s: input dwi1[%d] = %g\n", me, d, dwi1[d]);
      }
!     tenEstimateLinearSingle(ten, &_B0,
! 			    dwi1, emat, DD, knownB0, thresh, soft, b);
!     if (nB0P) {
!       *B0 = _B0;
!     }
!     if (tenVerbose) {
        fprintf(stderr, "%s: output ten = (%g) %g,%g,%g  %g,%g  %g\n", me,
  	      ten[0], ten[1], ten[2], ten[3], ten[4], ten[5], ten[6]);
+     }
      if (nterrP) {
        te = 0;
!       if (knownB0) {
! 	tenSimulateOne(dwi2, _B0, ten, bmat, DD, b);
! 	for (d=1; d<DD; d++) {
! 	  d1 = AIR_MAX(dwi1[d], 1);
! 	  d2 = AIR_MAX(dwi2[d], 1);
! 	  te += (d1 - d2)*(d1 - d2);
! 	}
! 	te /= (DD-1);
!       } else {
! 	tenSimulateOne(dwi2, _B0, ten, bmat, DD+1, b);
! 	for (d=0; d<DD; d++) {
! 	  d1 = AIR_MAX(dwi1[d], 1);
! 	  /* tenSimulateOne always puts the B0 in the beginning of
! 	     the dwi vector, but in this case we didn't have it in
! 	     the input dwi vecctor */
! 	  d2 = AIR_MAX(dwi2[d+1], 1);
! 	  te += (d1 - d2)*(d1 - d2);
! 	}
! 	te /= DD;
        }
        *terr = sqrt(te);
        terr += 1;
!     }  
      ten += 7;
      if (B0) {
***************
*** 425,428 ****
--- 429,433 ----
    /* tenEigenvalueClamp(nten, nten, 0, AIR_NAN); */
  
+   ELL_4V_SET(amap, -1, 1, 2, 3);
    nrrdAxisInfoCopy(nten, ndwi, amap, NRRD_AXIS_INFO_NONE);
  
***************
*** 434,444 ****
  ******** tenSimulateOne
  **
! ** simulate a diffusion weighted measurement
  **
  */
  void
! tenSimulateOne(float *dwi, float B0, float *ten,
! 	       double *bmat, int DD, float b) {
!   double v[_TEN_MAX_DWI_NUM];
    int i, j;
    
--- 439,456 ----
  ******** tenSimulateOne
  **
! ** given a tensor, simulate the set of diffusion weighted measurements
! ** represented by the given B matrix
  **
+ ** NOTE: the mindset if this function is very much "knownB0==true":
+ ** B0 is required as an argument (and its always copied to dwi[0]),
+ ** and the given bmat is assumed to have DD-1 rows,
+ **  so dwi[0] through dwi[DD-1] (DD values total) are set in the output.
  */
  void
! tenSimulateOne(float *dwi,
! 	       float B0, float *ten, double *bmat, int DD, float b) {
!   double vv;
!   /* this is how we multiply the off-diagonal entries by 2 */
!   double matwght[6] = {1, 2, 2, 1, 2, 1};
    int i, j;
    
***************
*** 449,459 ****
    }
    for (i=0; i<DD-1; i++) {
!     v[i] = 0;
      for (j=0; j<6; j++) {
!       v[i] += bmat[j + 6*i]*ten[j+1];
      }
!     dwi[i+1] = AIR_MAX(B0, 1)*exp(-b*v[i]);
      if (tenVerbose) {
!       fprintf(stderr, "v[%d] = %g --> dwi = %g\n", i, v[i], dwi[i+1]);
      }
    }
--- 461,471 ----
    }
    for (i=0; i<DD-1; i++) {
!     vv = 0;
      for (j=0; j<6; j++) {
!       vv += matwght[j]*bmat[j + 6*i]*ten[j+1];
      }
!     dwi[i+1] = AIR_MAX(B0, 1)*exp(-b*vv);
      if (tenVerbose) {
!       fprintf(stderr, "v[%d] = %g --> dwi = %g\n", i, vv, dwi[i+1]);
      }
    }

[Teem-commit] teem/src/ten epireg.c,1.25,1.26

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17843

Modified Files:
	epireg.c 
Log Message:
changed tweaking heuristic in automatic threshold detection

Index: epireg.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/epireg.c,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** epireg.c	27 Feb 2004 10:23:56 -0000	1.25
--- epireg.c	7 Mar 2004 00:49:06 -0000	1.26
***************
*** 191,195 ****
  
  int
! _tenEpiRegFindThresh(float *DWthrP, Nrrd **nin, int ninLen) {
    char me[]="_tenEpiRegFindThresh", err[AIR_STRLEN_MED];
    Nrrd *nhist, *ntmp;
--- 191,195 ----
  
  int
! _tenEpiRegFindThresh(float *DWthrP, Nrrd **nin, int ninLen, int save) {
    char me[]="_tenEpiRegFindThresh", err[AIR_STRLEN_MED];
    Nrrd *nhist, *ntmp;
***************
*** 232,236 ****
      }
    }
!   if (_tenFindValley(DWthrP, nhist, 0.85)) {
      sprintf(err, "%s: problem finding DWI histogram valley", me);
      biffAdd(TEN, err); airMopError(mop); return 1;
--- 232,239 ----
      }
    }
!   if (save) {
!     nrrdSave("regtmp-dwihist.nrrd", nhist, NULL);
!   }
!   if (_tenFindValley(DWthrP, nhist, 0.65, save)) {
      sprintf(err, "%s: problem finding DWI histogram valley", me);
      biffAdd(TEN, err); airMopError(mop); return 1;
***************
*** 244,248 ****
  int
  _tenEpiRegThreshold(Nrrd **nthresh, Nrrd **nblur, int ninLen,
! 		    float DWthr, int verb) {
    char me[]="_tenEpiRegThreshold", err[AIR_STRLEN_MED];
    airArray *mop;
--- 247,251 ----
  int
  _tenEpiRegThreshold(Nrrd **nthresh, Nrrd **nblur, int ninLen,
! 		    float DWthr, int verb, int progress) {
    char me[]="_tenEpiRegThreshold", err[AIR_STRLEN_MED];
    airArray *mop;
***************
*** 252,256 ****
  
    if (!( AIR_EXISTS(DWthr) )) {
!     if (_tenEpiRegFindThresh(&DWthr, nblur, ninLen)) {
        sprintf(err, "%s: trouble with automatic threshold determination", me);
        biffAdd(TEN, err); return 1;
--- 255,259 ----
  
    if (!( AIR_EXISTS(DWthr) )) {
!     if (_tenEpiRegFindThresh(&DWthr, nblur, ninLen, progress)) {
        sprintf(err, "%s: trouble with automatic threshold determination", me);
        biffAdd(TEN, err); return 1;
***************
*** 932,936 ****
    /* ------ threshold */
    if (_tenEpiRegThreshold(nbuffB, nbuffA, ninLen, 
! 			  DWthr, verbose)) {
      sprintf(err, "%s: trouble thresholding", me);
      biffAdd(TEN, err); airMopError(mop); return 1;
--- 935,939 ----
    /* ------ threshold */
    if (_tenEpiRegThreshold(nbuffB, nbuffA, ninLen, 
! 			  DWthr, verbose, progress)) {
      sprintf(err, "%s: trouble thresholding", me);
      biffAdd(TEN, err); airMopError(mop); return 1;

[Teem-commit] teem/src/ten ten.h,1.78,1.79 miscTen.c,1.22,1.23

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17631

Modified Files:
	ten.h miscTen.c 
Log Message:
can now optionally tell _tenFindValley to save filtered histogram

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.78
retrieving revision 1.79
diff -C2 -d -r1.78 -r1.79
*** ten.h	27 Feb 2004 12:50:37 -0000	1.78
--- ten.h	7 Mar 2004 00:48:13 -0000	1.79
***************
*** 471,475 ****
  			  int aniso, int scaleByAniso);
  TEEM_API int tenBMatrixCheck(Nrrd *nbmat);
! TEEM_API int _tenFindValley(float *valP, Nrrd *nhist, float tweak);
  
  /* fiberMethods.c */
--- 471,476 ----
  			  int aniso, int scaleByAniso);
  TEEM_API int tenBMatrixCheck(Nrrd *nbmat);
! TEEM_API int _tenFindValley(float *valP, Nrrd *nhist,
! 			    float tweak, int save);
  
  /* fiberMethods.c */

Index: miscTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/miscTen.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** miscTen.c	27 Feb 2004 10:23:56 -0000	1.22
--- miscTen.c	7 Mar 2004 00:48:13 -0000	1.23
***************
*** 215,219 ****
  */
  int
! _tenFindValley(float *valP, Nrrd *nhist, float tweak) {
    char me[]="_tenFindValley", err[AIR_STRLEN_MED];
    double gparm[NRRD_KERNEL_PARMS_NUM], dparm[NRRD_KERNEL_PARMS_NUM];
--- 215,219 ----
  */
  int
! _tenFindValley(float *valP, Nrrd *nhist, float tweak, int save) {
    char me[]="_tenFindValley", err[AIR_STRLEN_MED];
    double gparm[NRRD_KERNEL_PARMS_NUM], dparm[NRRD_KERNEL_PARMS_NUM];
***************
*** 238,242 ****
  
    bins = nhist->axis[0].size;
!   gparm[0] = bins/50;  /* wacky heuristic for gaussian stdev */
    gparm[1] = 3;        /* how many stdevs to cut-off at */
    dparm[0] = 1.0;      /* unit spacing */
--- 238,242 ----
  
    bins = nhist->axis[0].size;
!   gparm[0] = bins/128;  /* wacky heuristic for gaussian stdev */
    gparm[1] = 3;        /* how many stdevs to cut-off at */
    dparm[0] = 1.0;      /* unit spacing */
***************
*** 253,256 ****
--- 253,260 ----
      biffMove(TEN, err, NRRD), airMopError(mop); return 1;
    }
+   if (save) {
+     nrrdSave("tmp-histA.nrrd", ntmpA, NULL);
+     nrrdSave("tmp-histB.nrrd", ntmpB, NULL);
+   }
    hist = (float*)(ntmpB->data);
    histD = (float*)(nhistD->data);
***************
*** 281,282 ****
--- 285,287 ----
    return 0;
  }
+ 

[Teem-commit] teem/src/ten tendEstim.c,1.12,1.13

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17496

Modified Files:
	tendEstim.c 
Log Message:
fixed typo in usage info

Index: tendEstim.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendEstim.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** tendEstim.c	7 Jan 2004 15:34:31 -0000	1.12
--- tendEstim.c	7 Mar 2004 00:47:36 -0000	1.13
***************
*** 66,70 ****
  	     "confidence boundary is perfectly sharp");
    hestOptAdd(&hopt, "scale", "scale", airTypeFloat, 1, 1, &scale, "1",
! 	     "Ffter estimating the tensor, scale all of its elements "
  	     "(but not the confidence value) by this amount.  Can help with "
  	     "downstream numerical precision if values are very large "
--- 66,70 ----
  	     "confidence boundary is perfectly sharp");
    hestOptAdd(&hopt, "scale", "scale", airTypeFloat, 1, 1, &scale, "1",
! 	     "After estimating the tensor, scale all of its elements "
  	     "(but not the confidence value) by this amount.  Can help with "
  	     "downstream numerical precision if values are very large "

[Teem-commit] teem/src/ten bimod.c,1.6,1.7

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17353

Modified Files:
	bimod.c 
Log Message:
vain efforts to make this work on real DWI histograms...

Index: bimod.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/bimod.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** bimod.c	7 Jan 2004 15:34:31 -0000	1.6
--- bimod.c	7 Mar 2004 00:46:42 -0000	1.7
***************
*** 312,318 ****
    _tenEMBimodalPP(biparm);
    f1 = _tenEMBimodalNewFraction1(biparm);
!   if (1 == biparm->stage) {
      _tenEMBimodalNewMean(&m1, &m2, biparm);
!   }
    _tenEMBimodalNewSigma(&s1, &s2, m1, m2, biparm);
  
--- 312,318 ----
    _tenEMBimodalPP(biparm);
    f1 = _tenEMBimodalNewFraction1(biparm);
!   /*   if (1 == biparm->stage) { */
      _tenEMBimodalNewMean(&m1, &m2, biparm);
!     /*   } */
    _tenEMBimodalNewSigma(&s1, &s2, m1, m2, biparm);
  
***************
*** 420,424 ****
  tenEMBimodal(tenEMBimodalParm *biparm, Nrrd *_nhisto) {
    char me[]="tenEMBimodal", err[AIR_STRLEN_MED];
!   int done;
    
    if (!(biparm && _nhisto)) {
--- 420,424 ----
  tenEMBimodal(tenEMBimodalParm *biparm, Nrrd *_nhisto) {
    char me[]="tenEMBimodal", err[AIR_STRLEN_MED];
!   int done, _iter;
    
    if (!(biparm && _nhisto)) {
***************
*** 441,447 ****
         biparm->stage <= (biparm->twoStage ? 2 : 1);
         biparm->stage++) {
!     for (; 
  	 biparm->iteration <= biparm->maxIteration; 
! 	 biparm->iteration++) {
        if (_tenEMBimodalIterate(biparm)    /* sets delta */
  	  || _tenEMBimodalConfThresh(biparm)
--- 441,447 ----
         biparm->stage <= (biparm->twoStage ? 2 : 1);
         biparm->stage++) {
!     for (_iter=0; 
  	 biparm->iteration <= biparm->maxIteration; 
! 	 biparm->iteration++, _iter++) {
        if (_tenEMBimodalIterate(biparm)    /* sets delta */
  	  || _tenEMBimodalConfThresh(biparm)
***************
*** 451,455 ****
  	biffAdd(TEN, err); return 1;
        }
!       if (biparm->delta < biparm->minDelta) {
  	done = AIR_TRUE;
  	break;
--- 451,456 ----
  	biffAdd(TEN, err); return 1;
        }
!       if (biparm->delta < biparm->minDelta
! 	  && (!biparm->twoStage || 1 == biparm->stage || _iter > 10) ) {
  	done = AIR_TRUE;
  	break;

[Teem-commit] teem/src/moss privateMoss.h,1.3,1.4 xform.c,1.13,1.14

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/moss
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20107/moss

Modified Files:
	privateMoss.h xform.c 
Log Message:
propogated change in ell from column-major to row-major

Index: privateMoss.h
===================================================================
RCS file: /cvsroot/teem/teem/src/moss/privateMoss.h,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** privateMoss.h	7 Jan 2004 15:34:30 -0000	1.3
--- privateMoss.h	4 Mar 2004 23:57:22 -0000	1.4
***************
*** 18,25 ****
  */
  
! #define MOSS_MAT_SET(mat, a, b, c, d, x, y) \
!   (mat)[0]=(a); (mat)[1]=(b); \
!   (mat)[2]=(c); (mat)[3]=(d); \
!   (mat)[4]=(x); (mat)[5]=(y)
  
  #define MOSS_MAT_COPY(m2, m1) \
--- 18,24 ----
  */
  
! #define MOSS_MAT_SET(mat, a, b, x, c, d, y) \
!   (mat)[0]=(a); (mat)[1]=(b); (mat)[2]=(x); \
!   (mat)[3]=(c); (mat)[4]=(d); (mat)[5]=(y)
  
  #define MOSS_MAT_COPY(m2, m1) \
***************
*** 28,37 ****
  
  #define MOSS_MAT_6TO9(m2, m1) \
!   ELL_3V_SET((m2)+0, (m1)[0], (m1)[1], 0); \
!   ELL_3V_SET((m2)+3, (m1)[2], (m1)[3], 0); \
!   ELL_3V_SET((m2)+6, (m1)[4], (m1)[5], 1)
  
  #define MOSS_MAT_9TO6(m2, m1) \
!   MOSS_MAT_SET(m2, (m1)[0], (m1)[1], (m1)[3], (m1)[4], (m1)[6], (m1)[7])
  
  
--- 27,36 ----
  
  #define MOSS_MAT_6TO9(m2, m1) \
!   ELL_3V_COPY((m2)+0, (m1)+0); \
!   ELL_3V_COPY((m2)+3, (m1)+3); \
!   ELL_3V_SET((m2)+6, 0, 0, 1)
  
  #define MOSS_MAT_9TO6(m2, m1) \
!   MOSS_MAT_SET(m2, (m1)[0], (m1)[1], (m1)[2], (m1)[3], (m1)[4], (m1)[5])
  
  

Index: xform.c
===================================================================
RCS file: /cvsroot/teem/teem/src/moss/xform.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** xform.c	19 Feb 2004 06:45:12 -0000	1.13
--- xform.c	4 Mar 2004 23:57:22 -0000	1.14
***************
*** 23,29 ****
  /*
  
!  0  3  6
!  1  4  7
!  2  5  8
  
   a  c  tx
--- 23,29 ----
  /*
  
!  0  1  2
!  3  4  5
!  6  7  8
  
   a  c  tx
***************
*** 31,36 ****
   0  0  1
  
!  0  2  4
!  1  3  5
  
  */
--- 31,36 ----
   0  0  1
  
!  0  1  2
!  3  4  5
  
  */
***************
*** 40,46 ****
  
    fprintf(f, "% 15.7f % 15.7f % 15.7f\n", 
! 	  (float)mat[0], (float)mat[2], (float)mat[4]);
    fprintf(f, "% 15.7f % 15.7f % 15.7f\n", 
! 	  (float)mat[1], (float)mat[3], (float)mat[5]);
  }
  
--- 40,46 ----
  
    fprintf(f, "% 15.7f % 15.7f % 15.7f\n", 
! 	  (float)mat[0], (float)mat[1], (float)mat[2]);
    fprintf(f, "% 15.7f % 15.7f % 15.7f\n", 
! 	  (float)mat[3], (float)mat[4], (float)mat[5]);
  }
  
***************
*** 80,84 ****
  mossMatIdentitySet (double *mat) {
  
!   MOSS_MAT_SET(mat, 1, 0, 0, 1, 0, 0);
    return mat;
  }
--- 80,84 ----
  mossMatIdentitySet (double *mat) {
  
!   MOSS_MAT_SET(mat, 1, 0, 0, 0, 1, 0);
    return mat;
  }
***************
*** 87,91 ****
  mossMatTranslateSet (double *mat, double tx, double ty) {
  
!   MOSS_MAT_SET(mat, 1, 0, 0, 1, tx, ty);
    return mat;
  }
--- 87,91 ----
  mossMatTranslateSet (double *mat, double tx, double ty) {
  
!   MOSS_MAT_SET(mat, 1, 0, tx, 0, 1, ty);
    return mat;
  }
***************
*** 95,99 ****
  
    angle *= AIR_PI/180.0;
!   MOSS_MAT_SET(mat, cos(angle), sin(angle), -sin(angle), cos(angle), 0, 0);
    return mat;
  }
--- 95,99 ----
  
    angle *= AIR_PI/180.0;
!   MOSS_MAT_SET(mat, cos(angle), -sin(angle), 0, sin(angle), cos(angle), 0);
    return mat;
  }
***************
*** 103,107 ****
    double rot[6], flip[6];
  
!   MOSS_MAT_SET(flip, -1, 0, 0, 1, 0, 0);
    mossMatIdentitySet(mat);
    mossMatLeftMultiply(mat, mossMatRotateSet(rot, -angle));
--- 103,107 ----
    double rot[6], flip[6];
  
!   MOSS_MAT_SET(flip, -1, 0, 0, 0, 1, 0);
    mossMatIdentitySet(mat);
    mossMatLeftMultiply(mat, mossMatRotateSet(rot, -angle));
***************
*** 115,119 ****
    double rot[6], shear[6];
  
!   MOSS_MAT_SET(shear, 1, 0, amount, 1, 0, 0);
    mossMatIdentitySet(mat);
    mossMatLeftMultiply(mat, mossMatRotateSet(rot, -angleFixed));
--- 115,119 ----
    double rot[6], shear[6];
  
!   MOSS_MAT_SET(shear, 1, amount, 0, 0, 1, 0);
    mossMatIdentitySet(mat);
    mossMatLeftMultiply(mat, mossMatRotateSet(rot, -angleFixed));
***************
*** 126,130 ****
  mossMatScaleSet (double *mat, double sx, double sy) {
  
!   MOSS_MAT_SET(mat, sx, 0, 0, sy, 0, 0);
    return mat;
  }
--- 126,130 ----
  mossMatScaleSet (double *mat, double sx, double sy) {
  
!   MOSS_MAT_SET(mat, sx, 0, 0, 0, sy, 0);
    return mat;
  }
***************
*** 133,138 ****
  mossMatApply (double *ox, double *oy, double *mat, double ix, double iy) {
    
!   *ox = mat[0]*ix + mat[2]*iy + mat[4];
!   *oy = mat[1]*ix + mat[3]*iy + mat[5];
  }
  
--- 133,138 ----
  mossMatApply (double *ox, double *oy, double *mat, double ix, double iy) {
    
!   *ox = mat[0]*ix + mat[1]*iy + mat[2];
!   *oy = mat[3]*ix + mat[4]*iy + mat[5];
  }
  

[Teem-commit] teem/src/bin ilk.c,1.9,1.10

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20107/bin

Modified Files:
	ilk.c 
Log Message:
propogated change in ell from column-major to row-major

Index: ilk.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/ilk.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** ilk.c	7 Jan 2004 15:34:28 -0000	1.9
--- ilk.c	4 Mar 2004 23:57:22 -0000	1.10
***************
*** 71,75 ****
  	     "\b\bo \"flip:ang\": flip along axis an angle <ang> degrees from "
  	     "the X axis\n "
! 	     "\b\bo \"a,b,c,d,tx,ty\": specify the transform explicitly ",
  	     &matListLen, NULL, mossHestTransform);
    hestOptAdd(&hopt, "k", "kernel", airTypeOther, 1, 1, &ksp,
--- 71,76 ----
  	     "\b\bo \"flip:ang\": flip along axis an angle <ang> degrees from "
  	     "the X axis\n "
! 	     "\b\bo \"a,b,tx,c,d,ty\": specify the transform explicitly "
! 	     "in row-major order (opposite of PostScript) ",
  	     &matListLen, NULL, mossHestTransform);
    hestOptAdd(&hopt, "k", "kernel", airTypeOther, 1, 1, &ksp,

[Teem-commit] teem/src/bin miter.c,1.25,1.26

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12973

Modified Files:
	miter.c 
Log Message:
changed some stuff

Index: miter.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/miter.c,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** miter.c	26 Feb 2004 18:41:51 -0000	1.25
--- miter.c	4 Mar 2004 14:04:52 -0000	1.26
***************
*** 34,39 ****
    hestParm *hparm=NULL;
    miteUser *muu;
!   char *me, *errS, *outS, *shadeStr;
!   int renorm, baseDim;
    int E, Ecode;
    float ads[3];
--- 34,39 ----
    hestParm *hparm=NULL;
    miteUser *muu;
!   char *me, *errS, *outS, *shadeStr, *normalStr;
!   int renorm, baseDim, verbPix[2];
    int E, Ecode;
    float ads[3];
***************
*** 86,90 ****
    hestOptAdd(&hopt, "ss", "shading spec", airTypeString, 1, 1, &shadeStr,
  	     "phong:gage(scalar:n)", "how to do shading");
!   hestOptAdd(&hopt, "ns", "normal side", airTypeInt, 1, 1, &(muu->normalSide),
  	     "1", "how to interpret gradients as normals:\n "
  	     "\b\bo \"1\": normal points to lower values (higher == "
--- 86,93 ----
    hestOptAdd(&hopt, "ss", "shading spec", airTypeString, 1, 1, &shadeStr,
  	     "phong:gage(scalar:n)", "how to do shading");
!   hestOptAdd(&hopt, "ns", "normal spec", airTypeString, 1, 1, &normalStr,
! 	     "", "\"normal\" to use for those miteVal's that need one");
!   hestOptAdd(&hopt, "side", "normal side", airTypeInt, 1, 1,
! 	     &(muu->normalSide),
  	     "1", "how to interpret gradients as normals:\n "
  	     "\b\bo \"1\": normal points to lower values (higher == "
***************
*** 105,108 ****
--- 108,113 ----
  	     "0.01", "\"reference\" step size (world space) for doing "
  	     "opacity correction in compositing");
+   hestOptAdd(&hopt, "vp", "verbose pixel", airTypeInt, 2, 2, verbPix,
+ 	     "-1 -1", "pixel for which to turn on verbose messages");
    hestOptAdd(&hopt, "n1", "near1", airTypeDouble, 1, 1, &(muu->opacNear1),
  	     "0.99", "opacity close enough to 1.0 to terminate ray");
***************
*** 141,144 ****
--- 146,151 ----
    gageParmSet(muu->gctx0, gageParmGradMagCurvMin, gmc);
    gageParmSet(muu->gctx0, gageParmRenormalize, renorm);
+   muu->verbUi = verbPix[0];
+   muu->verbVi = verbPix[1];
  
    muu->nout = nrrdNew();  
***************
*** 155,158 ****
--- 162,166 ----
    }
    strncpy(muu->shadeStr, shadeStr, AIR_STRLEN_MED-1);
+   strncpy(muu->normalStr, normalStr, AIR_STRLEN_MED-1);
    muu->shadeStr[AIR_STRLEN_MED-1] = 0;
    muu->hctx->volSize[0] = nin->axis[baseDim+0].size;

[Teem-commit] teem/src/mite kindnot.c,1.2,1.3 mite.h,1.28,1.29 ray.c,1.19,1.20 renderMite.c,1.12,1.13 thread.c,1.12,1.13 txf.c,1.19,1.20 user.c,1.16,1.17

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12816

Modified Files:
	kindnot.c mite.h ray.c renderMite.c thread.c txf.c user.c 
Log Message:
refined semantics of normal specification, and added storage of ray depth when opacity reaches muu->opacMatters

Index: kindnot.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/kindnot.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** kindnot.c	29 Feb 2004 13:42:41 -0000	1.2
--- kindnot.c	4 Mar 2004 14:04:07 -0000	1.3
***************
*** 32,39 ****
    "Tw",
    "Ti",
    "NdotV",
    "NdotL",
-   "GTdotV",
    "VrefN",
    "VdefT",
    "VdefTdotV"
--- 32,41 ----
    "Tw",
    "Ti",
+   "V",
+   "N",
    "NdotV",
    "NdotL",
    "VrefN",
+   "GTdotV",
    "VdefT",
    "VdefTdotV"
***************
*** 51,58 ****
    miteValTw,
    miteValTi,
    miteValNdotV,
    miteValNdotL,
-   miteValGTdotV,
    miteValVrefN,
    miteValVdefT,
    miteValVdefTdotV
--- 53,62 ----
    miteValTw,
    miteValTi,
+   miteValView,
+   miteValNormal,
    miteValNdotV,
    miteValNdotL,
    miteValVrefN,
+   miteValGTdotV,
    miteValVdefT,
    miteValVdefTdotV
***************
*** 69,76 ****
    "tw",
    "ti",
    "ndotv", "vdotn",
    "ndotl", "ldotn",
-   "gtdotv",
    "vrefn",
    "vdeft",
    "vdeftdotv"
--- 73,82 ----
    "tw",
    "ti",
+   "view", "v",
+   "normal", "n", 
    "ndotv", "vdotn",
    "ndotl", "ldotn",
    "vrefn",
+   "gtdotv",
    "vdeft",
    "vdeftdotv"
***************
*** 88,95 ****
    miteValTw,
    miteValTi,
    miteValNdotV, miteValNdotV,
    miteValNdotL, miteValNdotL,
-   miteValGTdotV,
    miteValVrefN,
    miteValVdefT,
    miteValVdefTdotV
--- 94,103 ----
    miteValTw,
    miteValTi,
+   miteValView, miteValView, 
+   miteValNormal, miteValNormal,
    miteValNdotV, miteValNdotV,
    miteValNdotL, miteValNdotL,
    miteValVrefN,
+   miteValGTdotV,
    miteValVdefT,
    miteValVdefTdotV
***************
*** 125,132 ****
    {miteValTw,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValTi,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValNdotV,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValNdotL,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
-   {miteValGTdotV,        1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVrefN,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVdefT,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVdefTdotV,     1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1}
--- 133,142 ----
    {miteValTw,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValTi,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
+   {miteValView,          3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
+   {miteValNormal,        3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValNdotV,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValNdotL,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVrefN,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
+   {miteValGTdotV,        1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVdefT,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVdefTdotV,     1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1}

Index: mite.h
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/mite.h,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** mite.h	29 Feb 2004 13:42:41 -0000	1.28
--- mite.h	4 Mar 2004 14:04:08 -0000	1.29
***************
*** 120,124 ****
  			    any of the ntxf[i] */
    int ntxfNum;           /* allocated and valid length of ntxf[] */
!   char shadeStr[AIR_STRLEN_MED];  /* how to do shading */
    /* for each possible element of the txf range, what value should it
       start at prior to rendering. Mainly needed to store non-unity values
--- 120,140 ----
  			    any of the ntxf[i] */
    int ntxfNum;           /* allocated and valid length of ntxf[] */
!   /* the issue of regular shading, txf-based shading, and surface normals:
!      phong and lit-tensor shading ("regular shading") methods need to specify
!      one or more vectors that are used for shading calculations.  These will
!      be parsed from muu->shadeStr into mrr->shadeSpec, which in turn will 
!      determine the pointer values of mtt->shade{Vec,Scl}{0,1}.
!      ENTIRELY SEPERATE FROM THIS, a "surface normal" can be specified in
!      muu->normalStr, which (if non-empty), will be parsed into mrr->normalSpec,
!      which in turn will determine the pointer values of mtt->normal.  This
!      normal is used for the miteVal quantities involving "N".  
!      Both shading and normal specifications can be given, since they are
!      used in seperate computations.  If the user wants to do miteVal-based
!      stuff with the same quantity specified in (say) a phong shading 
!      specification, its up to them to verify that the normalStr and the
!      shadeStr refer to the same vector.
!   */
!   char shadeStr[AIR_STRLEN_MED], /* how to do shading */
!     normalStr[AIR_STRLEN_MED];   /* what is the "surface normal" */
    /* for each possible element of the txf range, what value should it
       start at prior to rendering. Mainly needed to store non-unity values
***************
*** 218,222 ****
  				 volumes in the gageContext's array of
  				 gagePerVolumes.  Probably a hack */
!   miteShadeSpec *shpec;       /* information based on muu->shadeStr */
    double time0;               /* rendering start time */
    gageQuery queryMite;        /* record of the miteVal quantities which 
--- 234,239 ----
  				 volumes in the gageContext's array of
  				 gagePerVolumes.  Probably a hack */
!   miteShadeSpec *shadeSpec;   /* information based on muu->shadeStr */
!   gageItemSpec *normalSpec;   /* information based on muu->normalStr */
    double time0;               /* rendering start time */
    gageQuery queryMite;        /* record of the miteVal quantities which 
***************
*** 236,251 ****
  ******** miteStageOp* enum
  **
! ** the kinds of things we can do per txf to modify the range variables.
! ** previously mite only supported seperable transfer functions (i.e.,
! ** multiplication only)
  */
  enum {
!   miteStageOpUnknown,
!   miteStageOpMin,
!   miteStageOpMax,
!   miteStageOpAdd,
!   miteStageOpMultiply,
    miteStageOpLast
  };
  
  typedef struct {
--- 253,276 ----
  ******** miteStageOp* enum
  **
! ** the kinds of things we can do per txf to modify the range
! ** variables.  previously mite only supported seperable transfer
! ** functions (i.e., multiplication only).  It is tempting to use all
! ** the operations available as nrrdBinaryOps, but that would lead to
! ** goofy ones like Mod and GreaterThan, which either require or create
! ** integral values which aren't of much use in transfer functions.
! ** More generality in how opacities and colors are assigned will
! ** likely be supported by some simple programmability, supported by
! ** the likes of the funk library, which will be entirely seperate from
! ** the miteStageOp mechanism.
  */
  enum {
!   miteStageOpUnknown,   /* 0 */
!   miteStageOpMin,       /* 1 */
!   miteStageOpMax,       /* 2 */
!   miteStageOpAdd,       /* 3 */
!   miteStageOpMultiply,  /* 4 */
    miteStageOpLast
  };
+ #define MITE_STAGE_OP_MAX  4
  
  typedef struct {
***************
*** 295,315 ****
    miteValTw,            /*  6: "Tw", ray position (gage_t[1]) */
    miteValTi,            /*  7: "Ti", ray index (ray sample #) (gage_t[1]) */
!   miteValNdotV,         /*  8: "NdotV", surface normal dotted w/ view vector
! 			        (towards eye) (gage_t[1]) */
!   miteValNdotL,         /*  9: "NdotL", surface normal dotted w/ light vector
! 			        (towards the light source) (gage_t[1]) */
!   miteValGTdotV,        /* 10: "GTdotV", normal curvature in view direction,
! 			        the contraction of the geometry tensor along
! 				the view vector (gage_t[1]) */
!   miteValVrefN,         /* 11: "VrefN", view vector (towards eye) reflected
! 			       across surface normal (gage_t[3]) */
!   miteValVdefT,         /* 12: "VdefT", view direction, deflected by tensor,
  			       then normalized (gage_t[3]) */
!   miteValVdefTdotV,     /* 13: "VdefTdotV", VdefT dotted back with V, not the
  			       same as the tensor contraction along V,
  			       (gage_t[1]) */
    miteValLast
  };
! #define MITE_VAL_ITEM_MAX  13
  
  /*
--- 320,345 ----
    miteValTw,            /*  6: "Tw", ray position (gage_t[1]) */
    miteValTi,            /*  7: "Ti", ray index (ray sample #) (gage_t[1]) */
!   miteValView,          /*  8: "V", the view vector (gage_t[3]) */
!   miteValNormal,        /*  9: "N", the nominal surface normal, as measured
! 			       by a scalar, vector, or tensor kind, and then
! 			       determined by the semantics of
! 			       muu->normalSide */
!   miteValNdotV,         /* 10: "NdotV", surface normal dotted w/ view vector
! 			       (towards eye) (gage_t[1]) */
!   miteValNdotL,         /* 11: "NdotL", surface normal dotted w/ light vector
! 			       (towards the light source) (gage_t[1]) */
!   miteValVrefN,         /* 12: "VrefN", view vector reflected across normal
! 			       (gage_t[3]) */
!   miteValGTdotV,        /* 13: "GTdotV", normal curvature in view direction,
! 			       the contraction of the geometry tensor along
! 				he view vector (gage_t[1]) */
!   miteValVdefT,         /* 14: "defT", view direction, deflected by tensor,
  			       then normalized (gage_t[3]) */
!   miteValVdefTdotV,     /* 15: "VdefTdotV", VdefT dotted back with V, not the
  			       same as the tensor contraction along V,
  			       (gage_t[1]) */
    miteValLast
  };
! #define MITE_VAL_ITEM_MAX  15
  
  /*
***************
*** 328,331 ****
--- 358,365 ----
  				   mite instead of by gage */
      **directAnsMiteVal,         /* pointers into ansMiteVal */
+     *_normal,                   /* pointer into ans{Scl,Vec,Ten} array above,
+ 				   (NOT ansMiteVal); this will determine the
+ 				   value of miteValNormal according to the
+ 				   semantics of muu->normalSide */
      *shadeVec0, *shadeVec1, 
      *shadeScl0, *shadeScl1;     /* pointers into the ans* arrays above,
***************
*** 344,348 ****
  				   each ray to enable sampling on planes) */
      V[3],                       /* per-ray view direction */
!     RR, GG, BB, TT;             /* per-ray composited values */
  } miteThread;
  
--- 378,384 ----
  				   each ray to enable sampling on planes) */
      V[3],                       /* per-ray view direction */
!     RR, GG, BB, TT,             /* per-ray composited values */
!     ZZ;                         /* for storing ray-depth when opacity passed
! 				   muu->opacMatters */
  } miteThread;
  
***************
*** 360,363 ****
--- 396,400 ----
  
  /* txf.c */
+ TEEM_API airEnum *miteStageOp;
  TEEM_API char miteRangeChar[MITE_RANGE_NUM];
  TEEM_API int miteVariableParse(gageItemSpec *isp, const char *label);

Index: ray.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/ray.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** ray.c	29 Feb 2004 13:42:41 -0000	1.19
--- ray.c	4 Mar 2004 14:04:08 -0000	1.20
***************
*** 39,42 ****
--- 39,43 ----
    mtt->RR = mtt->GG = mtt->BB = 0.0;
    mtt->TT = 1.0;
+   mtt->ZZ = -1.0;
    ELL_3V_SCALE(mtt->V, -1, rayDirWorld);
  
***************
*** 62,78 ****
    ks = mtt->range[miteRangeKs];
    ELL_3V_SCALE(ad, ka, muu->lit->amb);
!   switch (mrr->shpec->method) {
    case miteShadeMethodNone:
      /* nothing to do */
      break;
    case miteShadeMethodPhong:
-     /* this is dicey- we're *writing* to the answer buffer */
      if (kd || ks) {
!       ELL_3V_NORM(mtt->shadeVec0, mtt->shadeVec0, tmp);
!       if (muu->normalSide) {
! 	ELL_3V_SCALE(N, -muu->normalSide, mtt->shadeVec0);
!       } else {
! 	ELL_3V_COPY(N, mtt->shadeVec0);
        }
        if (kd) {
  	LdotN = ELL_3V_DOT(muu->lit->dir[0], N);
--- 63,78 ----
    ks = mtt->range[miteRangeKs];
    ELL_3V_SCALE(ad, ka, muu->lit->amb);
!   switch (mrr->shadeSpec->method) {
    case miteShadeMethodNone:
      /* nothing to do */
      break;
    case miteShadeMethodPhong:
      if (kd || ks) {
!       ELL_3V_NORM(N, mtt->shadeVec0, tmp);
!       if (1 == muu->normalSide) {
! 	ELL_3V_SCALE(N, -1, N);
        }
+       /* else -1==side --> N = -1*-1*N = N
+ 	 or 0==side --> N = N, so there's nothing to do */
        if (kd) {
  	LdotN = ELL_3V_DOT(muu->lit->dir[0], N);
***************
*** 104,108 ****
    default:
      fprintf(stderr, "!%s: PANIC, shadeMethod %d unimplemented\n", 
! 	    me, mrr->shpec->method);
      exit(1);
      break;
--- 104,108 ----
    default:
      fprintf(stderr, "!%s: PANIC, shadeMethod %d unimplemented\n", 
! 	    me, mrr->shadeSpec->method);
      exit(1);
      break;
***************
*** 132,136 ****
    char me[]="miteSample", err[AIR_STRLEN_MED];
    mite_t R, G, B, A;
!   double kn[3], knd[3], len;
  
    if (!inside) {
--- 132,137 ----
    char me[]="miteSample", err[AIR_STRLEN_MED];
    mite_t R, G, B, A;
!   gage_t *NN;
!   double NdotV, kn[3], knd[3], ref[3], len;
  
    if (!inside) {
***************
*** 152,155 ****
--- 153,157 ----
      biffAdd(MITE, err); return AIR_NAN;
    }
+   
    if (mrr->queryMiteNonzero) {
      /* There is some optimal trade-off between slowing things down
***************
*** 165,182 ****
      mtt->directAnsMiteVal[miteValTw][0] = rayT;
      mtt->directAnsMiteVal[miteValTi][0] = num;
  
!     if (mtt->shadeVec0 && 
! 	(GAGE_QUERY_ITEM_TEST(mrr->queryMite, miteValNdotV)
! 	 || GAGE_QUERY_ITEM_TEST(mrr->queryMite, miteValNdotL))) {
        mtt->directAnsMiteVal[miteValNdotV][0] =
! 	-muu->normalSide*ELL_3V_DOT(mtt->shadeVec0, mtt->V);
        mtt->directAnsMiteVal[miteValNdotL][0] =
! 	-muu->normalSide*ELL_3V_DOT(mtt->shadeVec0, muu->lit->dir[0]);
        if (!muu->normalSide) {
! 	mtt->directAnsMiteVal[miteValNdotV][0] = 
  	  AIR_ABS(mtt->directAnsMiteVal[miteValNdotV][0]);
  	mtt->directAnsMiteVal[miteValNdotL][0] = 
  	  AIR_ABS(mtt->directAnsMiteVal[miteValNdotL][0]);
        }
      }
  
--- 167,194 ----
      mtt->directAnsMiteVal[miteValTw][0] = rayT;
      mtt->directAnsMiteVal[miteValTi][0] = num;
+     ELL_3V_COPY(mtt->directAnsMiteVal[miteValView], mtt->V);
+     NN = mtt->directAnsMiteVal[miteValNormal];
+     if (1 == muu->normalSide) {
+       ELL_3V_SCALE(NN, -1, mtt->_normal);
+     } else {
+       ELL_3V_COPY(NN, mtt->_normal);
+     }
  
!     if ((GAGE_QUERY_ITEM_TEST(mrr->queryMite, miteValNdotV)
! 	 || GAGE_QUERY_ITEM_TEST(mrr->queryMite, miteValNdotL)
! 	 || GAGE_QUERY_ITEM_TEST(mrr->queryMite, miteValVrefN))) {
        mtt->directAnsMiteVal[miteValNdotV][0] =
! 	ELL_3V_DOT(NN, mtt->V);
        mtt->directAnsMiteVal[miteValNdotL][0] =
! 	ELL_3V_DOT(NN, muu->lit->dir[0]);
        if (!muu->normalSide) {
! 	mtt->directAnsMiteVal[miteValNdotV][0] =
  	  AIR_ABS(mtt->directAnsMiteVal[miteValNdotV][0]);
  	mtt->directAnsMiteVal[miteValNdotL][0] = 
  	  AIR_ABS(mtt->directAnsMiteVal[miteValNdotL][0]);
        }
+       NdotV = mtt->directAnsMiteVal[miteValNdotV][0];
+       ELL_3V_SCALE_ADD2(ref, 2*NdotV, NN, -1, mtt->V);
+       ELL_3V_NORM(mtt->directAnsMiteVal[miteValVrefN], ref, len);
      }
  
***************
*** 185,189 ****
        ELL_3V_NORM(kn, kn, len);
        ELL_3MV_MUL(knd, mtt->geomTens, kn);
!       mtt->ansMiteVal[miteValGTdotV] = ELL_3V_DOT(knd, kn);
      }
    }
--- 197,201 ----
        ELL_3V_NORM(kn, kn, len);
        ELL_3MV_MUL(knd, mtt->geomTens, kn);
!       mtt->directAnsMiteVal[miteValGTdotV][0] = ELL_3V_DOT(knd, kn);
      }
    }
***************
*** 212,215 ****
--- 224,232 ----
    }
  
+   /* set Z if it hasn't been set already */
+   if (1-mtt->TT >= muu->opacMatters && mtt->ZZ < 0) {
+     mtt->ZZ = rayT;
+   }
+ 
    return mtt->rayStep;
  }
***************
*** 218,222 ****
  miteRayEnd(miteThread *mtt, miteRender *mrr, miteUser *muu) {
    int idx;
!   mite_t *imgData, A;
    
    idx = mtt->ui + (muu->nout->axis[1].size)*mtt->vi;
--- 235,240 ----
  miteRayEnd(miteThread *mtt, miteRender *mrr, miteUser *muu) {
    int idx;
!   mite_t *imgData;
!   double A;
    
    idx = mtt->ui + (muu->nout->axis[1].size)*mtt->vi;
***************
*** 224,230 ****
    A = 1 - mtt->TT;
    if (A) {
!     ELL_4V_SET(imgData + 5*idx, mtt->RR/A, mtt->GG/A, mtt->BB/A, A);
    } else {
!     ELL_4V_SET(imgData + 5*idx, 0, 0, 0, 0);
    }
    return 0;
--- 242,249 ----
    A = 1 - mtt->TT;
    if (A) {
!     ELL_5V_SET(imgData + 5*idx, mtt->RR/A, mtt->GG/A, mtt->BB/A,
! 	       A, mtt->ZZ);
    } else {
!     ELL_5V_SET(imgData + 5*idx, 0, 0, 0, 0, -1);
    }
    return 0;

Index: renderMite.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/renderMite.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** renderMite.c	29 Feb 2004 13:42:41 -0000	1.12
--- renderMite.c	4 Mar 2004 14:04:08 -0000	1.13
***************
*** 37,42 ****
      mrr->vecPvlIdx = -1;
      mrr->tenPvlIdx = -1;
!     mrr->shpec = miteShadeSpecNew();
!     airMopAdd(mrr->rmop, mrr->shpec,
  	      (airMopper)miteShadeSpecNix, airMopAlways);
      mrr->time0 = AIR_NAN;
--- 37,45 ----
      mrr->vecPvlIdx = -1;
      mrr->tenPvlIdx = -1;
!     mrr->normalSpec = gageItemSpecNew();
!     airMopAdd(mrr->rmop, mrr->normalSpec,
! 	      (airMopper)gageItemSpecNix, airMopAlways);
!     mrr->shadeSpec = miteShadeSpecNew();
!     airMopAdd(mrr->rmop, mrr->shadeSpec,
  	      (airMopper)miteShadeSpecNix, airMopAlways);
      mrr->time0 = AIR_NAN;
***************
*** 92,98 ****
      }
    }
!   miteShadeSpecParse((*mrrP)->shpec, muu->shadeStr);
    miteShadeSpecQueryAdd(queryScl, queryVec, queryTen, (*mrrP)->queryMite,
! 			(*mrrP)->shpec);
    (*mrrP)->queryMiteNonzero = GAGE_QUERY_NONZERO((*mrrP)->queryMite);
  
--- 95,104 ----
      }
    }
!   miteVariableParse((*mrrP)->normalSpec, muu->normalStr);
!   miteQueryAdd(queryScl, queryVec, queryTen, (*mrrP)->queryMite,
! 	       (*mrrP)->normalSpec);
!   miteShadeSpecParse((*mrrP)->shadeSpec, muu->shadeStr);
    miteShadeSpecQueryAdd(queryScl, queryVec, queryTen, (*mrrP)->queryMite,
! 			(*mrrP)->shadeSpec);
    (*mrrP)->queryMiteNonzero = GAGE_QUERY_NONZERO((*mrrP)->queryMite);
  

Index: thread.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/thread.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** thread.c	29 Feb 2004 15:49:10 -0000	1.12
--- thread.c	4 Mar 2004 14:04:08 -0000	1.13
***************
*** 35,38 ****
--- 35,39 ----
    mtt->gctx = NULL;
    mtt->ansScl = mtt->ansVec = mtt->ansTen = NULL;
+   mtt->_normal = NULL;
    mtt->shadeVec0 = NULL;
    mtt->shadeVec1 = NULL;
***************
*** 119,140 ****
    (*mttP)->samples = 0;
    (*mttP)->verbose = 0;
    
    /* set up shading answers */
!   switch(mrr->shpec->method) {
    case miteShadeMethodNone:
      /* nothing to do */
      break;
    case miteShadeMethodPhong:
!     (*mttP)->shadeVec0 = _miteAnswerPointer(*mttP, mrr->shpec->vec0);
      break;
    case miteShadeMethodLitTen:
!     (*mttP)->shadeVec0 = _miteAnswerPointer(*mttP, mrr->shpec->vec0);
!     (*mttP)->shadeVec1 = _miteAnswerPointer(*mttP, mrr->shpec->vec1);
!     (*mttP)->shadeScl0 = _miteAnswerPointer(*mttP, mrr->shpec->scl0);
!     (*mttP)->shadeScl1 = _miteAnswerPointer(*mttP, mrr->shpec->scl1);
      break;
    default:
      sprintf(err, "%s: shade method %d not implemented!",
! 	    me, mrr->shpec->method);
      biffAdd(MITE, err); return 1;
      break;
--- 120,142 ----
    (*mttP)->samples = 0;
    (*mttP)->verbose = 0;
+   (*mttP)->_normal = _miteAnswerPointer(*mttP, mrr->normalSpec);
    
    /* set up shading answers */
!   switch(mrr->shadeSpec->method) {
    case miteShadeMethodNone:
      /* nothing to do */
      break;
    case miteShadeMethodPhong:
!     (*mttP)->shadeVec0 = _miteAnswerPointer(*mttP, mrr->shadeSpec->vec0);
      break;
    case miteShadeMethodLitTen:
!     (*mttP)->shadeVec0 = _miteAnswerPointer(*mttP, mrr->shadeSpec->vec0);
!     (*mttP)->shadeVec1 = _miteAnswerPointer(*mttP, mrr->shadeSpec->vec1);
!     (*mttP)->shadeScl0 = _miteAnswerPointer(*mttP, mrr->shadeSpec->scl0);
!     (*mttP)->shadeScl1 = _miteAnswerPointer(*mttP, mrr->shadeSpec->scl1);
      break;
    default:
      sprintf(err, "%s: shade method %d not implemented!",
! 	    me, mrr->shadeSpec->method);
      biffAdd(MITE, err); return 1;
      break;

Index: txf.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/txf.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** txf.c	3 Mar 2004 13:14:08 -0000	1.19
--- txf.c	4 Mar 2004 14:04:08 -0000	1.20
***************
*** 29,32 ****
--- 29,79 ----
  miteRangeChar[MITE_RANGE_NUM] = "ARGBEadsp";
  
+ char
+ _miteStageOpStr[][AIR_STRLEN_SMALL] = {
+   "(unknown miteStageOp)",
+   "min",
+   "max",
+   "add",
+   "multiply"
+ };
+ 
+ int
+ _miteStageOpVal[] = {
+   miteStageOpUnknown,
+   miteStageOpMin,
+   miteStageOpMax,
+   miteStageOpAdd,
+   miteStageOpMultiply
+ };
+ 
+ char
+ _miteStageOpStrEqv[][AIR_STRLEN_SMALL] = {
+   "min",
+   "max",
+   "add", "+",
+   "multiply", "*", "x"
+ };
+ 
+ int
+ _miteStageOpValEqv[] = {
+   miteStageOpUnknown,
+   miteStageOpMin,
+   miteStageOpMax,
+   miteStageOpAdd, miteStageOpAdd,
+   miteStageOpMultiply, miteStageOpMultiply, miteStageOpMultiply
+ };
+ 
+ airEnum
+ _miteStageOp = {
+   "miteStageOp",
+   MITE_STAGE_OP_MAX+1,
+   _miteStageOpStr, _miteStageOpVal,
+   NULL,
+   _miteStageOpStrEqv, _miteStageOpValEqv,
+   AIR_FALSE
+ };
+ airEnum *
+ miteStageOp = &_miteStageOp;
+ 
  /*
  ******** miteVariableParse()
***************
*** 36,39 ****
--- 83,87 ----
  ** kind and item).  The valid formats are:
  **
+ **   ""                  : NULL kind, -1 item
  **   <item>              : miteValGageKind (DEPRECATED)
  **   mite(<item>)        : miteValGageKind
***************
*** 57,60 ****
--- 105,116 ----
      biffAdd(MITE, err); return 1;
    }
+   if (0 == strlen(label)) {
+     /* nothing was specified; we try to indicate that by mimicing 
+        the return of gageItemSpecNew() */
+     isp->item = -1;
+     isp->kind = NULL;
+     return 0;
+   }
+   /* else given string was non-empty */
    mop = airMopNew();
    buff = airStrdup(label);
***************
*** 144,151 ****
  miteVariablePrint(char *buff, const gageItemSpec *isp) {
    char me[]="miteVariablePrint";
!   
!   if (gageKindScl == isp->kind
!       || gageKindVec == isp->kind
!       || tenGageKind == isp->kind) {
      sprintf(buff, "gage(%s:%s)", isp->kind->name, 
  	    airEnumStr(isp->kind->enm, isp->item));
--- 200,209 ----
  miteVariablePrint(char *buff, const gageItemSpec *isp) {
    char me[]="miteVariablePrint";
! 
!   if (!(isp->kind)) {
!     strcpy(buff, "");
!   } else if (gageKindScl == isp->kind
! 	     || gageKindVec == isp->kind
! 	     || tenGageKind == isp->kind) {
      sprintf(buff, "gage(%s:%s)", isp->kind->name, 
  	    airEnumStr(isp->kind->enm, isp->item));
***************
*** 281,285 ****
    char me[]="miteQueryAdd";
    
!   if (gageKindScl == isp->kind) {
      GAGE_QUERY_ITEM_ON(queryScl, isp->item);
    } else if (gageKindVec == isp->kind) {
--- 339,345 ----
    char me[]="miteQueryAdd";
    
!   if (NULL == isp->kind) {
!     /* nothing to add */
!   } else if (gageKindScl == isp->kind) {
      GAGE_QUERY_ITEM_ON(queryScl, isp->item);
    } else if (gageKindVec == isp->kind) {
***************
*** 298,313 ****
         (for instance, using the gradient of fractional anisotropy) */
      switch(isp->item) {
      case miteValNdotV: 
-       GAGE_QUERY_ITEM_ON(queryScl, gageSclNormal);
-       break;
      case miteValNdotL:
!       GAGE_QUERY_ITEM_ON(queryScl, gageSclNormal);
        break;
      case miteValGTdotV:
        GAGE_QUERY_ITEM_ON(queryScl, gageSclGeomTens);
        break;
-     case miteValVrefN:
-       GAGE_QUERY_ITEM_ON(queryScl, gageSclNormal);
-       break;
      case miteValVdefT:
        GAGE_QUERY_ITEM_ON(queryTen, tenGageTensor);
--- 358,372 ----
         (for instance, using the gradient of fractional anisotropy) */
      switch(isp->item) {
+     case miteValVrefN:
      case miteValNdotV: 
      case miteValNdotL:
!       /* the "N" can be a normalized vector from any of the
! 	 available kinds (except miteValGageKind!), and its
! 	 associated query will be handled elsewhere, so there's
! 	 nothing to add here */
        break;
      case miteValGTdotV:
        GAGE_QUERY_ITEM_ON(queryScl, gageSclGeomTens);
        break;
      case miteValVdefT:
        GAGE_QUERY_ITEM_ON(queryTen, tenGageTensor);
***************
*** 317,321 ****
      }
    } else {
!     fprintf(stderr, "%s: PANIC: unrecognized non-null gageKind\n", me);
      exit(1);
    }
--- 376,380 ----
      }
    } else {
!     fprintf(stderr, "%s: PANIC: unrecognized non-NULL gageKind\n", me);
      exit(1);
    }
***************
*** 350,356 ****
--- 409,418 ----
        biffAdd(MITE, err); return 1;
      }
+     /* note that key/values need to be copied for the sake of
+        identifying a non-default miteStageOp */
      switch(muu->ntxf[ni]->type) {
      case nrrdTypeUChar:
        if (!E) E |= nrrdUnquantize(mrr->ntxf[ni], muu->ntxf[ni], nrrdTypeUChar);
+       if (!E) E |= nrrdKeyValueCopy(mrr->ntxf[ni], muu->ntxf[ni]);
        break;
      case mite_nt:
***************
*** 359,362 ****
--- 421,425 ----
      default:  /* will be either float or double (whatever mite_nt isn't) */
        if (!E) E |= nrrdConvert(mrr->ntxf[ni], muu->ntxf[ni], mite_nt);
+       if (!E) E |= nrrdKeyValueCopy(mrr->ntxf[ni], muu->ntxf[ni]);
        break;
      }
***************
*** 434,437 ****
--- 497,506 ----
    gage_t *ret;
  
+   if (!isp->kind) {
+     /* we got a NULL kind (as happens with output of
+        gageItemSpecNew()); only NULL return is sensible */
+     return NULL;
+   }
+ 
    if (gageKindScl == isp->kind) {
      ret = mtt->ansScl;
***************
*** 457,461 ****
  int
  _miteStageSet(miteThread *mtt, miteRender *mrr) {
!   char me[]="_miteStageSet", err[AIR_STRLEN_MED];
    int ni, di, stageIdx, rii, stageNum, log2;
    Nrrd *ntxf;
--- 526,530 ----
  int
  _miteStageSet(miteThread *mtt, miteRender *mrr) {
!   char me[]="_miteStageSet", err[AIR_STRLEN_MED], *value;
    int ni, di, stageIdx, rii, stageNum, log2;
    Nrrd *ntxf;
***************
*** 492,496 ****
        } else {
  	stage->data = ntxf->data;
! 	stage->op = miteStageOpMultiply;
  	if (1 == isp.kind->table[isp.item].answerLength) {
  	  stage->qn = NULL;
--- 561,573 ----
        } else {
  	stage->data = ntxf->data;
! 	value = nrrdKeyValueGet(ntxf, "miteStageOp");
! 	if (value) {
! 	  stage->op = airEnumVal(miteStageOp, value);
! 	  if (miteStageOpUnknown == stage->op) {
! 	    stage->op = miteStageOpMultiply;
! 	  }
! 	} else {
! 	  stage->op = miteStageOpMultiply;
! 	}
  	if (1 == isp.kind->table[isp.item].answerLength) {
  	  stage->qn = NULL;

Index: user.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/user.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** user.c	29 Feb 2004 13:42:42 -0000	1.16
--- user.c	4 Mar 2004 14:04:08 -0000	1.17
***************
*** 38,41 ****
--- 38,42 ----
    muu->ntxfNum = 0;
    muu->shadeStr[0] = 0;
+   muu->normalStr[0] = 0;
    for (i=0; i<MITE_RANGE_NUM; i++) {
      muu->rangeInit[i] = 1.0;
***************
*** 96,99 ****
--- 97,102 ----
    GAGE_QUERY_RESET(queryTen);
    GAGE_QUERY_RESET(queryMite);  /* not actually used here */
+ 
+   /* add on all queries associated with transfer functions */
    for (T=0; T<muu->ntxfNum; T++) {
      if (miteNtxfCheck(muu->ntxf[T])) {
***************
*** 117,120 ****
--- 120,141 ----
  	    "************************\n\n\n", me);
    }
+ 
+   /* add on "normal"-based queries */
+   if (airStrlen(muu->normalStr)) {
+     miteVariableParse(&isp, muu->normalStr);
+     if (miteValGageKind == isp.kind) {
+       sprintf(err, "%s: normalStr \"%s\" refers to a miteVal "
+ 	      "(normal must be data-intrinsic)", me, muu->normalStr);
+       biffAdd(MITE, err); airMopError(mop); return 1;
+     }
+     if (3 != isp.kind->table[isp.item].answerLength) {
+       sprintf(err, "%s: %s not a vector: can't be used as normal",
+ 	      me, muu->normalStr);
+       biffAdd(MITE, err); return 1;
+     }
+     miteQueryAdd(queryScl, queryVec, queryTen, queryMite, &isp);
+   }
+ 
+   /* add on shading-based queries */
    shpec = miteShadeSpecNew();
    airMopAdd(mop, shpec, (airMopper)miteShadeSpecNix, airMopAlways);
***************
*** 125,128 ****
--- 146,162 ----
    }
    miteShadeSpecQueryAdd(queryScl, queryVec, queryTen, queryMite, shpec);
+ 
+   /* see if anyone asked for an unspecified normal */
+   if ((GAGE_QUERY_ITEM_TEST(queryMite, miteValNdotV)
+        || GAGE_QUERY_ITEM_TEST(queryMite, miteValNdotL)
+        || GAGE_QUERY_ITEM_TEST(queryMite, miteValVrefN))
+       && !airStrlen(muu->normalStr)) {
+     sprintf(err, "%s: txf or shading requested a miteVal's use of the "
+ 	    "\"normal\", but one has not been specified in muu->normalStr",
+ 	    me);
+     biffAdd(MITE, err); airMopError(mop); return 1;
+   }
+ 
+   /* see if we have volumes for requested queries */
    if (GAGE_QUERY_NONZERO(queryScl) && !(muu->nsin)) {
      sprintf(err, "%s: txf or shading require %s volume, but don't have one",
***************
*** 140,147 ****
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
!   if (!muu->nout) {
!     sprintf(err, "%s: rendered image nrrd is NULL", me);
!     biffAdd(MITE, err); airMopError(mop); return 1;
!   }
    if (muu->nsin) {
      if (gageVolumeCheck(muu->gctx0, muu->nsin, gageKindScl)) {
--- 174,179 ----
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
! 
!   /* check appropriateness of given volumes */
    if (muu->nsin) {
      if (gageVolumeCheck(muu->gctx0, muu->nsin, gageKindScl)) {
***************
*** 165,168 ****
--- 197,205 ----
      }
    }
+ 
+   if (!muu->nout) {
+     sprintf(err, "%s: rendered image nrrd is NULL", me);
+     biffAdd(MITE, err); airMopError(mop); return 1;
+   }
    airMopOkay(mop); 
    return 0;

[Teem-commit] teem/src/mite txf.c,1.18,1.19

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11155/mite

Modified Files:
	txf.c 
Log Message:
added even-bit quantization methods based on Emil's octahdron unfolding, and renamed the odd-bit methods from checker to octa

Index: txf.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/txf.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** txf.c	29 Feb 2004 13:42:42 -0000	1.18
--- txf.c	3 Mar 2004 13:14:08 -0000	1.19
***************
*** 498,510 ****
  	  log2 = airLog2(ntxf->axis[di].size);
  	  switch(log2) {
! 	  case 8:  stage->qn = limnVtoQN_GT[ limnQN8checker]; break;
! 	  case 9:  stage->qn = limnVtoQN_GT[ limnQN9checker]; break;
! 	  case 10: stage->qn = limnVtoQN_GT[limnQN10checker]; break;
! 	  case 11: stage->qn = limnVtoQN_GT[limnQN11checker]; break;
! 	  case 12: stage->qn = limnVtoQN_GT[limnQN12checker]; break;
! 	  case 13: stage->qn = limnVtoQN_GT[limnQN13checker]; break;
! 	  case 14: stage->qn = limnVtoQN_GT[limnQN14checker]; break;
! 	  case 15: stage->qn = limnVtoQN_GT[limnQN15checker]; break;
! 	  case 16: stage->qn = limnVtoQN_GT[limnQN16checker]; break;
  	  default:
  	    sprintf(err, "%s: txf axis %d size %d not usable for vector "
--- 498,510 ----
  	  log2 = airLog2(ntxf->axis[di].size);
  	  switch(log2) {
! 	  case 8:  stage->qn = limnVtoQN_GT[ limnQN8octa]; break;
! 	  case 9:  stage->qn = limnVtoQN_GT[ limnQN9octa]; break;
! 	  case 10: stage->qn = limnVtoQN_GT[limnQN10octa]; break;
! 	  case 11: stage->qn = limnVtoQN_GT[limnQN11octa]; break;
! 	  case 12: stage->qn = limnVtoQN_GT[limnQN12octa]; break;
! 	  case 13: stage->qn = limnVtoQN_GT[limnQN13octa]; break;
! 	  case 14: stage->qn = limnVtoQN_GT[limnQN14octa]; break;
! 	  case 15: stage->qn = limnVtoQN_GT[limnQN15octa]; break;
! 	  case 16: stage->qn = limnVtoQN_GT[limnQN16octa]; break;
  	  default:
  	    sprintf(err, "%s: txf axis %d size %d not usable for vector "

[Teem-commit] teem/src/limn env.c,1.7,1.8 limn.h,1.50,1.51 qn.c,1.19,1.20 renderLimn.c,1.22,1.23

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/limn
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11155/limn

Modified Files:
	env.c limn.h qn.c renderLimn.c 
Log Message:
added even-bit quantization methods based on Emil's octahdron unfolding, and renamed the odd-bit methods from checker to octa

Index: env.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/env.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** env.c	27 Feb 2004 18:16:50 -0000	1.7
--- env.c	3 Mar 2004 13:14:08 -0000	1.8
***************
*** 37,67 ****
    switch(qnMethod) {
    case limnQN16checker:
      sx = sy = 256;
      break;
    case limnQN14checker:
      sx = sy = 128;
      break;
    case limnQN12checker:
      sx = sy = 64;
      break;
    case limnQN10checker:
      sx = sy = 32;
      break;
    case limnQN8checker:
      sx = sy = 16;
      break;
!   case limnQN15checker:
      sx = 128;
      sy = 256;
      break;
!   case limnQN13checker:
      sx = 64;
      sy = 128;
      break;
!   case limnQN11checker:
      sx = 32;
      sy = 64;
      break;
!   case limnQN9checker:
      sx = 16;
      sy = 32;
--- 37,72 ----
    switch(qnMethod) {
    case limnQN16checker:
+   case limnQN16octa:
      sx = sy = 256;
      break;
    case limnQN14checker:
+   case limnQN14octa:
      sx = sy = 128;
      break;
    case limnQN12checker:
+   case limnQN12octa:
      sx = sy = 64;
      break;
    case limnQN10checker:
+   case limnQN10octa:
      sx = sy = 32;
      break;
    case limnQN8checker:
+   case limnQN8octa:
      sx = sy = 16;
      break;
!   case limnQN15octa:
      sx = 128;
      sy = 256;
      break;
!   case limnQN13octa:
      sx = 64;
      sy = 128;
      break;
!   case limnQN11octa:
      sx = 32;
      sy = 64;
      break;
!   case limnQN9octa:
      sx = 16;
      sy = 32;

Index: limn.h
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/limn.h,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** limn.h	27 Feb 2004 16:42:53 -0000	1.50
--- limn.h	3 Mar 2004 13:14:08 -0000	1.51
***************
*** 274,288 ****
    limnQN16border1,   /*  2 */
    limnQN16checker,   /*  3 */
!   limnQN15checker,   /*  4 */
!   limnQN14checker,   /*  5 */
!   limnQN13checker,   /*  6 */
!   limnQN12checker,   /*  7 */
!   limnQN11checker,   /*  8 */
!   limnQN10checker,   /*  9 */
!   limnQN9checker,    /* 10 */
!   limnQN8checker,    /* 11 */
    limnQNLast
  };
! #define LIMN_QN_MAX     11
  
  enum {
--- 274,293 ----
    limnQN16border1,   /*  2 */
    limnQN16checker,   /*  3 */
!   limnQN16octa,      /*  4 */
!   limnQN15octa,      /*  5 */
!   limnQN14checker,   /*  6 */
!   limnQN14octa,      /*  7 */
!   limnQN13octa,      /*  8 */
!   limnQN12checker,   /*  9 */
!   limnQN12octa,      /* 10 */
!   limnQN11octa,      /* 11 */
!   limnQN10checker,   /* 12 */
!   limnQN10octa,      /* 13 */
!   limnQN9octa,       /* 14 */
!   limnQN8checker,    /* 15 */
!   limnQN8octa,       /* 16 */
    limnQNLast
  };
! #define LIMN_QN_MAX     16
  
  enum {

Index: qn.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/qn.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** qn.c	27 Feb 2004 18:16:50 -0000	1.19
--- qn.c	3 Mar 2004 13:14:08 -0000	1.20
***************
*** 163,167 ****
     the error due to quantization is unbiased */
  
! #define _EVEN_QtoV(HNB, vec, qn) \
    ui = (qn) & ((1<<HNB)-1); \
    vi = ((qn) >> HNB) & ((1<<HNB)-1); \
--- 163,167 ----
     the error due to quantization is unbiased */
  
! #define _EVEN_CHECK_QtoV(HNB, vec, qn) \
    ui = (qn) & ((1<<HNB)-1); \
    vi = ((qn) >> HNB) & ((1<<HNB)-1); \
***************
*** 178,182 ****
    (vec)[2] = z*n
  
! #define _EVEN_VtoQ(HNB, vec) \
    x = (vec)[0]; \
    y = (vec)[1]; \
--- 178,182 ----
    (vec)[2] = z*n
  
! #define _EVEN_CHECK_VtoQ(HNB, vec) \
    x = (vec)[0]; \
    y = (vec)[1]; \
***************
*** 204,208 ****
    return (vi << HNB) | ui
  
! #define _16_QtoV(vec, qn) \
    ui = (qn) & 0xFF; \
    vi = ((qn) >> 8) & 0xFF; \
--- 204,259 ----
    return (vi << HNB) | ui
  
! #define _EVEN_OCTA_QtoV(HNB, vec, qn) \
!   xi = (qn) & ((1<<HNB)-1); \
!   yi = ((qn) >> HNB) & ((1<<HNB)-1); \
!   x = AIR_AFFINE(-0.5, xi, ((1<<HNB)-1)+0.5, -1, 1); \
!   y = AIR_AFFINE(-0.5, yi, ((1<<HNB)-1)+0.5, -1, 1); \
!   z = 1 - AIR_ABS(x) - AIR_ABS(y); \
!   if (z < 0) { \
!     if (x > 0) { \
!       x += z; \
!     } else { \
!       x -= z; \
!     } \
!     if (y > 0) { \
!       y += z; \
!     } else { \
!       y -= z; \
!     } \
!   } \
!   n = 1.0/sqrt(x*x + y*y + z*z); \
!   (vec)[0] = x*n; \
!   (vec)[1] = y*n; \
!   (vec)[2] = z*n
! 
! #define _EVEN_OCTA_VtoQ(HNB, vec) \
!   x = (vec)[0]; \
!   y = (vec)[1]; \
!   z = (vec)[2]; \
!   L = AIR_ABS(x) + AIR_ABS(y) + AIR_ABS(z); \
!   if (!L) { \
!     return 0; \
!   } \
!   x /= L; \
!   y /= L; \
!   z /= L; \
!   if (z < 0) { \
!     if (x > 0) { \
!       x -= z; \
!     } else { \
!       x += z; \
!     } \
!     if (y > 0) { \
!       y -= z; \
!     } else { \
!       y += z; \
!     } \
!   } \
!   AIR_INDEX(-1, x, 1, (1<<HNB), xi); \
!   AIR_INDEX(-1, y, 1, (1<<HNB), yi); \
!   return (yi << HNB) | xi
! 
! /* _16_CHECK_QtoV and _16_CHECK_VtoQ are not actually used */
! #define _16_CHECK_QtoV(vec, qn) \
    ui = (qn) & 0xFF; \
    vi = ((qn) >> 8) & 0xFF; \
***************
*** 219,223 ****
    (vec)[2] = z*n
  
! #define _16_VtoQ(vec) \
    x = (vec)[0]; \
    y = (vec)[1]; \
--- 270,274 ----
    (vec)[2] = z*n
  
! #define _16_CHECK_VtoQ(vec) \
    x = (vec)[0]; \
    y = (vec)[1]; \
***************
*** 247,251 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(8, vec, qn);
  }
  
--- 298,302 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(8, vec, qn);
  }
  
***************
*** 255,259 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(8, vec, qn);
  }
  
--- 306,310 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(8, vec, qn);
  }
  
***************
*** 263,267 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(8, vec);
  }
  
--- 314,318 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(8, vec);
  }
  
***************
*** 271,275 ****
    int xi, yi, ui, vi;
  
!   _EVEN_VtoQ(8, vec);
  }
  
--- 322,360 ----
    int xi, yi, ui, vi;
  
!   _EVEN_CHECK_VtoQ(8, vec);
! }
! 
! /* ----------------------------------------------------------------  */
! 
! void
! _limnQN16octa_QNtoV_f(float *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(8, vec, qn);
! }
! 
! void
! _limnQN16octa_QNtoV_d(double *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(8, vec, qn);
! }
! 
! int
! _limnQN16octa_VtoQN_f(float *vec) {
!   double L, x, y, z;
!   int xi, yi;
!   
!   _EVEN_OCTA_VtoQ(8, vec);
! }
! 
! int
! _limnQN16octa_VtoQN_d(double *vec) {
!   double L, x, y, z;
!   int xi, yi;
! 
!   _EVEN_OCTA_VtoQ(8, vec);
  }
  
***************
*** 278,282 ****
  /* 15 bit --> HNB == 7 */
  
! #define _ODD_QtoV(HNB, vec, qn) \
    ui = qn & ((1<<HNB)-1); \
    vi = (qn >> HNB) & ((1<<HNB)-1); \
--- 363,367 ----
  /* 15 bit --> HNB == 7 */
  
! #define _ODD_OCTA_QtoV(HNB, vec, qn) \
    ui = qn & ((1<<HNB)-1); \
    vi = (qn >> HNB) & ((1<<HNB)-1); \
***************
*** 293,297 ****
    vec[2] = z*n
  
! #define _ODD_VtoQ(HNB, vec) \
    x = vec[0]; \
    y = vec[1]; \
--- 378,382 ----
    vec[2] = z*n
  
! #define _ODD_OCTA_VtoQ(HNB, vec) \
    x = vec[0]; \
    y = vec[1]; \
***************
*** 312,344 ****
  
  void
! _limnQN15checker_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_QtoV(7, vec, qn);
  }
  
  void
! _limnQN15checker_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_QtoV(7, vec, qn);
  }
  
  int
! _limnQN15checker_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(7, vec);
  }
  
  int
! _limnQN15checker_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(7, vec);
  }
  
--- 397,429 ----
  
  void
! _limnQN15octa_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(7, vec, qn);
  }
  
  void
! _limnQN15octa_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(7, vec, qn);
  }
  
  int
! _limnQN15octa_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(7, vec);
  }
  
  int
! _limnQN15octa_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(7, vec);
  }
  
***************
*** 350,354 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(7, vec, qn);
  }
  
--- 435,439 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(7, vec, qn);
  }
  
***************
*** 358,362 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(7, vec, qn);
  }
  
--- 443,447 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(7, vec, qn);
  }
  
***************
*** 366,370 ****
    int xi, yi, ui, vi;
  
!   _EVEN_VtoQ(7, vec);
  }
  
--- 451,455 ----
    int xi, yi, ui, vi;
  
!   _EVEN_CHECK_VtoQ(7, vec);
  }
  
***************
*** 374,378 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(7, vec);
  }
  
--- 459,497 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(7, vec);
! }
! 
! /* ----------------------------------------------------------------  */
! 
! void
! _limnQN14octa_QNtoV_f(float *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(7, vec, qn);
! }
! 
! void
! _limnQN14octa_QNtoV_d(double *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(7, vec, qn);
! }
! 
! int
! _limnQN14octa_VtoQN_f(float *vec) {
!   double L, x, y, z;
!   int xi, yi;
!   
!   _EVEN_OCTA_VtoQ(7, vec);
! }
! 
! int
! _limnQN14octa_VtoQN_d(double *vec) {
!   double L, x, y, z;
!   int xi, yi;
! 
!   _EVEN_OCTA_VtoQ(7, vec);
  }
  
***************
*** 380,412 ****
  
  void
! _limnQN13checker_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_QtoV(6, vec, qn);
  }
  
  void
! _limnQN13checker_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_QtoV(6, vec, qn);
  }
  
  int
! _limnQN13checker_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(6, vec);
  }
  
  int
! _limnQN13checker_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(6, vec);
  }
  
--- 499,531 ----
  
  void
! _limnQN13octa_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(6, vec, qn);
  }
  
  void
! _limnQN13octa_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(6, vec, qn);
  }
  
  int
! _limnQN13octa_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(6, vec);
  }
  
  int
! _limnQN13octa_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(6, vec);
  }
  
***************
*** 418,422 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(6, vec, qn);
  }
  
--- 537,541 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(6, vec, qn);
  }
  
***************
*** 426,430 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(6, vec, qn);
  }
  
--- 545,549 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(6, vec, qn);
  }
  
***************
*** 434,438 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(6, vec);
  }
  
--- 553,557 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(6, vec);
  }
  
***************
*** 442,446 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(6, vec);
  }
  
--- 561,599 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(6, vec);
! }
! 
! /* ----------------------------------------------------------------  */
! 
! void
! _limnQN12octa_QNtoV_f(float *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(6, vec, qn);
! }
! 
! void
! _limnQN12octa_QNtoV_d(double *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(6, vec, qn);
! }
! 
! int
! _limnQN12octa_VtoQN_f(float *vec) {
!   double L, x, y, z;
!   int xi, yi;
!   
!   _EVEN_OCTA_VtoQ(6, vec);
! }
! 
! int
! _limnQN12octa_VtoQN_d(double *vec) {
!   double L, x, y, z;
!   int xi, yi;
! 
!   _EVEN_OCTA_VtoQ(6, vec);
  }
  
***************
*** 448,480 ****
  
  void
! _limnQN11checker_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_QtoV(5, vec, qn);
  }
  
  void
! _limnQN11checker_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_QtoV(5, vec, qn);
  }
  
  int
! _limnQN11checker_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(5, vec);
  }
  
  int
! _limnQN11checker_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(5, vec);
  }
  
--- 601,633 ----
  
  void
! _limnQN11octa_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(5, vec, qn);
  }
  
  void
! _limnQN11octa_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(5, vec, qn);
  }
  
  int
! _limnQN11octa_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(5, vec);
  }
  
  int
! _limnQN11octa_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(5, vec);
  }
  
***************
*** 486,490 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(5, vec, qn);
  }
  
--- 639,643 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(5, vec, qn);
  }
  
***************
*** 494,498 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(5, vec, qn);
  }
  
--- 647,651 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(5, vec, qn);
  }
  
***************
*** 502,506 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(5, vec);
  }
  
--- 655,659 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(5, vec);
  }
  
***************
*** 510,547 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(5, vec);
  }
  
  /* ----------------------------------------------------------- */
  void
! _limnQN9checker_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_QtoV(4, vec, qn);
  }
  
  void
! _limnQN9checker_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_QtoV(4, vec, qn);
  }
  
  int
! _limnQN9checker_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(4, vec);
  }
  
  int
! _limnQN9checker_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_VtoQ(4, vec);
  }
  
--- 663,734 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(5, vec);
! }
! 
! /* ----------------------------------------------------------------  */
! 
! void
! _limnQN10octa_QNtoV_f(float *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(5, vec, qn);
! }
! 
! void
! _limnQN10octa_QNtoV_d(double *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(5, vec, qn);
! }
! 
! int
! _limnQN10octa_VtoQN_f(float *vec) {
!   double L, x, y, z;
!   int xi, yi;
!   
!   _EVEN_OCTA_VtoQ(5, vec);
! }
! 
! int
! _limnQN10octa_VtoQN_d(double *vec) {
!   double L, x, y, z;
!   int xi, yi;
! 
!   _EVEN_OCTA_VtoQ(5, vec);
  }
  
  /* ----------------------------------------------------------- */
  void
! _limnQN9octa_QNtoV_f(float *vec, int qn) {
    int ui, vi, zi;
    float u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(4, vec, qn);
  }
  
  void
! _limnQN9octa_QNtoV_d(double *vec, int qn) {
    int ui, vi, zi;
    double u, v, x, y, z, n;
    
!   _ODD_OCTA_QtoV(4, vec, qn);
  }
  
  int
! _limnQN9octa_VtoQN_f(float *vec) {
    float L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(4, vec);
  }
  
  int
! _limnQN9octa_VtoQN_d(double *vec) {
    double L, u, v, x, y, z;
    int ui, vi, zi;
    
!   _ODD_OCTA_VtoQ(4, vec);
  }
  
***************
*** 553,557 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(4, vec, qn);
  }
  
--- 740,744 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(4, vec, qn);
  }
  
***************
*** 561,565 ****
    double u, v, x, y, z, n;
  
!   _EVEN_QtoV(4, vec, qn);
  }
  
--- 748,752 ----
    double u, v, x, y, z, n;
  
!   _EVEN_CHECK_QtoV(4, vec, qn);
  }
  
***************
*** 569,573 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(4, vec);
  }
  
--- 756,760 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(4, vec);
  }
  
***************
*** 577,581 ****
    int xi, yi, ui, vi;
    
!   _EVEN_VtoQ(4, vec);
  }
  
--- 764,802 ----
    int xi, yi, ui, vi;
    
!   _EVEN_CHECK_VtoQ(4, vec);
! }
! 
! /* ----------------------------------------------------------------  */
! 
! void
! _limnQN8octa_QNtoV_f(float *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(4, vec, qn);
! }
! 
! void
! _limnQN8octa_QNtoV_d(double *vec, int qn) {
!   int xi, yi;
!   double x, y, z, n;
! 
!   _EVEN_OCTA_QtoV(4, vec, qn);
! }
! 
! int
! _limnQN8octa_VtoQN_f(float *vec) {
!   double L, x, y, z;
!   int xi, yi;
!   
!   _EVEN_OCTA_VtoQ(4, vec);
! }
! 
! int
! _limnQN8octa_VtoQN_d(double *vec) {
!   double L, x, y, z;
!   int xi, yi;
! 
!   _EVEN_OCTA_VtoQ(4, vec);
  }
  
***************
*** 588,599 ****
    _limnQN16border1_QNtoV_f,
    _limnQN16checker_QNtoV_f,
!   _limnQN15checker_QNtoV_f,
    _limnQN14checker_QNtoV_f,
!   _limnQN13checker_QNtoV_f,
    _limnQN12checker_QNtoV_f,
!   _limnQN11checker_QNtoV_f,
    _limnQN10checker_QNtoV_f,
!   _limnQN9checker_QNtoV_f,
!   _limnQN8checker_QNtoV_f
  };
    
--- 809,825 ----
    _limnQN16border1_QNtoV_f,
    _limnQN16checker_QNtoV_f,
!   _limnQN16octa_QNtoV_f,
!   _limnQN15octa_QNtoV_f,
    _limnQN14checker_QNtoV_f,
!   _limnQN14octa_QNtoV_f,
!   _limnQN13octa_QNtoV_f,
    _limnQN12checker_QNtoV_f,
!   _limnQN12octa_QNtoV_f,
!   _limnQN11octa_QNtoV_f,
    _limnQN10checker_QNtoV_f,
!   _limnQN10octa_QNtoV_f,
!   _limnQN9octa_QNtoV_f,
!   _limnQN8checker_QNtoV_f,
!   _limnQN8octa_QNtoV_f
  };
    
***************
*** 604,615 ****
    NULL,
    _limnQN16checker_QNtoV_d,
!   _limnQN15checker_QNtoV_d,
    _limnQN14checker_QNtoV_d,
!   _limnQN13checker_QNtoV_d,
    _limnQN12checker_QNtoV_d,
!   _limnQN11checker_QNtoV_d,
    _limnQN10checker_QNtoV_d,
!   _limnQN9checker_QNtoV_d,
!   _limnQN8checker_QNtoV_d
  };
    
--- 830,846 ----
    NULL,
    _limnQN16checker_QNtoV_d,
!   _limnQN16octa_QNtoV_d,
!   _limnQN15octa_QNtoV_d,
    _limnQN14checker_QNtoV_d,
!   _limnQN14octa_QNtoV_d,
!   _limnQN13octa_QNtoV_d,
    _limnQN12checker_QNtoV_d,
!   _limnQN12octa_QNtoV_d,
!   _limnQN11octa_QNtoV_d,
    _limnQN10checker_QNtoV_d,
!   _limnQN10octa_QNtoV_d,
!   _limnQN9octa_QNtoV_d,
!   _limnQN8checker_QNtoV_d,
!   _limnQN8octa_QNtoV_d
  };
    
***************
*** 620,631 ****
    _limnQN16border1_VtoQN_f,
    _limnQN16checker_VtoQN_f,
!   _limnQN15checker_VtoQN_f,
    _limnQN14checker_VtoQN_f,
!   _limnQN13checker_VtoQN_f,
    _limnQN12checker_VtoQN_f,
!   _limnQN11checker_VtoQN_f,
    _limnQN10checker_VtoQN_f,
!   _limnQN9checker_VtoQN_f,
!   _limnQN8checker_VtoQN_f
  };
  
--- 851,867 ----
    _limnQN16border1_VtoQN_f,
    _limnQN16checker_VtoQN_f,
!   _limnQN16octa_VtoQN_f,
!   _limnQN15octa_VtoQN_f,
    _limnQN14checker_VtoQN_f,
!   _limnQN14octa_VtoQN_f,
!   _limnQN13octa_VtoQN_f,
    _limnQN12checker_VtoQN_f,
!   _limnQN12octa_VtoQN_f,
!   _limnQN11octa_VtoQN_f,
    _limnQN10checker_VtoQN_f,
!   _limnQN10octa_VtoQN_f,
!   _limnQN9octa_VtoQN_f,
!   _limnQN8checker_VtoQN_f,
!   _limnQN8octa_VtoQN_f
  };
  
***************
*** 636,647 ****
    NULL,
    _limnQN16checker_VtoQN_d,
!   _limnQN15checker_VtoQN_d,
    _limnQN14checker_VtoQN_d,
!   _limnQN13checker_VtoQN_d,
    _limnQN12checker_VtoQN_d,
!   _limnQN11checker_VtoQN_d,
    _limnQN10checker_VtoQN_d,
!   _limnQN9checker_VtoQN_d,
!   _limnQN8checker_VtoQN_d
  };
  
--- 872,888 ----
    NULL,
    _limnQN16checker_VtoQN_d,
!   _limnQN16octa_VtoQN_d,
!   _limnQN15octa_VtoQN_d,
    _limnQN14checker_VtoQN_d,
!   _limnQN14octa_VtoQN_d,
!   _limnQN13octa_VtoQN_d,
    _limnQN12checker_VtoQN_d,
!   _limnQN12octa_VtoQN_d,
!   _limnQN11octa_VtoQN_d,
    _limnQN10checker_VtoQN_d,
!   _limnQN10octa_VtoQN_d,
!   _limnQN9octa_VtoQN_d,
!   _limnQN8checker_VtoQN_d,
!   _limnQN8octa_VtoQN_d
  };
  
***************
*** 652,662 ****
--- 893,908 ----
    (1 << 16),
    (1 << 16),
+   (1 << 16),
    (1 << 15),
    (1 << 14),
+   (1 << 14),
    (1 << 13),
    (1 << 12),
+   (1 << 12),
    (1 << 11),
    (1 << 10),
+   (1 << 10),
    (1 << 9),
+   (1 << 8),
    (1 << 8)
  };

Index: renderLimn.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/renderLimn.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** renderLimn.c	19 Feb 2004 06:45:12 -0000	1.22
--- renderLimn.c	3 Mar 2004 13:14:08 -0000	1.23
***************
*** 118,122 ****
    B = look->kads[0]*look->rgba[2];
    if (nmap) {
!     qn = limnVtoQN_f[limnQN16checker](face->worldNormal);
      map = nmap->data;
      R += look->kads[1]*look->rgba[0]*map[0 + 3*qn];
--- 118,122 ----
    B = look->kads[0]*look->rgba[2];
    if (nmap) {
!     qn = limnVtoQN_f[limnQN16octa](face->worldNormal);
      map = nmap->data;
      R += look->kads[1]*look->rgba[0]*map[0 + 3*qn];

[Teem-commit] teem/src/bin emap.c,1.10,1.11

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11155/bin

Modified Files:
	emap.c 
Log Message:
added even-bit quantization methods based on Emil's octahdron unfolding, and renamed the odd-bit methods from checker to octa

Index: emap.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/emap.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** emap.c	1 Mar 2004 10:17:43 -0000	1.10
--- emap.c	3 Mar 2004 13:14:08 -0000	1.11
***************
*** 87,99 ****
  
    switch(bits) {
!   case 16: method = limnQN16checker; break;
!   case 15: method = limnQN15checker; break;
!   case 14: method = limnQN14checker; break;
!   case 13: method = limnQN13checker; break;
!   case 12: method = limnQN12checker; break;
!   case 11: method = limnQN11checker; break;
!   case 10: method = limnQN10checker; break;
!   case 9: method = limnQN9checker; break;
!   case 8: method = limnQN8checker; break;
    default:
      fprintf(stderr, "%s: requested #bits (%d) not in valid range [8,16]\n",
--- 87,99 ----
  
    switch(bits) {
!   case 16: method = limnQN16octa; break;
!   case 15: method = limnQN15octa; break;
!   case 14: method = limnQN14octa; break;
!   case 13: method = limnQN13octa; break;
!   case 12: method = limnQN12octa; break;
!   case 11: method = limnQN11octa; break;
!   case 10: method = limnQN10octa; break;
!   case 9: method = limnQN9octa; break;
!   case 8: method = limnQN8octa; break;
    default:
      fprintf(stderr, "%s: requested #bits (%d) not in valid range [8,16]\n",

[Teem-commit] teem/src/limn/test off2eps.c,1.6,1.7

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/limn/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11155/limn/test

Modified Files:
	off2eps.c 
Log Message:
added even-bit quantization methods based on Emil's octahdron unfolding, and renamed the odd-bit methods from checker to octa

Index: off2eps.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/test/off2eps.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** off2eps.c	13 Feb 2004 22:57:30 -0000	1.6
--- off2eps.c	3 Mar 2004 13:14:08 -0000	1.7
***************
*** 59,63 ****
  	     "-1 1", "range in V direction of image plane");
    hestOptAdd(&hopt, "e", "envmap", airTypeOther, 1, 1, &nmap, "",
! 	     "16checker-based environment map",
  	     NULL, NULL, nrrdHestNrrd);
    hestOptAdd(&hopt, "ws", "winscale", airTypeFloat, 1, 1, &winscale,
--- 59,63 ----
  	     "-1 1", "range in V direction of image plane");
    hestOptAdd(&hopt, "e", "envmap", airTypeOther, 1, 1, &nmap, "",
! 	     "16octa-based environment map",
  	     NULL, NULL, nrrdHestNrrd);
    hestOptAdd(&hopt, "ws", "winscale", airTypeFloat, 1, 1, &winscale,

[Teem-commit] teem/src/ell eigen.c,1.18,1.19

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19188/ell

Modified Files:
	eigen.c 
Log Message:
bug fixes relating to switch from column-major to row-major

Index: eigen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/eigen.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** eigen.c	1 Mar 2004 10:19:44 -0000	1.18
--- eigen.c	1 Mar 2004 21:58:55 -0000	1.19
***************
*** 212,215 ****
--- 212,220 ----
  ** (evec+0)[], (evec+3)[], and (evec+6)[]
  **
+ ** NOTE: Even in the post-teem-1.7 switch from column-major to 
+ ** row-major- its still the case that the eigenvectors are at
+ ** evec+0, evec+3, evec+6: this means that they USED to be the
+ ** "columns" of the matrix, and NOW they're the rows.  
+ **
  ** The eigenvalues (and associated eigenvectors) are sorted in
  ** descending order.

[Teem-commit] teem/src/ten glyph.c,1.35,1.36 tensor.c,1.27,1.28

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19188/ten

Modified Files:
	glyph.c tensor.c 
Log Message:
bug fixes relating to switch from column-major to row-major

Index: glyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/glyph.c,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** glyph.c	27 Feb 2004 06:08:35 -0000	1.35
--- glyph.c	1 Mar 2004 21:59:03 -0000	1.36
***************
*** 165,169 ****
    airArray *mop;
    double pI[3], pW[3];
!   float cl, cp, *tdata, evec[9], eval[3], *cvec,
      aniso[TEN_ANISO_MAX+1], sRot[16], mA[16], mB[16],
      R, G, B, qA, qB, glyphAniso, sliceGray;
--- 165,169 ----
    airArray *mop;
    double pI[3], pW[3];
!   float cl, cp, *tdata, evec[9], rotEvec[9], eval[3], *cvec,
      aniso[TEN_ANISO_MAX+1], sRot[16], mA[16], mB[16],
      R, G, B, qA, qB, glyphAniso, sliceGray;
***************
*** 265,268 ****
--- 265,269 ----
      }
      tenEigensolve(eval, evec, tdata);
+     ELL_3M_TRANSPOSE(rotEvec, evec);
      tenAnisoCalc(aniso, eval);
      if (parm->doSlice
***************
*** 355,359 ****
      ELL_4M_SCALE_SET(mB, eval[0], eval[1], eval[2]);
      ell_4m_post_mul_f(mA, mB);
!     ELL_43M_INSET(mB, evec);                        /* rotate by evecs */
      ell_4m_post_mul_f(mA, mB);
      ELL_4M_TRANSLATE_SET(mB, pW[0], pW[1], pW[2]);  /* translate */
--- 356,360 ----
      ELL_4M_SCALE_SET(mB, eval[0], eval[1], eval[2]);
      ell_4m_post_mul_f(mA, mB);
!     ELL_43M_INSET(mB, rotEvec);                     /* rotate by evecs */
      ell_4m_post_mul_f(mA, mB);
      ELL_4M_TRANSLATE_SET(mB, pW[0], pW[1], pW[2]);  /* translate */

Index: tensor.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tensor.c,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** tensor.c	23 Feb 2004 02:40:24 -0000	1.27
--- tensor.c	1 Mar 2004 21:59:03 -0000	1.28
***************
*** 186,189 ****
--- 186,194 ----
  ** return is same as ell_3m_eigensolve_d, which is same as ell_cubic
  **
+ ** NOTE: Even in the post-teem-1.7 switch from column-major to 
+ ** row-major- its still the case that the eigenvectors are at
+ ** evec+0, evec+3, evec+6: this means that they USED to be the
+ ** "columns" of the matrix, and NOW they're the rows.  
+ **
  ** This does NOT use biff
  */
***************
*** 290,295 ****
    ELL_3M_DIAG_SET(diag, eval[0], eval[1], eval[2]);
    ELL_3M_TRANSPOSE(evecT, evec);
!   ELL_3M_MUL(tmpMat1, diag, evecT);
!   ELL_3M_MUL(tmpMat2, evec, tmpMat1);
    ten[0] = conf;
    TEN_MAT2LIST(ten, tmpMat2);
--- 295,300 ----
    ELL_3M_DIAG_SET(diag, eval[0], eval[1], eval[2]);
    ELL_3M_TRANSPOSE(evecT, evec);
!   ELL_3M_MUL(tmpMat1, diag, evec);
!   ELL_3M_MUL(tmpMat2, evecT, tmpMat1);
    ten[0] = conf;
    TEN_MAT2LIST(ten, tmpMat2);

[Teem-commit] teem/src/limn/test soid.c,1.10,1.11

[<kin...@us...>]

Update of /cvsroot/teem/teem/src/limn/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19188/limn/test

Modified Files:
	soid.c 
Log Message:
bug fixes relating to switch from column-major to row-major

Index: soid.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/test/soid.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** soid.c	13 Feb 2004 22:57:30 -0000	1.10
--- soid.c	1 Mar 2004 21:59:03 -0000	1.11
***************
*** 23,53 ****
  char *info = ("Save a single ellipsoid or superquadric into an OFF file.");
  
- void
- washQtoM3(float m[9], float q[4]) {
-   float p[4], w, x, y, z, len;
- 
-   ELL_4V_COPY(p, q);
-   len = ELL_4V_LEN(p);
-   ELL_4V_SCALE(p, 1.0/len, p);
-   w = p[0];
-   x = p[1];
-   y = p[2];
-   z = p[3];
-   /* mathematica work implies that we should be 
-      setting ROW vectors here */
-   ELL_3V_SET(m+0, 
- 	     1 - 2*(y*y + z*z),
- 	     2*(x*y - w*z),
- 	     2*(x*z + w*y));
-   ELL_3V_SET(m+3,
- 	     2*(x*y + w*z),
- 	     1 - 2*(x*x + z*z),
- 	     2*(y*z - w*x));
-   ELL_3V_SET(m+6,
- 	     2*(x*z - w*y),
- 	     2*(y*z + w*x),
- 	     1 - 2*(x*x + y*y));
- }
- 
  int
  main(int argc, char *argv[]) {
--- 23,26 ----
***************
*** 109,119 ****
    look->spow = 0;
  
!   q[0] = 1.0;
!   q[1] = p[0];
!   q[2] = p[1];
!   q[3] = p[2];
!   len = ELL_4V_LEN(q);
!   ELL_4V_SCALE(q, 1.0/len, q);
!   washQtoM3(mR, q);
  
    if (AIR_EXISTS(AB[0]) && AIR_EXISTS(AB[1])) {
--- 82,88 ----
    look->spow = 0;
  
!   ELL_4V_SET(q, 1, p[0], p[1], p[2]);
!   ELL_4V_NORM(q, q, len);
!   ell_q_to_3m_f(mR, q);
  
    if (AIR_EXISTS(AB[0]) && AIR_EXISTS(AB[1])) {