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[Teem-commit] teem/src/alan alan.h,1.14,1.15 coreAlan.c,1.18,1.19 methodsAlan.c,1.13,1.14

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

Update of /cvsroot/teem/teem/src/alan
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30921

Modified Files:
	alan.h coreAlan.c methodsAlan.c 
Log Message:
still hacking

Index: coreAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/coreAlan.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** coreAlan.c	26 Jul 2004 11:43:18 -0000	1.18
--- coreAlan.c	26 Jul 2004 21:00:54 -0000	1.19
***************
*** 213,219 ****
  void *
  _alanTuringWorker(void *_task) {
!   alan_t *tendata, *ten, Dxx, Dxy, Dyy, react, _react,
      *lev0, *lev1, *parm, deltaT, alpha, beta, A, B,
!     *v[27], lapA, lapB, deltaA, deltaB, diffA, diffB, change;
    int dim, iter, stop, startW, endW, idx,
      px, mx, py, my, pz, mz,
--- 213,222 ----
  void *
  _alanTuringWorker(void *_task) {
!   alan_t *tendata, *ten, react, _react,
!     Dxx, Dxy, Dyy, Dxz, Dyz,
!     *tpx, *tmx, *tpy, *tmy, *tpz, *tmz,
      *lev0, *lev1, *parm, deltaT, alpha, beta, A, B,
!     *v[27], lapA, lapB, corrA, corrB, 
!     deltaA, deltaB, diffA, diffB, change;
    int dim, iter, stop, startW, endW, idx,
      px, mx, py, my, pz, mz,
***************
*** 301,305 ****
  	    v[7] = lev0 + 2*( x + sx*(py));
  	    if (tendata) {
- 	      ten = tendata + 4*(x + sx*(y));
  	      /*
  	      **  0 1 2    Dxy/2          Dyy        -Dxy/2
--- 304,307 ----
***************
*** 311,314 ****
--- 313,317 ----
  	      v[6] = lev0 + 2*(mx + sx*(py));
  	      v[8] = lev0 + 2*(px + sx*(py));
+ 	      ten = tendata + 4*idx;
  	      Dxx = ten[1];
  	      Dxy = ten[2];
***************
*** 321,327 ****
--- 324,349 ----
  		      - 2*(Dxx + Dyy)*B);
  	      react = ten[0];
+ 	      if (task->actx->homogAniso) {
+ 		corrA = 0;
+ 		corrB = 0;
+ 	      } else {
+ 		tpx = tendata + 4*(px + sx*( y + sy*( z)));
+ 		tmx = tendata + 4*(mx + sx*( y + sy*( z)));
+ 		tpy = tendata + 4*( x + sx*(py + sy*( z)));
+ 		tmy = tendata + 4*( x + sx*(my + sy*( z)));
+ 		corrA = ((tpx[1] - tmx[1])*(v[5][0] - v[3][0])/4 +  /* Dxx,x * A,x */
+ 			 (tpx[2] - tmx[2])*(v[7][0] - v[1][0])/4 +  /* Dxy,x * A,y */
+ 			 (tpy[2] - tmy[2])*(v[5][0] - v[3][0])/4 +  /* Dxy,y * A,x */
+ 			 (tpy[3] - tmy[3])*(v[7][0] - v[1][0]));    /* Dyy,y * A,y */
+ 		corrB = ((tpx[1] - tmx[1])*(v[5][1] - v[3][1])/4 +  /* Dxx,x * B,x */
+ 			 (tpx[2] - tmx[2])*(v[7][1] - v[1][1])/4 +  /* Dxy,x * B,y */
+ 			 (tpy[2] - tmy[2])*(v[5][1] - v[3][1])/4 +  /* Dxy,y * B,x */
+ 			 (tpy[3] - tmy[3])*(v[7][1] - v[1][1]));    /* Dyy,y * B,y */
+ 	      }
  	    } else {
  	      lapA = v[1][0] + v[3][0] + v[5][0] + v[7][0] - 4*A;
  	      lapB = v[1][1] + v[3][1] + v[5][1] + v[7][1] - 4*B;
+ 	      corrA = 0;
+ 	      corrB = 0;
  	      react = 1;
  	    }
***************
*** 350,367 ****
  	    v[16] = lev0 + 2*( x + sx*(py + sy*( z)));
  	    v[22] = lev0 + 2*( x + sx*( y + sy*(pz)));
! 	    lapA = (v[ 4][0] + v[10][0] + v[12][0]
! 		    + v[14][0] + v[16][0] + v[22][0] - 6*A);
! 	    lapB = (v[ 4][1] + v[10][1] + v[12][1]
! 		    + v[14][1] + v[16][1] + v[22][1] - 6*B);
! 	    react = 1;
  	  }
  	  
  	  react *= _react;
! 	  deltaA = deltaT*(react*task->actx->K*(alpha - A*B) + diffA*lapA);
  	  if (AIR_ABS(deltaA) > task->actx->maxPixelChange) {
  	    stop = alanStopDiverged;
  	  }
  	  change += AIR_ABS(deltaA);
! 	  deltaB = deltaT*(react*task->actx->K*(A*B - B - beta) + diffB*lapB);
  	  if (!( AIR_EXISTS(deltaA) && AIR_EXISTS(deltaB) )) {
  	    stop = alanStopNonExist;
--- 372,403 ----
  	    v[16] = lev0 + 2*( x + sx*(py + sy*( z)));
  	    v[22] = lev0 + 2*( x + sx*( y + sy*(pz)));
! 	    if (tendata) {
! 
! 	      if (task->actx->homogAniso) {
! 		corrA = 0;
! 		corrB = 0;
! 	      } else {
! 		
! 	      }
! 	    } else {
! 	      lapA = (v[ 4][0] + v[10][0] + v[12][0]
! 		      + v[14][0] + v[16][0] + v[22][0] - 6*A);
! 	      lapB = (v[ 4][1] + v[10][1] + v[12][1]
! 		      + v[14][1] + v[16][1] + v[22][1] - 6*B);
! 	      corrA = 0;
! 	      corrB = 0;
! 	      react = 1;
! 	    }
  	  }
  	  
  	  react *= _react;
! 	  deltaA = deltaT*(react*task->actx->K*(alpha - A*B) 
! 			   + diffA*(lapA + corrA));
  	  if (AIR_ABS(deltaA) > task->actx->maxPixelChange) {
  	    stop = alanStopDiverged;
  	  }
  	  change += AIR_ABS(deltaA);
! 	  deltaB = deltaT*(react*task->actx->K*(A*B - B - beta)
! 			   + diffB*(lapB + corrB));
  	  if (!( AIR_EXISTS(deltaA) && AIR_EXISTS(deltaB) )) {
  	    stop = alanStopNonExist;

Index: methodsAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/methodsAlan.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** methodsAlan.c	26 Jul 2004 11:43:18 -0000	1.13
--- methodsAlan.c	26 Jul 2004 21:00:54 -0000	1.14
***************
*** 33,36 ****
--- 33,37 ----
      ELL_3V_SET(actx->size, 0, 0, 0);
      actx->oversample = 0;
+     actx->homogAniso = AIR_FALSE;
      actx->numThreads = 1;
      actx->frameInterval = 10;
***************
*** 184,187 ****
--- 185,189 ----
      biffAdd(ALAN, err); return 1;
    }
+ 
    actx->nten = nrrdNuke(actx->nten);
    actx->nten = nrrdNew();
***************
*** 194,197 ****
--- 196,201 ----
    if (3 == actx->dim) {
      actx->size[2] = oversample*nten->axis[3].size;
+   } else {
+     actx->size[2] = 1;
    }
  
***************
*** 242,245 ****
--- 246,253 ----
      actx->numThreads = parmI;
      break;
+   case alanParmHomogAniso:
+     parmI = parm;
+     actx->homogAniso = parmI;
+     break;
    case alanParmSaveInterval:
      parmI = parm;

Index: alan.h
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/alan.h,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** alan.h	26 Jul 2004 11:43:18 -0000	1.14
--- alan.h	26 Jul 2004 21:00:54 -0000	1.15
***************
*** 49,52 ****
--- 49,53 ----
    alanParmNumThreads,
    alanParmFrameInterval,
+   alanParmHomogAniso,
    alanParmSaveInterval,
    alanParmMaxIteration,
***************
*** 101,104 ****
--- 102,106 ----
      size[3],          /* number of texels in X, Y, (Z) */
      oversample,       /* oversampling of tensors to texels */
+     homogAniso,       /* homogenous anisotropy approximation */
      numThreads,       /* # of threads, if airThreadCapable */
      frameInterval,    /* # of iterations between which to an image */

[Teem-commit] teem/src/bin spots.c,1.6,1.7

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20232

Modified Files:
	spots.c 
Log Message:
still hacking

Index: spots.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/spots.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** spots.c	26 Jul 2004 07:26:17 -0000	1.6
--- spots.c	26 Jul 2004 11:43:38 -0000	1.7
***************
*** 39,43 ****
    alanContext *actx;
    int *size, sizeLen, fi, si, wrap, nt, cfn;
!   double deltaT, mch, xch, alphabeta[2], time0, time1, H;
    Nrrd *ninit=NULL, *nten=NULL, *nparm=NULL;
  
--- 39,43 ----
    alanContext *actx;
    int *size, sizeLen, fi, si, wrap, nt, cfn;
!   double deltaT, mch, xch, alphabeta[2], time0, time1, deltaX, react, rrange;
    Nrrd *ninit=NULL, *nten=NULL, *nparm=NULL;
  
***************
*** 59,73 ****
  	     "terms of the reaction-diffusion equations.  The default "
  	     "values were the ones published by Turing.");
    hestOptAdd(&hopt, "dt", "time", airTypeDouble, 1, 1, &deltaT, "1.0",
  	     "time-step size in Euler integration.  Can be larger, at "
  	     "risk of hitting divergent instability.");
!   hestOptAdd(&hopt, "dx", "size", airTypeDouble, 1, 1, &H, "1.3",
  	     "nominal size of simulation grid element.");
    hestOptAdd(&hopt, "mch", "change", airTypeDouble, 1, 1, &mch, "0.00001",
! 	     "the minimum significant change, averaged over the whole texture, in the "
! 	     "first morphogen: to signify convergence");
    hestOptAdd(&hopt, "xch", "change", airTypeDouble, 1, 1, &xch, "6",
! 	     "the maximum allowable change, averaged over the whole texture, in the "
! 	     "first morphogen: to signify divergence");
    hestOptAdd(&hopt, "fi", "frame inter", airTypeInt, 1, 1, &fi, "0",
  	     "the number of iterations between which to save out an 8-bit "
--- 59,77 ----
  	     "terms of the reaction-diffusion equations.  The default "
  	     "values were the ones published by Turing.");
+   hestOptAdd(&hopt, "sr", "react", airTypeDouble, 1, 1, &react, "1.0",
+ 	     "scaling of reaction term");
+   hestOptAdd(&hopt, "rr", "range range", airTypeDouble, 1, 1, &rrange, "4.0",
+ 	     "amount of random noise to add to inital textures");
    hestOptAdd(&hopt, "dt", "time", airTypeDouble, 1, 1, &deltaT, "1.0",
  	     "time-step size in Euler integration.  Can be larger, at "
  	     "risk of hitting divergent instability.");
!   hestOptAdd(&hopt, "dx", "size", airTypeDouble, 1, 1, &deltaX, "1.3",
  	     "nominal size of simulation grid element.");
    hestOptAdd(&hopt, "mch", "change", airTypeDouble, 1, 1, &mch, "0.00001",
! 	     "the minimum significant change (averaged over the whole "
! 	     "texture) in the first morphogen: to signify convergence");
    hestOptAdd(&hopt, "xch", "change", airTypeDouble, 1, 1, &xch, "6",
! 	     "the maximum allowable change (averaged over the whole "
! 	     "texture) in the first morphogen: to signify divergence");
    hestOptAdd(&hopt, "fi", "frame inter", airTypeInt, 1, 1, &fi, "0",
  	     "the number of iterations between which to save out an 8-bit "
***************
*** 115,127 ****
    if (alanParmSet(actx, alanParmVerbose, 1)
        || alanParmSet(actx, alanParmTextureType, alanTextureTypeTuring)
-       || alanParmSet(actx, alanParmRandRange, 4.0)
        || alanParmSet(actx, alanParmK, 0.0125)
-       || alanParmSet(actx, alanParmH, 1.2)
        || alanParmSet(actx, alanParmAlpha, alphabeta[0])
        || alanParmSet(actx, alanParmBeta, alphabeta[1])
        || alanParmSet(actx, alanParmDeltaT, deltaT)
!       || alanParmSet(actx, alanParmH, H)
        || alanParmSet(actx, alanParmMinAverageChange, mch)
        || alanParmSet(actx, alanParmMaxPixelChange, xch)
        || alanParmSet(actx, alanParmSaveInterval, si)
        || alanParmSet(actx, alanParmFrameInterval, fi)
--- 119,131 ----
    if (alanParmSet(actx, alanParmVerbose, 1)
        || alanParmSet(actx, alanParmTextureType, alanTextureTypeTuring)
        || alanParmSet(actx, alanParmK, 0.0125)
        || alanParmSet(actx, alanParmAlpha, alphabeta[0])
        || alanParmSet(actx, alanParmBeta, alphabeta[1])
+       || alanParmSet(actx, alanParmDeltaX, deltaX)
        || alanParmSet(actx, alanParmDeltaT, deltaT)
!       || alanParmSet(actx, alanParmReact, react)
        || alanParmSet(actx, alanParmMinAverageChange, mch)
        || alanParmSet(actx, alanParmMaxPixelChange, xch)
+       || alanParmSet(actx, alanParmRandRange, rrange)
        || alanParmSet(actx, alanParmSaveInterval, si)
        || alanParmSet(actx, alanParmFrameInterval, fi)

[Teem-commit] teem/src/alan alan.h,1.13,1.14 coreAlan.c,1.17,1.18 methodsAlan.c,1.12,1.13

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

Update of /cvsroot/teem/teem/src/alan
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20204

Modified Files:
	alan.h coreAlan.c methodsAlan.c 
Log Message:
still hacking

Index: coreAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/coreAlan.c,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** coreAlan.c	26 Jul 2004 07:26:03 -0000	1.17
--- coreAlan.c	26 Jul 2004 11:43:18 -0000	1.18
***************
*** 213,217 ****
  void *
  _alanTuringWorker(void *_task) {
!   alan_t *tendata, *ten, Dxx, Dxy, Dyy, react,
      *lev0, *lev1, *parm, deltaT, alpha, beta, A, B,
      *v[27], lapA, lapB, deltaA, deltaB, diffA, diffB, change;
--- 213,217 ----
  void *
  _alanTuringWorker(void *_task) {
!   alan_t *tendata, *ten, Dxx, Dxy, Dyy, react, _react,
      *lev0, *lev1, *parm, deltaT, alpha, beta, A, B,
      *v[27], lapA, lapB, deltaA, deltaB, diffA, diffB, change;
***************
*** 227,235 ****
    sz = (2 == dim ? 1 : task->actx->size[2]);
    parm = (alan_t*)(task->actx->nparm->data);
!   diffA = task->actx->diffA/pow(task->actx->H, dim);
!   diffB = task->actx->diffB/pow(task->actx->H, dim);
    startW = task->idx*sy/task->actx->numThreads;
    endW = (task->idx+1)*sy/task->actx->numThreads;
    tendata = task->actx->nten ? (alan_t *)task->actx->nten->data : NULL;
  
    if (2 == dim) {
--- 227,236 ----
    sz = (2 == dim ? 1 : task->actx->size[2]);
    parm = (alan_t*)(task->actx->nparm->data);
!   diffA = task->actx->diffA/pow(task->actx->deltaX, dim);
!   diffB = task->actx->diffB/pow(task->actx->deltaX, dim);
    startW = task->idx*sy/task->actx->numThreads;
    endW = (task->idx+1)*sy/task->actx->numThreads;
    tendata = task->actx->nten ? (alan_t *)task->actx->nten->data : NULL;
+   _react = task->actx->react;
  
    if (2 == dim) {
***************
*** 356,359 ****
--- 357,361 ----
  	  }
  	  
+ 	  react *= _react;
  	  deltaA = deltaT*(react*task->actx->K*(alpha - A*B) + diffA*lapA);
  	  if (AIR_ABS(deltaA) > task->actx->maxPixelChange) {

Index: methodsAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/methodsAlan.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** methodsAlan.c	26 Jul 2004 07:26:03 -0000	1.12
--- methodsAlan.c	26 Jul 2004 11:43:18 -0000	1.13
***************
*** 41,48 ****
      actx->K = AIR_NAN;
      actx->F = AIR_NAN;
!     actx->H = 1.25;
      actx->alpha = 16;
      actx->beta = 12;
      actx->deltaT = 1.0;
      actx->initA = actx->initB = 0;
      actx->diffA = actx->diffB = 0;
--- 41,49 ----
      actx->K = AIR_NAN;
      actx->F = AIR_NAN;
!     actx->deltaX = 1.25;
      actx->alpha = 16;
      actx->beta = 12;
      actx->deltaT = 1.0;
+     actx->react = 1.0;
      actx->initA = actx->initB = 0;
      actx->diffA = actx->diffB = 0;
***************
*** 260,263 ****
--- 261,270 ----
      actx->deltaT = parm;
      break;
+   case alanParmDeltaX:
+     actx->deltaX = parm;
+     break;
+   case alanParmReact:
+     actx->react = parm;
+     break;
    case alanParmDiffA:
      actx->diffA = parm;
***************
*** 275,281 ****
      actx->F = parm;
      break;
-   case alanParmH:
-     actx->H = parm;
-     break;
    case alanParmMinAverageChange:
      actx->minAverageChange = parm;
--- 282,285 ----

Index: alan.h
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/alan.h,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** alan.h	26 Jul 2004 07:26:03 -0000	1.13
--- alan.h	26 Jul 2004 11:43:18 -0000	1.14
***************
*** 53,61 ****
    alanParmRandRange,
    alanParmDeltaT,
    alanParmDiffA,
    alanParmDiffB,
    alanParmK,
    alanParmF,
-   alanParmH,
    alanParmMinAverageChange,
    alanParmMaxPixelChange,
--- 53,62 ----
    alanParmRandRange,
    alanParmDeltaT,
+   alanParmDeltaX,
    alanParmDiffA,
    alanParmDiffB,
+   alanParmReact,
    alanParmK,
    alanParmF,
    alanParmMinAverageChange,
    alanParmMaxPixelChange,
***************
*** 106,110 ****
      constFilename;    /* always use the same filename when saving frames */
    alan_t K, F,        /* simulation variables */
!     H,                /* size of spatial grid discretization */
      minAverageChange, /* min worthwhile "avergageChange" value (see below),
  			 assume convergence if it falls below this */
--- 107,111 ----
      constFilename;    /* always use the same filename when saving frames */
    alan_t K, F,        /* simulation variables */
!     deltaX,           /* size of spatial grid discretization */
      minAverageChange, /* min worthwhile "avergageChange" value (see below),
  			 assume convergence if it falls below this */
***************
*** 113,116 ****
--- 114,118 ----
  			 this is exceeded */
      alpha, beta,      /* variables for turing */
+     react,            /* additional scaling of reaction term */
      deltaT,           /* euler integration step size */
      initA, initB,     /* initial (constant) values for each morphogen */

[Teem-commit] teem/src/ten glyph.c,1.41,1.42

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16157

Modified Files:
	glyph.c 
Log Message:
tweaking ray tracing shadows

Index: glyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/glyph.c,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** glyph.c	23 Jun 2004 01:46:41 -0000	1.41
--- glyph.c	26 Jul 2004 07:30:42 -0000	1.42
***************
*** 335,339 ****
  	ELL_3V_COPY(((echoRectangle*)esquare)->edge1, edge1);
  	echoColorSet(esquare, sliceGray, sliceGray, sliceGray, 1);
! 	echoMatterPhongSet(glyphsEcho, esquare, 1, 0, 0, 40);
  	echoListAdd(list, esquare);
        }
--- 335,342 ----
  	ELL_3V_COPY(((echoRectangle*)esquare)->edge1, edge1);
  	echoColorSet(esquare, sliceGray, sliceGray, sliceGray, 1);
! 	/* this is pretty arbitrary- but I want shadows to have some effect.
! 	   Previously, the material was all ambient: (A,D,S) = (1,0,0),
! 	   which avoided all shadow effects. */
! 	echoMatterPhongSet(glyphsEcho, esquare, 0.4, 0.6, 0, 40);
  	echoListAdd(list, esquare);
        }

[Teem-commit] teem/src/echo color.c,1.26,1.27 renderEcho.c,1.27,1.28 sqd.c,1.5,1.6

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

Update of /cvsroot/teem/teem/src/echo
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16100

Modified Files:
	color.c renderEcho.c sqd.c 
Log Message:
alas, still debugging superquadric glyph ray intersection

Index: sqd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/echo/sqd.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** sqd.c	7 Jan 2004 15:34:28 -0000	1.5
--- sqd.c	26 Jul 2004 07:30:10 -0000	1.6
***************
*** 92,96 ****
  		     echoPos_t x, echoPos_t y, echoPos_t z,
  		     echoPos_t A, echoPos_t B) {
!   echoPos_t R, xxb, yya, zza;
  
    xxb = pow(x*x, 1/B);  yya = pow(y*y, 1/A);  zza = pow(z*z, 1/A);
--- 92,98 ----
  		     echoPos_t x, echoPos_t y, echoPos_t z,
  		     echoPos_t A, echoPos_t B) {
!   echoPos_t R, xxb, yya, zza, larg;
! 
!   echoPos_t ret;
  
    xxb = pow(x*x, 1/B);  yya = pow(y*y, 1/A);  zza = pow(z*z, 1/A);
***************
*** 100,104 ****
  	     2*yya/(B*y*(yya + zza + R)),
  	     2*zza/(B*z*(yya + zza + R)));
!   return log(pow(yya + zza, A/B) + xxb);
  }
  
--- 102,136 ----
  	     2*yya/(B*y*(yya + zza + R)),
  	     2*zza/(B*z*(yya + zza + R)));
!   larg = pow(yya + zza, A/B) + xxb;
!   ret= larg > 0 ? log(larg) : ECHO_POS_MIN;
!   /*
!   if (!( AIR_EXISTS(grad[0]) && AIR_EXISTS(grad[1]) && AIR_EXISTS(grad[2]) )) {
!     fprintf(stderr, "_echo_SuperquadX_lvg: PANIC\n");
!     fprintf(stderr, "x = %g, y = %g, z = %g, A = %g, B = %g\n",
! 	    x, y, z, A, B);
!     fprintf(stderr, "pow(%g * %g = %g, 1/%g = %g) = %g\n",
! 	    x, x, x*x, B, 1/B, pow(x*x, 1/B));
!     fprintf(stderr, "xxb = %g, yya = %g, zza = %g\n",
! 	    xxb, yya, zza);
!     fprintf(stderr, "R: pow(%g + %g = %g, 1-(%g/%g = %g) = %g) = %g*%g = %g\n",
! 	    yya, zza, yya + zza, 
! 	    A, B, A/B, 1-(A/B), 
! 	    pow(yya + zza, 1-(A/B)), xxb,
! 	    pow(yya + zza, 1-(A/B))*xxb);
!     fprintf(stderr, "grad[0]: 2/(%g * %g * (1 + pow(%g + %g = %g, %g/%g = %g)/%g = %g)) = %g\n",
! 	    B, x, yya, zza, yya+zza, A, B, A/B, xxb, 
! 	    pow(yya + zza, A/B)/xxb, grad[0]);
!     fprintf(stderr, "grad[1]: 2*%g/(%g*%g*(%g + %g + %g = %g) = %g) = %g\n",
! 	    yya, B, y, yya, zza, R, yya + zza + R,
! 	    B*y*(yya + zza + R),
! 	    2*yya/(B*y*(yya + zza + R)));
! 
!     fprintf(stderr, "log(pow(%g + %g = %g, %g) = %g + %g) = %g\n",
! 	    yya, zza, yya+zza, A/B, pow(yya + zza, A/B), xxb, ret);
!     fprintf(stderr, "grad = %g %g %g\n", grad[0], grad[1], grad[2]);
!     fprintf(stderr, "\n----------\n\n");
!   }
!   */
!   return ret;
  }
  
***************
*** 107,111 ****
  		     echoPos_t x, echoPos_t y, echoPos_t z,
  		     echoPos_t A, echoPos_t B) {
!   echoPos_t R, xxa, yyb, zza;
  
    xxa = pow(x*x, 1/A);  yyb = pow(y*y, 1/B);  zza = pow(z*z, 1/A);
--- 139,143 ----
  		     echoPos_t x, echoPos_t y, echoPos_t z,
  		     echoPos_t A, echoPos_t B) {
!   echoPos_t R, xxa, yyb, zza, larg;
  
    xxa = pow(x*x, 1/A);  yyb = pow(y*y, 1/B);  zza = pow(z*z, 1/A);
***************
*** 115,119 ****
  	     2/(B*y*(1 + pow(xxa + zza, A/B)/yyb)),
  	     2*zza/(B*z*(xxa + zza + R)));
!   return log(pow(xxa + zza, A/B) + yyb);
  }
  
--- 147,152 ----
  	     2/(B*y*(1 + pow(xxa + zza, A/B)/yyb)),
  	     2*zza/(B*z*(xxa + zza + R)));
!   larg = pow(xxa + zza, A/B) + yyb;
!   return larg > 0 ? log(larg) : ECHO_POS_MIN;
  }
  
***************
*** 122,126 ****
  		     echoPos_t x, echoPos_t y, echoPos_t z,
  		     echoPos_t A, echoPos_t B) {
!   echoPos_t R, xxa, yya, zzb;
  
    xxa = pow(x*x, 1/A);  yya = pow(y*y, 1/A);  zzb = pow(z*z, 1/B);
--- 155,161 ----
  		     echoPos_t x, echoPos_t y, echoPos_t z,
  		     echoPos_t A, echoPos_t B) {
!   echoPos_t R, xxa, yya, zzb, larg;
! 
!   echoPos_t ret;
  
    xxa = pow(x*x, 1/A);  yya = pow(y*y, 1/A);  zzb = pow(z*z, 1/B);
***************
*** 130,134 ****
  	     2*yya/(B*y*(xxa + yya + R)),
  	     2/(B*z*(1 + pow(xxa + yya, A/B)/zzb)));
!   return log(pow(xxa + yya, A/B) + zzb);
  }
  
--- 165,186 ----
  	     2*yya/(B*y*(xxa + yya + R)),
  	     2/(B*z*(1 + pow(xxa + yya, A/B)/zzb)));
!   larg = pow(xxa + yya, A/B) + zzb;
! 
!   ret = larg > 0 ? log(larg) : ECHO_POS_MIN;
!   /*
!   if (!AIR_EXISTS(ret)) {
!     fprintf(stderr, "_echo_SuperquadZ_lvg: PANIC\n");
!     fprintf(stderr, "x = %g, y = %g, z = %g, A = %g, B = %g\n",
! 	    x, y, z, A, B);
!     fprintf(stderr, "pow(%g*%g = %g, %g) = %g\n", 
! 	    x, x, x*x, 1/A, xxa);
!     fprintf(stderr, "pow(%g*%g = %g, %g) = %g\n", 
! 	    y, y, y*y, 1/A, yya);
!     fprintf(stderr, "log(pow(%g, %g) = %g + %g) = %g\n",
! 	    xxa + yya, A/B, pow(xxa + yya, A/B), zzb, ret);
!     exit(0);
!   }
!   */
!   return ret;
  }
  
***************
*** 294,298 ****
    TT = (Tmin + Tmax)/2;
    LVALGRAD(VV, dV, TT);
!   while (iter < parm->sqNRI && AIR_ABS(VV) > parm->sqTol) {
      if (tstate->verbose) {
        fprintf(stderr, "%s%s: iter = %d: TT = %g, VV = %g, dV = %g\n",
--- 346,352 ----
    TT = (Tmin + Tmax)/2;
    LVALGRAD(VV, dV, TT);
! 
!   while (iter < parm->sqNRI && AIR_ABS(VV) > parm->sqTol
! 	 && AIR_EXISTS(VV) && AIR_EXISTS(dV)) {
      if (tstate->verbose) {
        fprintf(stderr, "%s%s: iter = %d: TT = %g, VV = %g, dV = %g\n",
***************
*** 318,321 ****
--- 372,384 ----
    }
  
+   if (!( AIR_EXISTS(VV) && AIR_EXISTS(dV) )) {
+     /* we bailed out of the loop above because
+        we got screwed by numerical errors
+        --> pretend that there was no intersection,
+        and HEY this will have to be debugged later */
+     return AIR_FALSE;
+   }
+ 
+   /* else we succeedded in finding the intersection */
    intx->t = TT + saveTmin;
    VALGRAD(VV, dV, TT);   /* puts gradient into grad */

Index: renderEcho.c
===================================================================
RCS file: /cvsroot/teem/teem/src/echo/renderEcho.c,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** renderEcho.c	12 May 2004 11:07:24 -0000	1.27
--- renderEcho.c	26 Jul 2004 07:30:10 -0000	1.28
***************
*** 347,351 ****
        chan = arg->chanBuff;
  
!       /* arg->verbose = ( (160 == imgUi && 160 == imgVi) ); */
        
        if (arg->verbose) {
--- 347,351 ----
        chan = arg->chanBuff;
  
!       /* arg->verbose = ( (38 == imgUi && 121 == imgVi) ); */
        
        if (arg->verbose) {

Index: color.c
===================================================================
RCS file: /cvsroot/teem/teem/src/echo/color.c,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** color.c	26 May 2004 02:11:00 -0000	1.26
--- color.c	26 Jul 2004 07:30:10 -0000	1.27
***************
*** 130,133 ****
--- 130,138 ----
      ELL_3V_NORM(Ldir, Ldir, Ldist);
      Ldot = ELL_3V_DOT(Ldir, intx->norm);
+     /* HEY: HACK: we have to general per-object-type flag that says,
+        this kind of object has no notion of in-versus-out facing ... */
+     if (echoTypeRectangle == intx->obj->type) {
+       Ldot = AIR_ABS(Ldot);
+     }
      if (Ldot <= 0) {
        continue;
***************
*** 157,160 ****
--- 162,168 ----
      if (spec) {
        Ldot = ELL_3V_DOT(Ldir, intx->refl);
+       if (echoTypeRectangle == intx->obj->type) {
+ 	Ldot = AIR_ABS(Ldot);
+       }
        if (Ldot > 0) {
  	Ldot = pow(Ldot, sp);

[Teem-commit] teem/src/bin spots.c,1.5,1.6

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15481

Modified Files:
	spots.c 
Log Message:
working on 3D reaction-diffusion textures

Index: spots.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/spots.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** spots.c	7 Jan 2004 15:34:28 -0000	1.5
--- spots.c	26 Jul 2004 07:26:17 -0000	1.6
***************
*** 27,31 ****
  
  char *spotsInfo = ("Generate reaction-diffusion textures based on "
! 		   "Turing's formulation. ");
  
  int
--- 27,32 ----
  
  char *spotsInfo = ("Generate reaction-diffusion textures based on "
! 		   "Turing's second example formulation (page 65) of "
! 		   "his 1954 paper \"The Chemical Basis of Morphogenesis.\" ");
  
  int
***************
*** 38,42 ****
    alanContext *actx;
    int *size, sizeLen, fi, si, wrap, nt, cfn;
!   double speed, mch, alphabeta[2], time0, time1, H;
    Nrrd *ninit=NULL, *nten=NULL, *nparm=NULL;
  
--- 39,43 ----
    alanContext *actx;
    int *size, sizeLen, fi, si, wrap, nt, cfn;
!   double deltaT, mch, xch, alphabeta[2], time0, time1, H;
    Nrrd *ninit=NULL, *nten=NULL, *nparm=NULL;
  
***************
*** 58,62 ****
  	     "terms of the reaction-diffusion equations.  The default "
  	     "values were the ones published by Turing.");
!   hestOptAdd(&hopt, "dt", "time", airTypeDouble, 1, 1, &speed, "1.0",
  	     "time-step size in Euler integration.  Can be larger, at "
  	     "risk of hitting divergent instability.");
--- 59,63 ----
  	     "terms of the reaction-diffusion equations.  The default "
  	     "values were the ones published by Turing.");
!   hestOptAdd(&hopt, "dt", "time", airTypeDouble, 1, 1, &deltaT, "1.0",
  	     "time-step size in Euler integration.  Can be larger, at "
  	     "risk of hitting divergent instability.");
***************
*** 64,69 ****
  	     "nominal size of simulation grid element.");
    hestOptAdd(&hopt, "mch", "change", airTypeDouble, 1, 1, &mch, "0.00001",
! 	     "the minimum change, averaged over the whole texture, in the "
! 	     "first morphogen, that signifies convergence");
    hestOptAdd(&hopt, "fi", "frame inter", airTypeInt, 1, 1, &fi, "0",
  	     "the number of iterations between which to save out an 8-bit "
--- 65,73 ----
  	     "nominal size of simulation grid element.");
    hestOptAdd(&hopt, "mch", "change", airTypeDouble, 1, 1, &mch, "0.00001",
! 	     "the minimum significant change, averaged over the whole texture, in the "
! 	     "first morphogen: to signify convergence");
!   hestOptAdd(&hopt, "xch", "change", airTypeDouble, 1, 1, &xch, "6",
! 	     "the maximum allowable change, averaged over the whole texture, in the "
! 	     "first morphogen: to signify divergence");
    hestOptAdd(&hopt, "fi", "frame inter", airTypeInt, 1, 1, &fi, "0",
  	     "the number of iterations between which to save out an 8-bit "
***************
*** 116,122 ****
        || alanParmSet(actx, alanParmAlpha, alphabeta[0])
        || alanParmSet(actx, alanParmBeta, alphabeta[1])
!       || alanParmSet(actx, alanParmSpeed, speed)
        || alanParmSet(actx, alanParmH, H)
        || alanParmSet(actx, alanParmMinAverageChange, mch)
        || alanParmSet(actx, alanParmSaveInterval, si)
        || alanParmSet(actx, alanParmFrameInterval, fi)
--- 120,127 ----
        || alanParmSet(actx, alanParmAlpha, alphabeta[0])
        || alanParmSet(actx, alanParmBeta, alphabeta[1])
!       || alanParmSet(actx, alanParmDeltaT, deltaT)
        || alanParmSet(actx, alanParmH, H)
        || alanParmSet(actx, alanParmMinAverageChange, mch)
+       || alanParmSet(actx, alanParmMaxPixelChange, xch)
        || alanParmSet(actx, alanParmSaveInterval, si)
        || alanParmSet(actx, alanParmFrameInterval, fi)

[Teem-commit] teem/src/alan alan.h,1.12,1.13 coreAlan.c,1.16,1.17 methodsAlan.c,1.11,1.12

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

Update of /cvsroot/teem/teem/src/alan
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15443

Modified Files:
	alan.h coreAlan.c methodsAlan.c 
Log Message:
working on 3D reaction-diffusion textures

Index: coreAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/coreAlan.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** coreAlan.c	12 May 2004 21:52:37 -0000	1.16
--- coreAlan.c	26 Jul 2004 07:26:03 -0000	1.17
***************
*** 47,52 ****
      biffAdd(ALAN, err); return 1;
    }
!   if (0 == actx->speed) {
!     sprintf(err, "%s: speed == 0", me);
      biffAdd(ALAN, err); return 1;
    }
--- 47,52 ----
      biffAdd(ALAN, err); return 1;
    }
!   if (0 == actx->deltaT) {
!     sprintf(err, "%s: deltaT == 0", me);
      biffAdd(ALAN, err); return 1;
    }
***************
*** 158,162 ****
        parm[2 + 3*I] = parmInit[2 + 3*I];
      } else {
!       parm[0 + 3*I] = actx->speed;
        parm[1 + 3*I] = actx->alpha;
        parm[2 + 3*I] = actx->beta;
--- 158,162 ----
        parm[2 + 3*I] = parmInit[2 + 3*I];
      } else {
!       parm[0 + 3*I] = actx->deltaT;
        parm[1 + 3*I] = actx->alpha;
        parm[2 + 3*I] = actx->beta;
***************
*** 170,174 ****
    char me[]="_alanPerIteration", fname[AIR_STRLEN_MED];
    Nrrd *nslc, *nimg;
! 
    if (!(actx->saveInterval || actx->frameInterval)) {
      if (actx->verbose && !(iter % 100)) {
--- 170,174 ----
    char me[]="_alanPerIteration", fname[AIR_STRLEN_MED];
    Nrrd *nslc, *nimg;
!   
    if (!(actx->saveInterval || actx->frameInterval)) {
      if (actx->verbose && !(iter % 100)) {
***************
*** 186,190 ****
      nrrdSlice(nslc=nrrdNew(), actx->_nlev[(iter+1) % 2], 0, 0);
      nrrdQuantize(nimg=nrrdNew(), nslc, NULL, 8);
!     sprintf(fname, "%06d.png", actx->constFilename ? 0 : iter);
      nrrdSave(fname, nimg, NULL);
      fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
--- 186,191 ----
      nrrdSlice(nslc=nrrdNew(), actx->_nlev[(iter+1) % 2], 0, 0);
      nrrdQuantize(nimg=nrrdNew(), nslc, NULL, 8);
!     sprintf(fname, (2 == actx->dim ? "%06d.png" : "%06d.nrrd"),
! 	    actx->constFilename ? 0 : iter);
      nrrdSave(fname, nimg, NULL);
      fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
***************
*** 211,231 ****
  
  void *
! _alanTuring2DWorker(void *_task) {
    alan_t *tendata, *ten, Dxx, Dxy, Dyy, react,
!     *lev0, *lev1, *parm, speed, alpha, beta, A, B,
!     *v[9], lapA, lapB, deltaA, deltaB, diffA, diffB, change;
!   int iter, stop, startY, endY, idx, px, mx, py, my, sx, sy, x, y;
    alanTask *task;
  
    task = (alanTask *)_task;
    sx = task->actx->size[0];
    sy = task->actx->size[1];
    parm = (alan_t*)(task->actx->nparm->data);
!   diffA = task->actx->diffA/(task->actx->H*task->actx->H);
!   diffB = task->actx->diffB/(task->actx->H*task->actx->H);
!   startY = task->idx*sy/task->actx->numThreads;
!   endY = (task->idx+1)*sy/task->actx->numThreads;
    tendata = task->actx->nten ? (alan_t *)task->actx->nten->data : NULL;
  
    for (iter = 0; 
         alanStopNot == task->actx->stop && iter < task->actx->maxIteration; 
--- 212,248 ----
  
  void *
! _alanTuringWorker(void *_task) {
    alan_t *tendata, *ten, Dxx, Dxy, Dyy, react,
!     *lev0, *lev1, *parm, deltaT, alpha, beta, A, B,
!     *v[27], lapA, lapB, deltaA, deltaB, diffA, diffB, change;
!   int dim, iter, stop, startW, endW, idx,
!     px, mx, py, my, pz, mz,
!     startY, endY, startZ, endZ, sx, sy, sz, x, y, z;
    alanTask *task;
  
    task = (alanTask *)_task;
+   dim = task->actx->dim;
    sx = task->actx->size[0];
    sy = task->actx->size[1];
+   sz = (2 == dim ? 1 : task->actx->size[2]);
    parm = (alan_t*)(task->actx->nparm->data);
!   diffA = task->actx->diffA/pow(task->actx->H, dim);
!   diffB = task->actx->diffB/pow(task->actx->H, dim);
!   startW = task->idx*sy/task->actx->numThreads;
!   endW = (task->idx+1)*sy/task->actx->numThreads;
    tendata = task->actx->nten ? (alan_t *)task->actx->nten->data : NULL;
  
+   if (2 == dim) {
+     startZ = 0;
+     endZ = 1;
+     startY = startW;
+     endY = endW;
+   } else {
+     startZ = startW;
+     endZ = endW;
+     startY = 0;
+     endY = sy;
+   }
+ 
    for (iter = 0; 
         alanStopNot == task->actx->stop && iter < task->actx->maxIteration; 
***************
*** 240,316 ****
      stop = alanStopNot;
      change = 0;
!     for (y = startY; y < endY; y++) {
        if (task->actx->wrap) {
! 	py = AIR_MOD(y+1, sy);
! 	my = AIR_MOD(y-1, sy);
        } else {
! 	py = AIR_MIN(y+1, sy-1);
! 	my = AIR_MAX(y-1, 0);
        }
!       for (x = 0; x < sx; x++) {
  	if (task->actx->wrap) {
! 	  px = AIR_MOD(x+1, sx);
! 	  mx = AIR_MOD(x-1, sx);
! 	} else {
! 	  px = AIR_MIN(x+1, sx-1);
! 	  mx = AIR_MAX(x-1, 0);
! 	}
! 	idx = x + sx*(y);
! 	ten = tendata + 4*(x + sx*(y));
! 	A = lev0[0 + 2*idx];
! 	B = lev0[1 + 2*idx];
! 	speed = parm[0 + 3*idx];
! 	alpha = parm[1 + 3*idx];
! 	beta = parm[2 + 3*idx];
! 	v[1] = lev0 + 2*( x + sx*(my));
! 	v[3] = lev0 + 2*(mx + sx*( y));
! 	v[5] = lev0 + 2*(px + sx*( y));
! 	v[7] = lev0 + 2*( x + sx*(py));
! 	if (tendata) {
! 	  /*
! 	  **  0 1 2    Dxy/2          Dyy        -Dxy/2
! 	  **  3 4 5     Dxx     -2*(Dxx + Dyy)     Dxx
! 	  **  6 7 8   -Dxy/2          Dyy         Dxy/2
! 	  */
! 	  v[0] = lev0 + 2*(mx + sx*(my));
! 	  v[2] = lev0 + 2*(px + sx*(my));
! 	  v[6] = lev0 + 2*(mx + sx*(py));
! 	  v[8] = lev0 + 2*(px + sx*(py));
! 	  Dxx = ten[1];
! 	  Dxy = ten[2];
! 	  Dyy = ten[3];
! 	  lapA = (Dxy*(v[0][0] + v[8][0] - v[2][0] - v[6][0])/2
! 		  + Dxx*(v[3][0] + v[5][0]) + Dyy*(v[1][0] + v[7][0])
! 		  - 2*(Dxx + Dyy)*A);
! 	  lapB = (Dxy*(v[0][1] + v[8][1] - v[2][1] - v[6][1])/2
! 		  + Dxx*(v[3][1] + v[5][1]) + Dyy*(v[1][1] + v[7][1])
! 		  - 2*(Dxx + Dyy)*B);
! 	  react = ten[0];
  	} else {
! 	  lapA = v[1][0] + v[3][0] + v[5][0] + v[7][0] - 4*A;
! 	  lapB = v[1][1] + v[3][1] + v[5][1] + v[7][1] - 4*B;
! 	  react = 1;
! 	}
! 	
! 	deltaA = speed*(react*task->actx->K*(alpha - A*B) + diffA*lapA);
! 	if (AIR_ABS(deltaA) > task->actx->maxPixelChange) {
! 	  stop = alanStopDiverged;
  	}
! 	change += AIR_ABS(deltaA);
! 	deltaB = speed*(react*task->actx->K*(A*B - B - beta) + diffB*lapB);
! 	if (!( AIR_EXISTS(deltaA) && AIR_EXISTS(deltaB) )) {
! 	  stop = alanStopNonExist;
  	}
- 	
- 	A += deltaA;
- 	B = AIR_MAX(0, B + deltaB);
- 	lev1[0 + 2*idx] = A;
- 	lev1[1 + 2*idx] = B; 
        }
      }
! 
      /* add change to global sum in a threadsafe way */
      airThreadMutexLock(task->actx->changeMutex);
!     task->actx->averageChange += change/(sx*sy);
      task->actx->changeCount += 1;
      if (task->actx->changeCount == task->actx->numThreads) {
--- 257,380 ----
      stop = alanStopNot;
      change = 0;
!     for (z = startZ; z < endZ; z++) {
        if (task->actx->wrap) {
! 	pz = AIR_MOD(z+1, sz);
! 	mz = AIR_MOD(z-1, sz);
        } else {
! 	pz = AIR_MIN(z+1, sz-1);
! 	mz = AIR_MAX(z-1, 0);
        }
!       for (y = startY; y < endY; y++) {
  	if (task->actx->wrap) {
! 	  py = AIR_MOD(y+1, sy);
! 	  my = AIR_MOD(y-1, sy);
  	} else {
! 	  py = AIR_MIN(y+1, sy-1);
! 	  my = AIR_MAX(y-1, 0);
  	}
! 	for (x = 0; x < sx; x++) {
! 	  if (task->actx->wrap) {
! 	    px = AIR_MOD(x+1, sx);
! 	    mx = AIR_MOD(x-1, sx);
! 	  } else {
! 	    px = AIR_MIN(x+1, sx-1);
! 	    mx = AIR_MAX(x-1, 0);
! 	  }
! 	  idx = x + sx*(y + sy*z);
! 	  A = lev0[0 + 2*idx];
! 	  B = lev0[1 + 2*idx];
! 	  deltaT = parm[0 + 3*idx];
! 	  alpha = parm[1 + 3*idx];
! 	  beta = parm[2 + 3*idx];
! 	  if (2 == dim) {
! 	    /*
! 	    **  0 1 2 ----> X
! 	    **  3 4 5
! 	    **  6 7 8
!             **  |
! 	    **  v Y
! 	    */
! 	    v[1] = lev0 + 2*( x + sx*(my));
! 	    v[3] = lev0 + 2*(mx + sx*( y));
! 	    v[5] = lev0 + 2*(px + sx*( y));
! 	    v[7] = lev0 + 2*( x + sx*(py));
! 	    if (tendata) {
! 	      ten = tendata + 4*(x + sx*(y));
! 	      /*
! 	      **  0 1 2    Dxy/2          Dyy        -Dxy/2
! 	      **  3 4 5     Dxx     -2*(Dxx + Dyy)     Dxx
! 	      **  6 7 8   -Dxy/2          Dyy         Dxy/2
! 	      */
! 	      v[0] = lev0 + 2*(mx + sx*(my));
! 	      v[2] = lev0 + 2*(px + sx*(my));
! 	      v[6] = lev0 + 2*(mx + sx*(py));
! 	      v[8] = lev0 + 2*(px + sx*(py));
! 	      Dxx = ten[1];
! 	      Dxy = ten[2];
! 	      Dyy = ten[3];
! 	      lapA = (Dxy*(v[0][0] + v[8][0] - v[2][0] - v[6][0])/2
! 		      + Dxx*(v[3][0] + v[5][0]) + Dyy*(v[1][0] + v[7][0])
! 		      - 2*(Dxx + Dyy)*A);
! 	      lapB = (Dxy*(v[0][1] + v[8][1] - v[2][1] - v[6][1])/2
! 		      + Dxx*(v[3][1] + v[5][1]) + Dyy*(v[1][1] + v[7][1])
! 		      - 2*(Dxx + Dyy)*B);
! 	      react = ten[0];
! 	    } else {
! 	      lapA = v[1][0] + v[3][0] + v[5][0] + v[7][0] - 4*A;
! 	      lapB = v[1][1] + v[3][1] + v[5][1] + v[7][1] - 4*B;
! 	      react = 1;
! 	    }
! 	  } else {
! 	    /* 3 == dim */
! 	    /*
! 	    **          0   1   2   ---- X
! 	    **        3   4   5
! 	    **      6   7   8
! 	    **    /
! 	    **  /       9  10  11
! 	    ** Y     12  13  14
! 	    **     15  16  17
! 	    **
! 	    **         18  19  20
! 	    **       21  22  23
! 	    **     24  25  26
! 	    **         |
! 	    **         |
! 	    **         Z
! 	    */
! 	    v[ 4] = lev0 + 2*( x + sx*( y + sy*(mz)));
! 	    v[10] = lev0 + 2*( x + sx*(my + sy*( z)));
! 	    v[12] = lev0 + 2*(mx + sx*( y + sy*( z)));
! 	    v[14] = lev0 + 2*(px + sx*( y + sy*( z)));
! 	    v[16] = lev0 + 2*( x + sx*(py + sy*( z)));
! 	    v[22] = lev0 + 2*( x + sx*( y + sy*(pz)));
! 	    lapA = (v[ 4][0] + v[10][0] + v[12][0]
! 		    + v[14][0] + v[16][0] + v[22][0] - 6*A);
! 	    lapB = (v[ 4][1] + v[10][1] + v[12][1]
! 		    + v[14][1] + v[16][1] + v[22][1] - 6*B);
! 	    react = 1;
! 	  }
! 	  
! 	  deltaA = deltaT*(react*task->actx->K*(alpha - A*B) + diffA*lapA);
! 	  if (AIR_ABS(deltaA) > task->actx->maxPixelChange) {
! 	    stop = alanStopDiverged;
! 	  }
! 	  change += AIR_ABS(deltaA);
! 	  deltaB = deltaT*(react*task->actx->K*(A*B - B - beta) + diffB*lapB);
! 	  if (!( AIR_EXISTS(deltaA) && AIR_EXISTS(deltaB) )) {
! 	    stop = alanStopNonExist;
! 	  }
! 	  
! 	  A += deltaA;
! 	  B = AIR_MAX(0, B + deltaB);
! 	  lev1[0 + 2*idx] = A;
! 	  lev1[1 + 2*idx] = B; 
  	}
        }
      }
!     
      /* add change to global sum in a threadsafe way */
      airThreadMutexLock(task->actx->changeMutex);
!     task->actx->averageChange += change/(sx*sy*sz);
      task->actx->changeCount += 1;
      if (task->actx->changeCount == task->actx->numThreads) {
***************
*** 378,382 ****
      task[tid].idx = tid;
      task[tid].thread = airThreadNew();
!     airThreadStart(task[tid].thread, _alanTuring2DWorker,
  		   (void *)&(task[tid]));
    }
--- 442,446 ----
      task[tid].idx = tid;
      task[tid].thread = airThreadNew();
!     airThreadStart(task[tid].thread, _alanTuringWorker,
  		   (void *)&(task[tid]));
    }

Index: methodsAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/methodsAlan.c,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** methodsAlan.c	7 Jan 2004 15:34:27 -0000	1.11
--- methodsAlan.c	26 Jul 2004 07:26:03 -0000	1.12
***************
*** 44,48 ****
      actx->alpha = 16;
      actx->beta = 12;
!     actx->speed = 1.0;
      actx->initA = actx->initB = 0;
      actx->diffA = actx->diffB = 0;
--- 44,48 ----
      actx->alpha = 16;
      actx->beta = 12;
!     actx->deltaT = 1.0;
      actx->initA = actx->initB = 0;
      actx->diffA = actx->diffB = 0;
***************
*** 257,262 ****
      actx->constFilename = parmI;
      break;
!   case alanParmSpeed:
!     actx->speed = parm;
      break;
    case alanParmDiffA:
--- 257,262 ----
      actx->constFilename = parmI;
      break;
!   case alanParmDeltaT:
!     actx->deltaT = parm;
      break;
    case alanParmDiffA:

Index: alan.h
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/alan.h,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** alan.h	19 Feb 2004 03:44:08 -0000	1.12
--- alan.h	26 Jul 2004 07:26:03 -0000	1.13
***************
*** 52,56 ****
    alanParmMaxIteration,
    alanParmRandRange,
!   alanParmSpeed,
    alanParmDiffA,
    alanParmDiffB,
--- 52,56 ----
    alanParmMaxIteration,
    alanParmRandRange,
!   alanParmDeltaT,
    alanParmDiffA,
    alanParmDiffB,
***************
*** 113,117 ****
  			 this is exceeded */
      alpha, beta,      /* variables for turing */
!     speed,            /* euler integration step size */
      initA, initB,     /* initial (constant) values for each morphogen */
      diffA, diffB,     /* base diffusion rates for each morphogen */
--- 113,117 ----
  			 this is exceeded */
      alpha, beta,      /* variables for turing */
!     deltaT,           /* euler integration step size */
      initA, initB,     /* initial (constant) values for each morphogen */
      diffA, diffB,     /* base diffusion rates for each morphogen */

[Teem-commit] teem/src/unrrdu 1op.c,1.19,1.20

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2425/unrrdu

Modified Files:
	1op.c 
Log Message:
added usage note about log base 2, which has always been there

Index: 1op.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/1op.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** 1op.c	12 May 2004 21:30:04 -0000	1.19
--- 1op.c	26 Jul 2004 01:22:04 -0000	1.20
***************
*** 39,42 ****
--- 39,43 ----
  	     "same as in C\n "
  	     "\b\bo \"exp\", \"log\", \"log10\", \"log1p\": same as in C\n "
+ 	     "\b\bo \"log2\": log base 2\n "
  	     "\b\bo \"sqrt\", \"cbrt\", \"ceil\", \"floor\": same as in C\n "
  	     "\b\bo \"erf\": error function (integral of Gaussian)\n "

[Teem-commit] teem/src/nrrd nrrdEnums.h,1.47,1.48 enumsNrrd.c,1.36,1.37 arith.c,1.36,1.37

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2342/nrrd

Modified Files:
	nrrdEnums.h enumsNrrd.c arith.c 
Log Message:
added signed exponentiation

Index: arith.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/arith.c,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** arith.c	12 May 2004 10:05:56 -0000	1.36
--- arith.c	26 Jul 2004 01:21:19 -0000	1.37
***************
*** 229,232 ****
--- 229,233 ----
  double _nrrdBinaryOpDivide(double a, double b)    {return a / b;}
  double _nrrdBinaryOpPow(double a, double b)       {return pow(a,b);}
+ double _nrrdBinaryOpSgnPow(double a, double b)    {return airSgnPow(a,b);}
  double _nrrdBinaryOpMod(double a, double b) {
    return AIR_MOD((int)a,(int)b);}
***************
*** 253,256 ****
--- 254,258 ----
    _nrrdBinaryOpDivide,
    _nrrdBinaryOpPow,
+   _nrrdBinaryOpSgnPow,
    _nrrdBinaryOpMod,
    _nrrdBinaryOpFmod,

Index: nrrdEnums.h
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/nrrdEnums.h,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** nrrdEnums.h	23 Jun 2004 01:43:46 -0000	1.47
--- nrrdEnums.h	26 Jul 2004 01:21:19 -0000	1.48
***************
*** 429,448 ****
    nrrdBinaryOpDivide,     /*  4 */
    nrrdBinaryOpPow,        /*  5 */
!   nrrdBinaryOpMod,        /*  6 */
!   nrrdBinaryOpFmod,       /*  7 */
!   nrrdBinaryOpAtan2,      /*  8 */
!   nrrdBinaryOpMin,        /*  9 */
!   nrrdBinaryOpMax,        /* 10 */
!   nrrdBinaryOpLT,         /* 11 */
!   nrrdBinaryOpLTE,        /* 12 */
!   nrrdBinaryOpGT,         /* 13 */
!   nrrdBinaryOpGTE,        /* 14 */
!   nrrdBinaryOpCompare,    /* 15 */
!   nrrdBinaryOpEqual,      /* 16 */
!   nrrdBinaryOpNotEqual,   /* 17 */
!   nrrdBinaryOpExists,     /* 18 */
    nrrdBinaryOpLast
  };
! #define NRRD_BINARY_OP_MAX   18
  
  /*
--- 429,449 ----
    nrrdBinaryOpDivide,     /*  4 */
    nrrdBinaryOpPow,        /*  5 */
!   nrrdBinaryOpSgnPow,     /*  6 */
!   nrrdBinaryOpMod,        /*  7 */
!   nrrdBinaryOpFmod,       /*  8 */
!   nrrdBinaryOpAtan2,      /*  9 */
!   nrrdBinaryOpMin,        /* 10 */
!   nrrdBinaryOpMax,        /* 11 */
!   nrrdBinaryOpLT,         /* 12 */
!   nrrdBinaryOpLTE,        /* 13 */
!   nrrdBinaryOpGT,         /* 14 */
!   nrrdBinaryOpGTE,        /* 15 */
!   nrrdBinaryOpCompare,    /* 16 */
!   nrrdBinaryOpEqual,      /* 17 */
!   nrrdBinaryOpNotEqual,   /* 18 */
!   nrrdBinaryOpExists,     /* 19 */
    nrrdBinaryOpLast
  };
! #define NRRD_BINARY_OP_MAX   19
  
  /*

Index: enumsNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/enumsNrrd.c,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** enumsNrrd.c	23 Jun 2004 01:42:14 -0000	1.36
--- enumsNrrd.c	26 Jul 2004 01:21:19 -0000	1.37
***************
*** 854,857 ****
--- 854,858 ----
    "/",
    "^",
+   "spow",
    "%",
    "fmod",
***************
*** 877,880 ****
--- 878,882 ----
    "divide",
    "power",
+   "signed power",
    "integer modulo",
    "fractional modulo",
***************
*** 897,900 ****
--- 899,903 ----
  #define nbDiv nrrdBinaryOpDivide
  #define nbPow nrrdBinaryOpPow
+ #define nbSpw nrrdBinaryOpSgnPow
  #define nbMod nrrdBinaryOpMod
  #define nbFmd nrrdBinaryOpFmod
***************
*** 918,921 ****
--- 921,925 ----
    "/", "divide", "quotient",
    "^", "pow", "power",
+   "spow", "sgnpow", "sgnpower",
    "%", "mod", "modulo",
    "fmod",
***************
*** 941,944 ****
--- 945,949 ----
    nbDiv, nbDiv, nbDiv, 
    nbPow, nbPow, nbPow,
+   nbSpw, nbSpw, nbSpw,
    nbMod, nbMod, nbMod, 
    nbFmd,

[Teem-commit] teem/src/unrrdu 2op.c,1.23,1.24

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2342/unrrdu

Modified Files:
	2op.c 
Log Message:
added signed exponentiation

Index: 2op.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/2op.c,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** 2op.c	7 Jan 2004 15:34:31 -0000	1.23
--- 2op.c	26 Jul 2004 01:21:18 -0000	1.24
***************
*** 43,46 ****
--- 43,47 ----
  	     "add, subtract, multiply, divide\n "
  	     "\b\bo \"^\": exponentiation (pow)\n "
+ 	     "\b\bo \"spow\": signed exponentiation: sgn(x)pow(abs(x),p)\n "
  	     "\b\bo \"%\": integer modulo\n "
  	     "\b\bo \"fmod\": same as fmod() in C\n "

[Teem-commit] NrrdIO biffbiff.c,1.2,1.3 encodingHex.c,1.2,1.3 enum.c,1.3,1.4 methodsNrrd.c,1.2,1.3 parseNrrd.c,1.2,1.3 simple.c,1.3,1.4 string.c,1.2,1.3

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

Update of /cvsroot/teem/NrrdIO
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20043

Modified Files:
	biffbiff.c encodingHex.c enum.c methodsNrrd.c parseNrrd.c 
	simple.c string.c 
Log Message:
fixing warnings

Index: methodsNrrd.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/methodsNrrd.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** methodsNrrd.c	26 May 2004 12:52:21 -0000	1.2
--- methodsNrrd.c	13 Jul 2004 21:41:45 -0000	1.3
***************
*** 93,97 ****
    nio->dataFN = airFree(nio->dataFN);
    nio->line = airFree(nio->line);
!   nio = airFree(nio);
    /* the NrrdIoState never owned nio->oldData; we don't free it */
    return NULL;
--- 93,97 ----
    nio->dataFN = airFree(nio->dataFN);
    nio->line = airFree(nio->line);
!   airFree(nio);  /* no NULL assignment, else compile warnings */
    /* the NrrdIoState never owned nio->oldData; we don't free it */
    return NULL;
***************
*** 210,214 ****
      nrrdKeyValueClear(nrrd);
      nrrd->kvpArr = airArrayNix(nrrd->kvpArr);
!     nrrd = airFree(nrrd);
    }
    return NULL;
--- 210,214 ----
      nrrdKeyValueClear(nrrd);
      nrrd->kvpArr = airArrayNix(nrrd->kvpArr);
!     airFree(nrrd);  /* no NULL assignment, else compile warnings */
    }
    return NULL;

Index: enum.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/enum.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** enum.c	26 May 2004 12:52:21 -0000	1.3
--- enum.c	13 Jul 2004 21:41:45 -0000	1.4
***************
*** 80,84 ****
  char *
  airEnumStr(airEnum *enm, int val) {
!   int idx = 0;
  
    idx = _airEnumIndex(enm, val);
--- 80,84 ----
  char *
  airEnumStr(airEnum *enm, int val) {
!   int idx;
  
    idx = _airEnumIndex(enm, val);
***************
*** 88,92 ****
  char *
  airEnumDesc(airEnum *enm, int val) {
!   int idx = 0;
  
    idx = _airEnumIndex(enm, val);
--- 88,92 ----
  char *
  airEnumDesc(airEnum *enm, int val) {
!   int idx;
  
    idx = _airEnumIndex(enm, val);

Index: simple.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/simple.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** simple.c	26 May 2004 13:10:19 -0000	1.3
--- simple.c	13 Jul 2004 21:41:45 -0000	1.4
***************
*** 129,133 ****
    sprintf(nout->content, "%s(%s%s%s)", func, content,
  	  airStrlen(buff) ? "," : "", buff);
!   buff = airFree(buff);
    return 0;
  }
--- 129,133 ----
    sprintf(nout->content, "%s(%s%s%s)", func, content,
  	  airStrlen(buff) ? "," : "", buff);
!   airFree(buff);  /* no NULL assignment, else compile warnings */
    return 0;
  }

Index: biffbiff.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/biffbiff.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** biffbiff.c	26 May 2004 12:52:21 -0000	1.2
--- biffbiff.c	13 Jul 2004 21:41:45 -0000	1.3
***************
*** 322,326 ****
  biffGet(const char *key) {
    int i, max, len, sum;
!   char me[] = "biffGet", *ret = NULL, *buf;
    _biffEntry *e;
  
--- 322,326 ----
  biffGet(const char *key) {
    int i, max, len, sum;
!   char me[] = "biffGet", *ret, *buf;
    _biffEntry *e;
  
***************
*** 356,360 ****
      strcat(ret, buf);
    }
!   free(buf);
  
    return(ret);
--- 356,360 ----
      strcat(ret, buf);
    }
!   free(buf); /* no NULL assignment, else compile warnings */
  
    return(ret);

Index: string.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/string.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** string.c	26 May 2004 12:52:21 -0000	1.2
--- string.c	13 Jul 2004 21:41:45 -0000	1.3
***************
*** 143,147 ****
        t = airStrtok(NULL, ct, &l);
      }
!     s = airFree(s);
    }
    return n;
--- 143,147 ----
        t = airStrtok(NULL, ct, &l);
      }
!     airFree(s);  /* no NULL assignment to s, else compile warnings */
    }
    return n;

Index: parseNrrd.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/parseNrrd.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** parseNrrd.c	26 May 2004 12:52:21 -0000	1.2
--- parseNrrd.c	13 Jul 2004 21:41:45 -0000	1.3
***************
*** 645,649 ****
    char me[]="_nrrdReadNrrdParseField", err[AIR_STRLEN_MED], *next,
      *buff, *colon, *keysep;
!   int fld=nrrdField_unknown, noField=AIR_FALSE, badField=AIR_FALSE;
    
    next = nio->line + nio->pos;
--- 645,649 ----
    char me[]="_nrrdReadNrrdParseField", err[AIR_STRLEN_MED], *next,
      *buff, *colon, *keysep;
!   int fld=nrrdField_unknown, noField, badField=AIR_FALSE;
    
    next = nio->line + nio->pos;

Index: encodingHex.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/encodingHex.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** encodingHex.c	26 May 2004 12:52:21 -0000	1.2
--- encodingHex.c	13 Jul 2004 21:41:45 -0000	1.3
***************
*** 85,89 ****
    nibIdx = 0;
    nibNum = 2*nrrdElementNumber(nrrd)*nrrdElementSize(nrrd);
!   if (nibNum/nrrdElementNumber(nrrd) != 2*nrrdElementSize(nrrd)) {
      sprintf(err, "%s: size_t can't hold 2*(#bytes in array)\n", me);
      biffAdd(NRRD, err); return 1;
--- 85,89 ----
    nibIdx = 0;
    nibNum = 2*nrrdElementNumber(nrrd)*nrrdElementSize(nrrd);
!   if (nibNum/nrrdElementNumber(nrrd) != (size_t)(2*nrrdElementSize(nrrd))) {
      sprintf(err, "%s: size_t can't hold 2*(#bytes in array)\n", me);
      biffAdd(NRRD, err); return 1;

[Teem-commit] teem/src/air enum.c,1.7,1.8 string.c,1.8,1.9

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

Update of /cvsroot/teem/teem/src/air
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19641/air

Modified Files:
	enum.c string.c 
Log Message:
fixing warnings in NrrdIO-related code

Index: enum.c
===================================================================
RCS file: /cvsroot/teem/teem/src/air/enum.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** enum.c	13 Feb 2004 03:40:58 -0000	1.7
--- enum.c	13 Jul 2004 21:40:20 -0000	1.8
***************
*** 69,73 ****
  char *
  airEnumStr(airEnum *enm, int val) {
!   int idx = 0;
  
    idx = _airEnumIndex(enm, val);
--- 69,73 ----
  char *
  airEnumStr(airEnum *enm, int val) {
!   int idx;
  
    idx = _airEnumIndex(enm, val);
***************
*** 77,81 ****
  char *
  airEnumDesc(airEnum *enm, int val) {
!   int idx = 0;
  
    idx = _airEnumIndex(enm, val);
--- 77,81 ----
  char *
  airEnumDesc(airEnum *enm, int val) {
!   int idx;
  
    idx = _airEnumIndex(enm, val);

Index: string.c
===================================================================
RCS file: /cvsroot/teem/teem/src/air/string.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** string.c	13 Mar 2004 20:03:08 -0000	1.8
--- string.c	13 Jul 2004 21:40:20 -0000	1.9
***************
*** 132,136 ****
        t = airStrtok(NULL, ct, &l);
      }
!     s = airFree(s);
    }
    return n;
--- 132,136 ----
        t = airStrtok(NULL, ct, &l);
      }
!     airFree(s);  /* no NULL assignment to s, else compile warnings */
    }
    return n;

[Teem-commit] teem/src/nrrd encodingHex.c,1.6,1.7 methodsNrrd.c,1.43,1.44 parseNrrd.c,1.22,1.23 simple.c,1.61,1.62

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19641/nrrd

Modified Files:
	encodingHex.c methodsNrrd.c parseNrrd.c simple.c 
Log Message:
fixing warnings in NrrdIO-related code

Index: parseNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/parseNrrd.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** parseNrrd.c	30 Mar 2004 19:25:09 -0000	1.22
--- parseNrrd.c	13 Jul 2004 21:40:21 -0000	1.23
***************
*** 634,638 ****
    char me[]="_nrrdReadNrrdParseField", err[AIR_STRLEN_MED], *next,
      *buff, *colon, *keysep;
!   int fld=nrrdField_unknown, noField=AIR_FALSE, badField=AIR_FALSE;
    
    next = nio->line + nio->pos;
--- 634,638 ----
    char me[]="_nrrdReadNrrdParseField", err[AIR_STRLEN_MED], *next,
      *buff, *colon, *keysep;
!   int fld=nrrdField_unknown, noField, badField=AIR_FALSE;
    
    next = nio->line + nio->pos;

Index: encodingHex.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/encodingHex.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** encodingHex.c	7 Jan 2004 15:34:30 -0000	1.6
--- encodingHex.c	13 Jul 2004 21:40:21 -0000	1.7
***************
*** 74,78 ****
    nibIdx = 0;
    nibNum = 2*nrrdElementNumber(nrrd)*nrrdElementSize(nrrd);
!   if (nibNum/nrrdElementNumber(nrrd) != 2*nrrdElementSize(nrrd)) {
      sprintf(err, "%s: size_t can't hold 2*(#bytes in array)\n", me);
      biffAdd(NRRD, err); return 1;
--- 74,78 ----
    nibIdx = 0;
    nibNum = 2*nrrdElementNumber(nrrd)*nrrdElementSize(nrrd);
!   if (nibNum/nrrdElementNumber(nrrd) != (size_t)(2*nrrdElementSize(nrrd))) {
      sprintf(err, "%s: size_t can't hold 2*(#bytes in array)\n", me);
      biffAdd(NRRD, err); return 1;

Index: methodsNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/methodsNrrd.c,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -d -r1.43 -r1.44
*** methodsNrrd.c	25 May 2004 15:41:52 -0000	1.43
--- methodsNrrd.c	13 Jul 2004 21:40:21 -0000	1.44
***************
*** 82,86 ****
    nio->dataFN = airFree(nio->dataFN);
    nio->line = airFree(nio->line);
!   nio = airFree(nio);
    /* the NrrdIoState never owned nio->oldData; we don't free it */
    return NULL;
--- 82,86 ----
    nio->dataFN = airFree(nio->dataFN);
    nio->line = airFree(nio->line);
!   airFree(nio);  /* no NULL assignment, else compile warnings */
    /* the NrrdIoState never owned nio->oldData; we don't free it */
    return NULL;
***************
*** 293,297 ****
      nrrdKeyValueClear(nrrd);
      nrrd->kvpArr = airArrayNix(nrrd->kvpArr);
!     nrrd = airFree(nrrd);
    }
    return NULL;
--- 293,297 ----
      nrrdKeyValueClear(nrrd);
      nrrd->kvpArr = airArrayNix(nrrd->kvpArr);
!     airFree(nrrd);  /* no NULL assignment, else compile warnings */
    }
    return NULL;

Index: simple.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/simple.c,v
retrieving revision 1.61
retrieving revision 1.62
diff -C2 -d -r1.61 -r1.62
*** simple.c	26 May 2004 13:09:32 -0000	1.61
--- simple.c	13 Jul 2004 21:40:21 -0000	1.62
***************
*** 118,122 ****
    sprintf(nout->content, "%s(%s%s%s)", func, content,
  	  airStrlen(buff) ? "," : "", buff);
!   buff = airFree(buff);
    return 0;
  }
--- 118,122 ----
    sprintf(nout->content, "%s(%s%s%s)", func, content,
  	  airStrlen(buff) ? "," : "", buff);
!   airFree(buff);  /* no NULL assignment, else compile warnings */
    return 0;
  }

[Teem-commit] teem/src/biff biffbiff.c,1.2,1.3

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

Update of /cvsroot/teem/teem/src/biff
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19641/biff

Modified Files:
	biffbiff.c 
Log Message:
fixing warnings in NrrdIO-related code

Index: biffbiff.c
===================================================================
RCS file: /cvsroot/teem/teem/src/biff/biffbiff.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** biffbiff.c	7 Jan 2004 15:34:28 -0000	1.2
--- biffbiff.c	13 Jul 2004 21:40:21 -0000	1.3
***************
*** 311,315 ****
  biffGet(const char *key) {
    int i, max, len, sum;
!   char me[] = "biffGet", *ret = NULL, *buf;
    _biffEntry *e;
  
--- 311,315 ----
  biffGet(const char *key) {
    int i, max, len, sum;
!   char me[] = "biffGet", *ret, *buf;
    _biffEntry *e;
  
***************
*** 345,349 ****
      strcat(ret, buf);
    }
!   free(buf);
  
    return(ret);
--- 345,349 ----
      strcat(ret, buf);
    }
!   free(buf); /* no NULL assignment, else compile warnings */
  
    return(ret);

[Teem-commit] teem/src/ell/test wheel.c,1.3,1.4

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

Update of /cvsroot/teem/teem/src/ell/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19417

Modified Files:
	wheel.c 
Log Message:
more options, hooray

Index: wheel.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/test/wheel.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** wheel.c	23 Jun 2004 01:45:05 -0000	1.3
--- wheel.c	13 Jul 2004 21:39:09 -0000	1.4
***************
*** 216,220 ****
    airArray *mop;
    
!   double tval[6], ABC[3], geom[3], xroot[3], yroot[3], bbox[4], psc;
    wheelPS wps;
    int correct, labels;
--- 216,220 ----
    airArray *mop;
    
!   double tval[6], ABC[3], geom[3], xroot[3], yroot[3], bbox[4], htick, psc;
    wheelPS wps;
    int correct, labels;
***************
*** 240,243 ****
--- 240,245 ----
    hestOptAdd(&hopt, "labels", NULL, airTypeInt, 0, 0, &labels, NULL,
  	     "put little labels on things; fix with psfrag in LaTeX");
+   hestOptAdd(&hopt, "htick", "pos", airTypeDouble, 1, 1, &htick, "nan",
+ 	     "location of single tick mark on horizontal axis");
    hestOptAdd(&hopt, "bb", "bbox", airTypeDouble, 4, 4, bbox, 
  	     "nan nan nan nan", "bounding box, in world space around the "
***************
*** 344,347 ****
--- 346,354 ----
    wheelLine(&wps, xroot[1], -0.02*geom[1], xroot[1], 0.02*geom[1]);
    wheelLine(&wps, xroot[2], -0.02*geom[1], xroot[2], 0.02*geom[1]);
+   if (AIR_EXISTS(htick)) {
+     wheelWidth(&wps, 10);
+     wheelLine(&wps, htick, -0.04, htick, 0.04);
+   }
+ 
  
    /* labels, if wanted */

[Teem-commit] NrrdIO enumsNrrd.c,1.2,1.3 sane.c,1.3,1.4

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

Update of /cvsroot/teem/NrrdIO
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7720

Modified Files:
	enumsNrrd.c sane.c 
Log Message:
new sanity checks for nan, and fixes for nrrd kinds

Index: sane.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/sane.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** sane.c	26 May 2004 12:52:21 -0000	1.3
--- sane.c	30 Jun 2004 17:18:38 -0000	1.4
***************
*** 40,44 ****
  int
  airSanity(void) {
!   double nan, pinf, ninf;
    float nanF, pinfF, ninfF;
    int tmpI, sign, exp, frac, size;
--- 40,44 ----
  int
  airSanity(void) {
!   double nan, pinf, ninf, pzero;
    float nanF, pinfF, ninfF;
    int tmpI, sign, exp, frac, size;
***************
*** 90,94 ****
      return airInsane_nInfExists;
    }
!   nan = pinf/pinf;
    if (AIR_EXISTS(nan)) {
      return airInsane_NaNExists;
--- 90,95 ----
      return airInsane_nInfExists;
    }
!   pzero = 0.0;
!   nan = pzero/pzero;
    if (AIR_EXISTS(nan)) {
      return airInsane_NaNExists;

Index: enumsNrrd.c
===================================================================
RCS file: /cvsroot/teem/NrrdIO/enumsNrrd.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** enumsNrrd.c	26 May 2004 12:52:21 -0000	1.2
--- enumsNrrd.c	30 Jun 2004 17:18:38 -0000	1.3
***************
*** 360,377 ****
    "scalar",
    "complex",
!   "2-vector", "2vector",
!   "3-color", "3color",
!   "4-color", "4color",
!   "3-vector", "3vector",
!   "3-normal", "3normal",
!   "4-vector", "4vector",
!   "2D-sym-tensor", "2Dsymtensor",
!   "2D-mask-sym-tensor", "2Dmasksymtensor",
!   "2D-tensor", "2Dtensor",
!   "2D-mask-tensor", "2Dmasktensor",
!   "3D-sym-tensor", "3Dsymtensor", "6-tensor",
!   "3D-mask-sym-tensor", "3Dmasksymtensor", "7-tensor",
!   "3D-tensor", "3Dtensor", "9-tensor",
!   "3D-mask-tensor", "3Dmasktensor",
    ""
  };
--- 360,377 ----
    "scalar",
    "complex",
!   "2-vector",
!   "3-color",
!   "4-color",
!   "3-vector",
!   "3-normal",
!   "4-vector",
!   "2D-symmetric-tensor", "2D-sym-tensor",
!   "2D-masked-symmetric-tensor", "2D-masked-sym-tensor",
!   "2D-tensor",
!   "2D-masked-tensor",
!   "3D-symmetric-tensor", "3D-sym-tensor",
!   "3D-masked-symmetric-tensor", "3D-masked-sym-tensor",
!   "3D-tensor",
!   "3D-masked-tensor",
    ""
  };
***************
*** 385,402 ****
    nrrdKindComplex,
    nrrdKind2Vector,
!   nrrdKind3Color, nrrdKind3Color,
!   nrrdKind4Color, nrrdKind4Color,
!   nrrdKind3Vector, nrrdKind3Vector,
!   nrrdKind3Normal, nrrdKind3Normal,
!   nrrdKind4Vector, nrrdKind4Vector,
    nrrdKind2DSymTensor, nrrdKind2DSymTensor,
    nrrdKind2DMaskedSymTensor, nrrdKind2DMaskedSymTensor,
!   nrrdKind2DTensor, nrrdKind2DTensor,
!   nrrdKind2DMaskedTensor, nrrdKind2DMaskedTensor,
!   nrrdKind3DSymTensor, nrrdKind3DSymTensor, nrrdKind3DSymTensor,
    nrrdKind3DMaskedSymTensor, nrrdKind3DMaskedSymTensor,
!              nrrdKind3DMaskedSymTensor,
!   nrrdKind3DTensor, nrrdKind3DTensor, nrrdKind3DTensor,
!   nrrdKind3DMaskedTensor, nrrdKind3DMaskedTensor
  };
  
--- 385,401 ----
    nrrdKindComplex,
    nrrdKind2Vector,
!   nrrdKind3Color,
!   nrrdKind4Color,
!   nrrdKind3Vector,
!   nrrdKind3Normal,
!   nrrdKind4Vector,
    nrrdKind2DSymTensor, nrrdKind2DSymTensor,
    nrrdKind2DMaskedSymTensor, nrrdKind2DMaskedSymTensor,
!   nrrdKind2DTensor,
!   nrrdKind2DMaskedTensor,
!   nrrdKind3DSymTensor, nrrdKind3DSymTensor,
    nrrdKind3DMaskedSymTensor, nrrdKind3DMaskedSymTensor,
!   nrrdKind3DTensor,
!   nrrdKind3DMaskedTensor,
  };
  

[Teem-commit] teem/src/air sane.c,1.8,1.9

[Milan I. <ik...@us...>]

Update of /cvsroot/teem/teem/src/air
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23182

Modified Files:
	sane.c 
Log Message:
switched to M#% safe qnan checking (zero/zero instead of inf/inf)

Index: sane.c
===================================================================
RCS file: /cvsroot/teem/teem/src/air/sane.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** sane.c	9 Feb 2004 06:47:50 -0000	1.8
--- sane.c	28 Jun 2004 22:24:14 -0000	1.9
***************
*** 29,33 ****
  int
  airSanity(void) {
!   double nan, pinf, ninf;
    float nanF, pinfF, ninfF;
    int tmpI, sign, exp, frac, size;
--- 29,33 ----
  int
  airSanity(void) {
!   double nan, pinf, ninf, pzero;
    float nanF, pinfF, ninfF;
    int tmpI, sign, exp, frac, size;
***************
*** 79,83 ****
      return airInsane_nInfExists;
    }
!   nan = pinf/pinf;
    if (AIR_EXISTS(nan)) {
      return airInsane_NaNExists;
--- 79,84 ----
      return airInsane_nInfExists;
    }
!   pzero = 0.0;
!   nan = pzero/pzero;
    if (AIR_EXISTS(nan)) {
      return airInsane_NaNExists;

[Teem-commit] teem/src/unrrdu make.c,1.50,1.51

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3468

Modified Files:
	make.c 
Log Message:
clarified relationship between big-vs-little endian, and most-vs-least significant byte first

Index: make.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/make.c,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** make.c	30 Mar 2004 19:25:17 -0000	1.50
--- make.c	28 Jun 2004 10:04:43 -0000	1.51
***************
*** 95,99 ****
  
    /* so that long lists of filenames can be read from file */
-   airStrtokQuoting = AIR_TRUE;
    hparm->respFileEnable = AIR_TRUE;
    hparm->greedySingleString = AIR_TRUE;
--- 95,98 ----
***************
*** 161,166 ****
  	     "Endianness of data; relevent for any data with value "
  	     "representation bigger than 8 bits, with a non-ascii encoding: "
! 	     "\"little\" for Intel and "
! 	     "friends; \"big\" for everyone else. "
  	     "Defaults to endianness of this machine",
  	     NULL, airEndian);
--- 160,166 ----
  	     "Endianness of data; relevent for any data with value "
  	     "representation bigger than 8 bits, with a non-ascii encoding: "
! 	     "\"little\" for Intel and friends "
! 	     "(least significant byte first, at lower address); "
! 	     "\"big\" for everyone else (most significant byte first). "
  	     "Defaults to endianness of this machine",
  	     NULL, airEndian);
***************
*** 175,178 ****
--- 175,179 ----
  
    USAGE(_unrrdu_makeInfoL);
+   airStrtokQuoting = AIR_TRUE;
    PARSE();
    airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);

[Teem-commit] teem/src TODO.txt,1.17,1.18

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

Update of /cvsroot/teem/teem/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17382

Modified Files:
	TODO.txt 
Log Message:
the long road ahead

Index: TODO.txt
===================================================================
RCS file: /cvsroot/teem/teem/src/TODO.txt,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** TODO.txt	26 May 2004 17:10:00 -0000	1.17
--- TODO.txt	26 Jun 2004 09:50:35 -0000	1.18
***************
*** 3,6 ****
--- 3,40 ----
  Do you see the problem?  Grrr.
  
+ PLEASE figure out why I can't say
+ 
+    -t "unsigned char"
+ 
+ to unu make, unu convert and the like.
+ Does it have to do with airStrtokQuoting?
+ Why not? I hate this crap.
+ 
+ debug rendering of ML with windowed sinc
+ 
+ add { } commenting to hest
+ 
+ have to add more internal types to stuff in arith.c for these:
+ new nrrdBinaryOps: bit-wise and (&), or (|), xor (^)
+ new nrrdUnaryOps: bit-wise not (^), expm1
+ 
+ 
+ It would be good if per-axis field specifications failed (or at least warned) if there are more fields than there should be
+ 
+ SEGFAULT:  in muse/usr/sci/data/Medical/cat-array/bisti/rend
+ gkms hvol -s a:-1200,6000 a:0,3100 a:-1000,1000 -i CFC.nrrd -o CFC-hvol.nrrd 
+ 
+ speed up nrrdCCFind
+ 
+ finish updating bane tutorial
+ make nrrdMake from guts of "unu make"
+ re-modularize gage to facilitate probing bricked data
+ 
+ nrrdKernel*Parse should allocate the thing and return it, instead of returning an int error code
+ see if dyeColorParse should do the same
+ 
+ unu jhisto works with axis[0] elements when given a single nrrd
+ 
+ 
  FAQ on teem coding standards
  Banks's policy.txt:
***************
*** 58,59 ****
--- 92,94 ----
  air:  think about implementing a fabs() and dabs() with bitmasking
  
+ nrrd: figure out some framework for lazy evaluation stuff

[Teem-commit] teem/src/limn/test plot.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/limn/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5438

Modified Files:
	plot.c 
Log Message:
great, great, more cryptic command-line options

Index: plot.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/test/plot.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** plot.c	23 Jun 2004 00:53:41 -0000	1.1
--- plot.c	26 Jun 2004 08:29:41 -0000	1.2
***************
*** 32,41 ****
  
  typedef struct {
-   double axisThick;
    /* these are allocated per-graph BY HEST */
    double *graphThick, *graphGray, *dotDiameter, *dotGray;
    /* also hest-allocated */
    char *axisHorzLabel, *axisVertLabel;
    
    double dotInnerDiameterFraction;
    double axisOrig[2];
--- 32,46 ----
  
  typedef struct {
    /* these are allocated per-graph BY HEST */
    double *graphThick, *graphGray, *dotDiameter, *dotGray;
+ 
    /* also hest-allocated */
    char *axisHorzLabel, *axisVertLabel;
+   double *horzTick, *vertTick;
    
+   int numHorzTick, numVertTick;
+   int labelHorzTick, labelVertTick;
+   double axisThick, tickThick, tickLabelSize, tickLength;
+   double horzTickLabelOffset, vertTickLabelOffset;
    double dotInnerDiameterFraction;
    double axisOrig[2];
***************
*** 101,107 ****
  void
  plotLine(plotPS *pps, plotParm *pparm,
! 	 double width, double x0, double y0, double x1, double y1) {
    
-   fprintf(pps->file, "%g W\n", pps->psc*width);
    fprintf(pps->file, "%g %g M\n", PPS_X(x0), PPS_Y(y0));
    fprintf(pps->file, "%g %g L S\n", PPS_X(x1), PPS_Y(y1));
--- 106,111 ----
  void
  plotLine(plotPS *pps, plotParm *pparm,
! 	 double x0, double y0, double x1, double y1) {
    
    fprintf(pps->file, "%g %g M\n", PPS_X(x0), PPS_Y(y0));
    fprintf(pps->file, "%g %g L S\n", PPS_X(x1), PPS_Y(y1));
***************
*** 110,117 ****
  
  void
! plotLabel(plotPS *pps, plotParm *pparm,
  	  double x, double y, char *str) {
    
!   fprintf(pps->file, "%g %g M (%s) show\n", PPS_X(x), PPS_Y(y), str);
    return;
  }
--- 114,132 ----
  
  void
! plotLabel(plotPS *pps, plotParm *pparm, int centered, 
  	  double x, double y, char *str) {
    
!   fprintf(pps->file, "gsave\n");
!   plotWidth(pps, pparm, 0);
!   if (centered) {
!     fprintf(pps->file,  
! 	    "0 0 M (%s) false charpath pathbbox\n"
! 	    "exch 4 1 roll sub 2 div 3 1 roll sub -2 div\n"  /* don't ask */
! 	    "newpath %g add exch %g add M (%s) show\n",
! 	    str, PPS_X(x), PPS_Y(y), str);
!   } else {
!     fprintf(pps->file,  "%g %g M (%s) show\n", PPS_X(x), PPS_Y(y), str);
!   }
!   fprintf(pps->file, "grestore\n");
    return;
  }
***************
*** 119,132 ****
  void
  plotAxes(plotPS *pps, plotParm *pparm, Nrrd *ndata) {
!   double axX, axY;
    
!   axX = AIR_AFFINE(ndata->axis[1].min, pparm->axisOrig[0], ndata->axis[1].max,
  		   pps->bbox[0], pps->bbox[2]);
    axY = AIR_AFFINE(pparm->dbox[1], pparm->axisOrig[1], pparm->dbox[3],
  		   pps->bbox[1], pps->bbox[3]);
    plotGray(pps, pparm, 0);
!   plotLine(pps, pparm, pparm->axisThick,
  	   axX, pps->bbox[1], axX, pps->bbox[3]);
!   plotLine(pps, pparm, pparm->axisThick,
  	   pps->bbox[0], axY, pps->bbox[2], axY);
  
--- 134,150 ----
  void
  plotAxes(plotPS *pps, plotParm *pparm, Nrrd *ndata) {
!   double axX, axY, xx, yy, toff;
!   char buff[AIR_STRLEN_SMALL];
!   int ti;
    
!   axX = AIR_AFFINE(pparm->dbox[0], pparm->axisOrig[0], pparm->dbox[2],
  		   pps->bbox[0], pps->bbox[2]);
    axY = AIR_AFFINE(pparm->dbox[1], pparm->axisOrig[1], pparm->dbox[3],
  		   pps->bbox[1], pps->bbox[3]);
    plotGray(pps, pparm, 0);
!   plotWidth(pps, pparm, pparm->axisThick);
!   plotLine(pps, pparm,
  	   axX, pps->bbox[1], axX, pps->bbox[3]);
!   plotLine(pps, pparm,
  	   pps->bbox[0], axY, pps->bbox[2], axY);
  
***************
*** 134,141 ****
      fprintf(pps->file, "/Helvetica findfont 20 scalefont setfont\n");
      if (strlen(pparm->axisHorzLabel)) {
!       plotLabel(pps, pparm, pps->bbox[2], axY, pparm->axisHorzLabel);
      }
      if (strlen(pparm->axisVertLabel)) {
!       plotLabel(pps, pparm, axX, pps->bbox[3], pparm->axisVertLabel);
      }
    }
--- 152,208 ----
      fprintf(pps->file, "/Helvetica findfont 20 scalefont setfont\n");
      if (strlen(pparm->axisHorzLabel)) {
!       plotLabel(pps, pparm, AIR_FALSE, 
! 		pps->bbox[2], axY, pparm->axisHorzLabel);
      }
      if (strlen(pparm->axisVertLabel)) {
!       plotLabel(pps, pparm, AIR_FALSE, 
! 		axX, pps->bbox[3], pparm->axisVertLabel);
!     }
!   }
! 
!   if (pparm->numHorzTick) {
!     if (pparm->tickThick > 0) {
!       toff = pparm->tickLength/2;
!       plotGray(pps, pparm, 0);
!       plotWidth(pps, pparm, pparm->tickThick);
!       for (ti=0; ti<pparm->numHorzTick; ti++) {
! 	xx = AIR_AFFINE(pparm->dbox[0], pparm->horzTick[ti], pparm->dbox[2],
! 			pps->bbox[0], pps->bbox[2]);
! 	plotLine(pps, pparm, xx, axY - toff, xx, axY + toff);
!       }
!     }
!     if (pparm->tickLabelSize) {
!       fprintf(pps->file, "/Helvetica findfont %g scalefont setfont\n",
! 	      pparm->tickLabelSize);
!       for (ti=0; ti<pparm->numHorzTick; ti++) {
! 	xx = AIR_AFFINE(pparm->dbox[0], pparm->horzTick[ti], pparm->dbox[2],
! 			pps->bbox[0], pps->bbox[2]);
! 	yy = axY + pparm->horzTickLabelOffset;
! 	sprintf(buff, "%g", pparm->horzTick[ti]);
! 	plotLabel(pps, pparm, AIR_TRUE, xx, yy, buff);
!       }
!     }
!   }
!   if (pparm->numVertTick) {
!     if (pparm->tickThick > 0) {
!       toff = pparm->tickLength/2;
!       plotGray(pps, pparm, 0);
!       plotWidth(pps, pparm, pparm->tickThick);
!       for (ti=0; ti<pparm->numVertTick; ti++) {
! 	yy = AIR_AFFINE(pparm->dbox[1], pparm->vertTick[ti], pparm->dbox[3],
! 			pps->bbox[1], pps->bbox[3]);
! 	plotLine(pps, pparm, axX - toff, yy, axX + toff, yy);
!       }
!     }
!     if (pparm->tickLabelSize) {
!       fprintf(pps->file, "/Helvetica findfont %g scalefont setfont\n",
! 	      pparm->tickLabelSize);
!       for (ti=0; ti<pparm->numVertTick; ti++) {
! 	yy = AIR_AFFINE(pparm->dbox[1], pparm->vertTick[ti], pparm->dbox[3],
! 			pps->bbox[1], pps->bbox[3]);
! 	xx = axX + pparm->vertTickLabelOffset;
! 	sprintf(buff, "%g", pparm->vertTick[ti]);
! 	plotLabel(pps, pparm, AIR_TRUE, xx, yy, buff);
!       }
      }
    }
***************
*** 179,182 ****
--- 246,250 ----
  
    fprintf(pps->file, "gsave\n");
+   fprintf(pps->file, "newpath\n");
    plotWidth(pps, pparm, 0);
    data = (double *)(ndata[nidx]->data);
***************
*** 231,264 ****
  	     "input nrrd containing data to plot",
  	     &numNrrd, NULL, nrrdHestNrrd);
!   hestOptAdd(&hopt, "dbox", "minX minY maxX maxY", airTypeDouble, 4, 4, pparm.dbox, NULL,
  	     "bounding box, in data space");
    
!   hestOptAdd(&hopt, "bbox", "minX minY maxX maxY", airTypeDouble, 4, 4, pps.bbox, NULL,
  	     "bounding box, in graph space");
    hestOptAdd(&hopt, "psc", "PS scale", airTypeDouble, 1, 1, &(pps.psc), "300",
  	     "scaling from graph space to PostScript points");
! 
!   hestOptAdd(&hopt, "grth", "graph thickness", airTypeDouble, 1, -1, &(pparm.graphThick), "0.01",
! 	     "thickness of line for graph, or \"0\" for no graph line", &numGrth);
!   hestOptAdd(&hopt, "grgr", "graph gray", airTypeDouble, 1, -1, &(pparm.graphGray), "0",
  	     "grayscale to use for graph", &numGrgr);
!   hestOptAdd(&hopt, "dtdi", "dot diameter", airTypeDouble, 1, -1, &(pparm.dotDiameter), "0.1",
! 	     "radius of dot drawn at data points, or \"0\" for no dots", &numDtdi);
!   hestOptAdd(&hopt, "dtgr", "dot gray", airTypeDouble, 1, -1, &(pparm.dotGray), "0",
  	     "grayscale to use for dots", &numDtgr);
!   hestOptAdd(&hopt, "dtid", "dot inner diam frac", airTypeDouble, 1, 1,
! 	     &(pparm.dotInnerDiameterFraction), "0.0",
  	     "fractional radius of white dot drawn within dot");
  
!   hestOptAdd(&hopt, "axth", "axis thickness", airTypeDouble, 1, 1, &(pparm.axisThick), "0.01",
  	     "thickness of lines for axes");
!   hestOptAdd(&hopt, "axor", "axis origin", airTypeDouble, 2, 2, &(pparm.axisOrig), "0 0",
  	     "origin of lines for axes, in data space");
!   hestOptAdd(&hopt, "axhl", "horiz axis label", airTypeString, 1, 1, &(pparm.axisHorzLabel), "",
  	     "label on horizontal axis");
!   hestOptAdd(&hopt, "axvl", "vert axis label", airTypeString, 1, 1, &(pparm.axisVertLabel), "",
  	     "label on vertical axis");
  
!   hestOptAdd(&hopt, "o", "output PS", airTypeString, 1, 1, &outS, "out.ps",
  	     "output file to render postscript into");
    hestParseOrDie(hopt, argc-1, argv+1, NULL,
--- 299,369 ----
  	     "input nrrd containing data to plot",
  	     &numNrrd, NULL, nrrdHestNrrd);
!   hestOptAdd(&hopt, "dbox", "minX minY maxX maxY", airTypeDouble,
! 	     4, 4, pparm.dbox, NULL,
  	     "bounding box, in data space");
    
!   hestOptAdd(&hopt, "bbox", "minX minY maxX maxY", airTypeDouble,
! 	     4, 4, pps.bbox, NULL,
  	     "bounding box, in graph space");
    hestOptAdd(&hopt, "psc", "PS scale", airTypeDouble, 1, 1, &(pps.psc), "300",
  	     "scaling from graph space to PostScript points");
!   
!   hestOptAdd(&hopt, "grth", "graph thickness", airTypeDouble,
! 	     1, -1, &(pparm.graphThick), "0.01",
! 	     "thickness of line for graph, or \"0\" for no graph line", 
! 	     &numGrth);
!   hestOptAdd(&hopt, "grgr", "graph gray", airTypeDouble,
! 	     1, -1, &(pparm.graphGray), "0",
  	     "grayscale to use for graph", &numGrgr);
!   hestOptAdd(&hopt, "dtdi", "dot diameter", airTypeDouble,
! 	     1, -1, &(pparm.dotDiameter), "0.1",
! 	     "radius of dot drawn at data points, or \"0\" for no dots",
! 	     &numDtdi);
!   hestOptAdd(&hopt, "dtgr", "dot gray", airTypeDouble,
! 	     1, -1, &(pparm.dotGray), "0",
  	     "grayscale to use for dots", &numDtgr);
!   hestOptAdd(&hopt, "dtid", "dot inner diam frac", airTypeDouble,
! 	     1, 1, &(pparm.dotInnerDiameterFraction), "0.0",
  	     "fractional radius of white dot drawn within dot");
  
!   hestOptAdd(&hopt, "tihz", "pos", airTypeDouble,
! 	     0, -1, &(pparm.horzTick), "",
! 	     "locations for tickmarks on horizontal axis",
! 	     &(pparm.numHorzTick));
!   hestOptAdd(&hopt, "tivt", "pos", airTypeDouble,
! 	     0, -1, &(pparm.vertTick), "",
! 	     "locations for tickmarks on vertical axis",
! 	     &(pparm.numVertTick));
!   hestOptAdd(&hopt, "tiho", "offset", airTypeDouble,
! 	     1, 1, &(pparm.horzTickLabelOffset), "0",
! 	     "horizontal tick label offset");
!   hestOptAdd(&hopt, "tivo", "offset", airTypeDouble,
! 	     1, 1, &(pparm.vertTickLabelOffset), "0",
! 	     "vertical tick label offset");
!   hestOptAdd(&hopt, "tils", "size", airTypeDouble,
! 	     1, 1, &(pparm.tickLabelSize), "0",
! 	     "font size for labels on tick marks, or \"0\" for no labels");
!   hestOptAdd(&hopt, "tith", "tick thickness", airTypeDouble,
! 	     1, 1, &(pparm.tickThick), "0.01",
! 	     "thickness of lines for tick marks");
!   hestOptAdd(&hopt, "tiln", "tick length", airTypeDouble,
! 	     1, 1, &(pparm.tickLength), "0.08",
! 	     "length of lines for tick marks");
! 
!   hestOptAdd(&hopt, "axth", "axis thickness", airTypeDouble,
! 	     1, 1, &(pparm.axisThick), "0.01",
  	     "thickness of lines for axes");
!   hestOptAdd(&hopt, "axor", "axis origin", airTypeDouble,
! 	     2, 2, &(pparm.axisOrig), "0 0",
  	     "origin of lines for axes, in data space");
!   hestOptAdd(&hopt, "axhl", "horiz axis label", airTypeString,
! 	     1, 1, &(pparm.axisHorzLabel), "",
  	     "label on horizontal axis");
!   hestOptAdd(&hopt, "axvl", "vert axis label", airTypeString,
! 	     1, 1, &(pparm.axisVertLabel), "",
  	     "label on vertical axis");
  
!   hestOptAdd(&hopt, "o", "output PS", airTypeString,
! 	     1, 1, &outS, "out.ps",
  	     "output file to render postscript into");
    hestParseOrDie(hopt, argc-1, argv+1, NULL,
***************
*** 285,289 ****
      if (!( (1 == _ndata[ni]->dim || 2 == _ndata[ni]->dim) 
  	   && nrrdTypeBlock != _ndata[ni]->type )) {
!       fprintf(stderr, "%s: input nrrd must be 1-D or 2-D array of scalars", me);
        airMopError(mop); return 1;
      }
--- 390,395 ----
      if (!( (1 == _ndata[ni]->dim || 2 == _ndata[ni]->dim) 
  	   && nrrdTypeBlock != _ndata[ni]->type )) {
!       fprintf(stderr, "%s: input nrrd must be 1-D or 2-D array of scalars",
! 	      me);
        airMopError(mop); return 1;
      }

[Teem-commit] teem/src/ten GNUmakefile,1.38,1.39 enumsTen.c,1.22,1.23 glyph.c,1.40,1.41 ten.h,1.86,1.87 tenGage.c,1.20,1.21 tenMacros.h,1.11,1.12 tendGlyph.c,1.31,1.32 tensor.c,1.31,1.32

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8676

Modified Files:
	GNUmakefile enumsTen.c glyph.c ten.h tenGage.c tenMacros.h 
	tendGlyph.c tensor.c 
Log Message:
phd-related hacking

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/GNUmakefile,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** GNUmakefile	27 Feb 2004 10:23:55 -0000	1.38
--- GNUmakefile	23 Jun 2004 01:46:41 -0000	1.39
***************
*** 55,59 ****
  	tendSlice.o tendEllipse.o tendEvecrgb.o tendNorm.o tendAnscale.o \
  	tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o
! $(L).TESTS = test/tg test/tt test/tem
  ####
  ####
--- 55,59 ----
  	tendSlice.o tendEllipse.o tendEvecrgb.o tendNorm.o tendAnscale.o \
  	tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o
! $(L).TESTS = test/tg test/tt test/tem test/rotedge
  ####
  ####

Index: glyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/glyph.c,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** glyph.c	26 May 2004 02:02:24 -0000	1.40
--- glyph.c	23 Jun 2004 01:46:41 -0000	1.41
***************
*** 92,95 ****
--- 92,99 ----
      biffAdd(TEN, err); return 1;
    }
+   if (!( parm->glyphScale > 0)) {
+     sprintf(err, "%s: glyphScale must be > 0 (not %g)", me, parm->glyphScale);
+     biffAdd(TEN, err); return 1;
+   }
    if (parm->nmask) {
      if (npos) {
***************
*** 254,257 ****
--- 258,265 ----
    for (idx=0; idx<numGlyphs; idx++, _idx = idx) {
      tdata = (float*)(nten->data) + 7*idx;
+     if (!( TEN_T_EXISTS(tdata) )) {
+       /* there's nothing we can do here */
+       continue;
+     }
      if (npos) {
        ELL_3V_COPY(pW, (float*)(npos->data) + 3*idx);

Index: tensor.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tensor.c,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** tensor.c	11 May 2004 02:39:54 -0000	1.31
--- tensor.c	23 Jun 2004 01:46:41 -0000	1.32
***************
*** 504,514 ****
  }
  
- void
- tenShapeGradients_d(double mean[7],
- 		    double var[7], double *varNorm,
- 		    double skew[7], double *skewNorm,
- 		    double evec[9], double eval[9], int *didEigen,
- 		    double ten[7]) {
-   double meanDot, varDot;
  #define Txx (ten[1])
  #define Txy (ten[2])
--- 504,507 ----
***************
*** 518,524 ****
  #define Tzz (ten[6])
  
!   /* 0.57735027 == 1/sqrt(3) */
    TEN_T_SET(mean, ten[0],
! 	    0.57735027, 0, 0, 
  	    0.57735027, 0, 
  	    0.57735027);
--- 511,534 ----
  #define Tzz (ten[6])
  
! /*
! ** eval and evec are given merely as space into which
! ** we may compute the eigensystem
! */
! void
! tenShapeGradients_d(double mean[7],
! 		    double var[7], double *varNorm,
! 		    double skew[7], double *skewNorm,
! 		    double eval[3], double evec[9], int *didEigen,
! 		    double ten[7]) {
!   double meanDot, varDot, dot, mev, third, matR[9],
!     matA[9], matB[9], norm, epsilon;
! 
!   /* largest allowable dot product betwen two normals */
!   epsilon = 0.00001;
! 
!   *didEigen = AIR_FALSE;
! 
    TEN_T_SET(mean, ten[0],
! 	    0.57735027, 0, 0,      /* sqrt(1/3) = 0.57735027 */
  	    0.57735027, 0, 
  	    0.57735027);
***************
*** 528,547 ****
  	    2*Tzz - Txx - Tyy);
    *varNorm = TEN_T_NORM(var);
!   if (*varNorm) {
      TEN_T_SCALE(var, 1.0/(*varNorm), var);
    }
!   TEN_T_SET(skew, ten[0],
! 	    Tyy*Tzz - Tyz*Tyz, Txz*Tyz - Txy*Tzz, Txy*Tyz - Txz*Tyy,
! 	    Txx*Tzz - Txz*Txz, Txy*Txz - Tyz*Txx,
! 	    Txx*Tyy - Txy*Txy);
!   meanDot = TEN_T_DOT(skew, mean);
!   varDot = TEN_T_DOT(skew, var);
!   TEN_T_SCALE_INCR2(skew, -meanDot, mean, -varDot, var);
!   *skewNorm = TEN_T_NORM(skew);
!   if (*skewNorm) {
!     TEN_T_SCALE(skew, 1.0/(*skewNorm), skew);
    }
    
-   *didEigen = AIR_FALSE;
    return;
  }
--- 538,679 ----
  	    2*Tzz - Txx - Tyy);
    *varNorm = TEN_T_NORM(var);
!   if (*varNorm < epsilon) {
!     /* they gave us a diagonal matrix */
!     TEN_T_SET(var, ten[0],
! 	      0, 0, 0,
! 	      0.707106781, 0,      /* sqrt(1/2) = 0.707106781 */
! 	      -0.707106781);
!     TEN_T_SET(skew, ten[0],
! 	      0.816496581, 0, 0,   /* sqrt(2/3) = 0.816496581 */
! 	      -0.408248290, 0,     /* sqrt(1/6) = 0.408248290 */
! 	      -0.408248290);
!     *skewNorm = 0;  /* have to invent a value, this works */
!   } else {
!     /* we have some variance */
      TEN_T_SCALE(var, 1.0/(*varNorm), var);
+     /* make damn sure var is orthogonal to mean */
+     dot = TEN_T_DOT(var, mean);
+     if (AIR_ABS(dot) > epsilon) {
+       TEN_T_SCALE_INCR(var, -dot, mean);
+       norm = TEN_T_NORM(var);
+       TEN_T_SCALE(var, 1.0/(norm), var);
+     }
+     TEN_T_SET(skew, ten[0],
+ 	      Tyy*Tzz - Tyz*Tyz, Txz*Tyz - Txy*Tzz, Txy*Tyz - Txz*Tyy,
+ 	      Txx*Tzz - Txz*Txz, Txy*Txz - Tyz*Txx,
+ 	      Txx*Tyy - Txy*Txy);
+     meanDot = TEN_T_DOT(skew, mean);
+     varDot = TEN_T_DOT(skew, var);
+     TEN_T_SCALE_INCR2(skew, -meanDot, mean, -varDot, var);
+     *skewNorm = TEN_T_NORM(skew);
+     if (*skewNorm < epsilon) {
+       /* skew is at an extremum, have to diagonalize */
+       tenEigensolve_d(eval, evec, ten);
+       *didEigen = AIR_TRUE;
+       mev = (eval[0] + eval[1] + eval[2])/3;
+       third = ((eval[0] - mev)*(eval[0] - mev)*(eval[0] - mev)
+ 	       + (eval[1] - mev)*(eval[1] - mev)*(eval[1] - mev)
+ 	       + (eval[2] - mev)*(eval[2] - mev)*(eval[2] - mev))/3;
+       if (third > 0) {
+ 	/* skew is positive: linear: eval[1] = eval[2] */
+ 	ELL_3V_SET(matA + 0*3, 0, 0, 0);
+ 	ELL_3V_SET(matA + 1*3, 0, 0.707106781, 0);
+ 	ELL_3V_SET(matA + 2*3, 0, 0, -0.707106781);
+       } else {
+ 	/* skew is negative: planar: eval[0] = eval[1] */
+ 	ELL_3V_SET(matA + 0*3, 0.707106781, 0, 0);
+ 	ELL_3V_SET(matA + 1*3, 0, -0.707106781, 0);
+ 	ELL_3V_SET(matA + 2*3, 0, 0, 0);
+       }
+       ELL_3M_TRANSPOSE(matR, evec);
+       ELL_3M_MUL(matB, matA, evec);
+       ELL_3M_MUL(matA, matR, matB);
+       TEN_M2T(skew, matA);
+     } else {
+       /* skew not at extremum */
+       TEN_T_SCALE(skew, 1.0/(*skewNorm), skew);
+       /* make damn sure skew is orthogonal to mean ... */
+       dot = TEN_T_DOT(skew, mean);
+       if (AIR_ABS(dot) > epsilon) {
+ 	TEN_T_SCALE_INCR(skew, -dot, mean);
+       }
+       /* ... and to var */
+       dot = TEN_T_DOT(skew, var);
+       if (AIR_ABS(dot) > epsilon) {
+ 	TEN_T_SCALE_INCR(skew, -dot, var);
+       }
+       norm = TEN_T_NORM(skew);
+       TEN_T_SCALE(skew, 1.0/(norm), skew);
+     }
    }
!   if (fabs(TEN_T_DOT(skew, mean)) > 0.7) {
!     fprintf(stderr, "tenShapeGradients_d : PANIC\n");
!     fprintf(stderr, "dots = %g %g %g\n",
! 	    TEN_T_DOT(mean, var),
! 	    TEN_T_DOT(mean, skew),
! 	    TEN_T_DOT(var, skew));
!     fprintf(stderr, "ten = (%g) %g %g %g   %g %g   %g\n",
! 	    ten[0],
! 	    ten[1], ten[2], ten[3],
! 	    ten[4], ten[5],
! 	    ten[6]);
!     fprintf(stderr, "varNorm = %g; var = (%g) %g %g %g   %g %g   %g\n",
! 	    *varNorm,
! 	    var[0],
! 	    var[1], var[2], var[3],
! 	    var[4], var[5],
! 	    var[6]);
!     fprintf(stderr, "skewNorm = %g; skew = (%g) %g %g %g   %g %g   %g\n",
! 	    *skewNorm,
! 	    skew[0],
! 	    skew[1], skew[2], skew[3],
! 	    skew[4], skew[5],
! 	    skew[6]);
!     exit(0);
    }
+ 
+   return;
+ }
+ 
+ /*
+ ** eval and evec must be pre-computed and given to us
+ */
+ void
+ tenRotationTangents_d(double ups1[7], double *ups1Mag,
+ 		      double ups2[7], double *ups2Mag,
+ 		      double ups3[7], double *ups3Mag,
+ 		      double eval[3], double evec[9],
+ 		      double ten[7]) {
+   double anti[9], mat[9], wM[9], Mw[9], diff[9];
+   int ii;
+ 
+   TEN_T2M(mat, ten);
+   for (ii=0; ii<=2; ii++) {
+     /* the matrix macros for setting/getting rows
+        are pretty stupid, so unfortunately they aren't
+        being used here */
+     ELL_3V_SET(anti + 0*3, 0, -(evec + ii*3)[2], (evec + ii*3)[1]);
+     ELL_3V_SET(anti + 1*3, (evec + ii*3)[2], 0, -(evec + ii*3)[0]);
+     ELL_3V_SET(anti + 2*3, -(evec + ii*3)[1], (evec + ii*3)[0], 0);
+     ELL_3M_MUL(wM, anti, mat);
+     ELL_3M_MUL(Mw, mat, anti);
+     ELL_3M_SUB(diff, wM, Mw);
+     switch (ii) {
+     case 0:
+       TEN_M2T(ups1, diff); ups1[0] = 1;
+       break;
+     case 1:
+       TEN_M2T(ups2, diff); ups2[0] = 1;
+       break;
+     case 2:
+       TEN_M2T(ups3, diff); ups3[0] = 1;
+       break;
+     }
+   }
+   *ups1Mag = eval[1] - eval[2];
+   *ups2Mag = eval[0] - eval[2];
+   *ups3Mag = eval[0] - eval[1];
    
    return;
  }
+ 

Index: tenMacros.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tenMacros.h,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** tenMacros.h	7 May 2004 19:13:34 -0000	1.11
--- tenMacros.h	23 Jun 2004 01:46:41 -0000	1.12
***************
*** 58,61 ****
--- 58,70 ----
                                       (t)[6] = (m)[8] )
  
+ #define TEN_T_EXISTS(t) ( \
+     AIR_EXISTS((t)[0]) \
+  && AIR_EXISTS((t)[1]) \
+  && AIR_EXISTS((t)[2]) \
+  && AIR_EXISTS((t)[3]) \
+  && AIR_EXISTS((t)[4]) \
+  && AIR_EXISTS((t)[5]) \
+  && AIR_EXISTS((t)[6]) )
+ 
  #define TEN_T_SET(t, conf, a, b, c, d, e, f) ( \
     (t)[0] = (conf), \

Index: enumsTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/enumsTen.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** enumsTen.c	22 Apr 2004 07:14:54 -0000	1.22
--- enumsTen.c	23 Jun 2004 01:46:41 -0000	1.23
***************
*** 125,128 ****
--- 125,135 ----
    "P normal",
  
+   "shape gradients",
+   "shape gradient mags",
+   "rotation tangents",
+   "rotation tangent mags",
+ 
+   "eigenvalue gradients",
+ 
    "anisotropies"
  };
***************
*** 174,177 ****
--- 181,189 ----
    "P grad mag",
    "P normal",
+   "shape gradients",
+   "shape gradient mags",
+   "rotation tangents",
+   "rotation tangent mags",
+   "eigenvalue gradients",
    "anisotropies"
  };
***************
*** 198,202 ****
    tenGageEvec1,         /* "evec1", medium eigenvectors of tensor: GT[3] */
    tenGageEvec2,         /* "evec2", minor eigenvectors of tensor: GT[3] */
!   tenGageTensorGrad,    /* "tg, all tensor component gradients: GT[21] */
    tenGageTraceGradVec,  /* "trgv": gradient (vector) of trace: GT[3] */
    tenGageTraceGradMag,  /* "trgm": gradient magnitude of trace: GT[1] */
--- 210,214 ----
    tenGageEvec1,         /* "evec1", medium eigenvectors of tensor: GT[3] */
    tenGageEvec2,         /* "evec2", minor eigenvectors of tensor: GT[3] */
!   tenGageTensorGrad,    /* "tg", all tensor component gradients: GT[21] */
    tenGageTraceGradVec,  /* "trgv": gradient (vector) of trace: GT[3] */
    tenGageTraceGradMag,  /* "trgm": gradient magnitude of trace: GT[1] */
***************
*** 223,226 ****
--- 235,243 ----
    tenGageThetaGradMag,  /* "thgm", gradient magnitude of P: GT[1] */
    tenGageThetaNormal,   /* "thn", normalized gradient of P: GT[3] */
+   tenGageShapeGrads,    /* "shgs" */
+   tenGageShapeGradMags, /* "shgms" */
+   tenGageRotTans,       /* "rts" */
+   tenGageRotTanMags,    /* "rtms" */
+   tenGageEvalGrads,     /* "evgs" */
    tenGageAniso          /* "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
  };
***************
*** 271,274 ****
--- 288,296 ----
    "thgm", "th grad mag",
    "thn", "th normal",
+   "shgs", "shape gradients",
+   "shgms", "shape gradient mags",
+   "rts", "rotation tangents",
+   "rtms", "rotation tangent mags",
+   "evgs", "eigenvalue gradients",
    "an", "aniso", "anisotropies",
    ""
***************
*** 320,323 ****
--- 342,350 ----
    tenGageThetaGradMag, tenGageThetaGradMag,
    tenGageThetaNormal, tenGageThetaNormal,
+   tenGageShapeGrads, tenGageShapeGrads,
+   tenGageShapeGradMags, tenGageShapeGradMags,
+   tenGageRotTans, tenGageRotTans,
+   tenGageRotTanMags, tenGageRotTanMags,
+   tenGageEvalGrads, tenGageEvalGrads,
    tenGageAniso, tenGageAniso, tenGageAniso
  };
***************
*** 352,356 ****
    "Weinstein-Kindlmann tensorlines",
    "based on tensor multiplication only",
!   "Zhukov's oriented tensors"
  };
  
--- 379,383 ----
    "Weinstein-Kindlmann tensorlines",
    "based on tensor multiplication only",
!   "Zhukov\'s oriented tensors"
  };
  

Index: tenGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tenGage.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** tenGage.c	11 May 2004 02:39:54 -0000	1.20
--- tenGage.c	23 Jun 2004 01:46:41 -0000	1.21
***************
*** 18,29 ****
  */
  
- extern void
- tenShapeGradients_d(double mean[7],
- 		    double var[7], double *varNorm,
- 		    double skew[7], double *skewNorm,
- 		    double evec[9], double eval[9], int *didEigen,
- 		    double ten[7]);
- 
- 
  #include "ten.h"
  #include "privateTen.h"
--- 18,21 ----
***************
*** 86,89 ****
--- 78,90 ----
    {tenGageThetaGradMag,        1,  1,  {tenGageThetaGradVec, -1, -1, -1, -1},                                                 -1,  -1},
    {tenGageThetaNormal,         3,  1,  {tenGageThetaGradVec, tenGageThetaGradMag, -1, -1, -1},                                -1,  -1},
+   
+   /* the ...Mags item doesn't actually require all of the previous item,
+      but its the easiest way to implement it for now */
+   {tenGageShapeGrads,          9,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},                                        -1,  -1},
+   {tenGageShapeGradMags,       3,  1,  {tenGageShapeGrads, -1, -1, -1, -1},                                                   -1,  -1},
+   {tenGageRotTans,             9,  1,  {tenGageTensor, tenGageTensorGrad, tenGageEval, tenGageEvec, -1},                      -1,  -1},
+   {tenGageRotTanMags,          3,  1,  {tenGageRotTans, -1, -1, -1, -1},                                                      -1,  -1},
+ 
+   {tenGageEvalGrads,           9,  1,  {tenGageTensorGrad, tenGageEval, tenGageEvec, -1},                                     -1,  -1},
  
    {tenGageAniso, TEN_ANISO_MAX+1,  0,  {tenGageEval0, tenGageEval1, tenGageEval2, -1, -1},                                    -1,  -1}
***************
*** 155,158 ****
--- 156,160 ----
      *gradDtA=NULL, *gradDtB=NULL, *gradDtC=NULL,
      *gradDtD=NULL, *gradDtE=NULL, *gradDtF=NULL,
+     gradDdXYZ[21],
      *gradCbS=NULL, *gradCbB=NULL, *gradCbQ=NULL, *gradCbR=NULL;
    double tmp0, tmp1, magTmp=0,
***************
*** 235,238 ****
--- 237,242 ----
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensorGrad)) {
      /* done if doD1 */
+     /* still have to set up point variables that item answers
+        below will rely on as short-cuts */
      vecTmp = pvl->directAnswer[tenGageTensorGrad];
      gradDtA = vecTmp + 1*3;
***************
*** 242,278 ****
      gradDtE = vecTmp + 5*3;
      gradDtF = vecTmp + 6*3;
!   }
! 
!   /* --- Trace --- */
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceGradVec)) {
!     /*
!     double tmpT[7], meanGrad[7], varGrad[7], varNorm, skewGrad[7], skewNorm,
!       copyT[7];
!     int didEigen=0;
!     
!     TEN_T_COPY(copyT, tenAns);
!     tenShapeGradients_d(meanGrad, 
! 			varGrad, &varNorm,
! 			skewGrad, &skewNorm,
! 			NULL, NULL, &didEigen,
! 			copyT);
!     vecTmp = pvl->directAnswer[tenGageTraceGradVec];
!     TEN_T_SET(tmpT, tenAns[0],
  	      gradDtA[0], gradDtB[0], gradDtC[0],
  	      gradDtD[0], gradDtE[0],
  	      gradDtF[0]);
!     vecTmp[0] = TEN_T_DOT(meanGrad, tmpT);
!     TEN_T_SET(tmpT, tenAns[0],
  	      gradDtA[1], gradDtB[1], gradDtC[1],
  	      gradDtD[1], gradDtE[1],
  	      gradDtF[1]);
!     vecTmp[1] = TEN_T_DOT(meanGrad, tmpT);
!     TEN_T_SET(tmpT, tenAns[0],
  	      gradDtA[2], gradDtB[2], gradDtC[2],
  	      gradDtD[2], gradDtE[2],
  	      gradDtF[2]);
!     vecTmp[2] = TEN_T_DOT(meanGrad, tmpT);
!     */
  
      vecTmp = pvl->directAnswer[tenGageTraceGradVec];
      ELL_3V_ADD3(vecTmp, gradDtA, gradDtD, gradDtF);
--- 246,265 ----
      gradDtE = vecTmp + 5*3;
      gradDtF = vecTmp + 6*3;
!     TEN_T_SET(gradDdXYZ + 0*7, tenAns[0],
  	      gradDtA[0], gradDtB[0], gradDtC[0],
  	      gradDtD[0], gradDtE[0],
  	      gradDtF[0]);
!     TEN_T_SET(gradDdXYZ + 1*7, tenAns[0],
  	      gradDtA[1], gradDtB[1], gradDtC[1],
  	      gradDtD[1], gradDtE[1],
  	      gradDtF[1]);
!     TEN_T_SET(gradDdXYZ + 2*7, tenAns[0],
  	      gradDtA[2], gradDtB[2], gradDtC[2],
  	      gradDtD[2], gradDtE[2],
  	      gradDtF[2]);
!   }
  
+   /* --- Trace --- */
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceGradVec)) {
      vecTmp = pvl->directAnswer[tenGageTraceGradVec];
      ELL_3V_ADD3(vecTmp, gradDtA, gradDtD, gradDtF);
***************
*** 344,376 ****
    /* --- Q --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQGradVec)) {
-     /*
-     double tmpT[7], meanGrad[7], varGrad[7], varNorm, skewGrad[7], skewNorm,
-       copyT[7];
-     int didEigen=0;
-     
-     TEN_T_COPY(copyT, tenAns);
-     tenShapeGradients_d(meanGrad, 
- 			varGrad, &varNorm,
- 			skewGrad, &skewNorm,
- 			NULL, NULL, &didEigen,
- 			copyT);
-     gradCbQ = vecTmp = pvl->directAnswer[tenGageQGradVec];
-     TEN_T_SET(tmpT, tenAns[0],
- 	      gradDtA[0], gradDtB[0], gradDtC[0],
- 	      gradDtD[0], gradDtE[0],
- 	      gradDtF[0]);
-     vecTmp[0] = TEN_T_DOT(varGrad, tmpT);
-     TEN_T_SET(tmpT, tenAns[0],
- 	      gradDtA[1], gradDtB[1], gradDtC[1],
- 	      gradDtD[1], gradDtE[1],
- 	      gradDtF[1]);
-     vecTmp[1] = TEN_T_DOT(varGrad, tmpT);
-     TEN_T_SET(tmpT, tenAns[0],
- 	      gradDtA[2], gradDtB[2], gradDtC[2],
- 	      gradDtD[2], gradDtE[2],
- 	      gradDtF[2]);
-     vecTmp[2] = TEN_T_DOT(varGrad, tmpT);
-     */
- 
      gradCbQ = vecTmp = pvl->directAnswer[tenGageQGradVec];
      ELL_3V_SCALE_ADD2(vecTmp,
--- 331,334 ----
***************
*** 437,440 ****
--- 395,470 ----
  		 1.0/(epsilon + magTmp), vecTmp);
    }
+   /* --- Shape gradients + rotation tangents --- */
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageShapeGrads)
+       || GAGE_QUERY_ITEM_TEST(pvl->query, tenGageShapeGradMags)) {
+     double meanGrad[7], varGrad[7], varNorm,
+       skewGrad[7], skewNorm, copyT[7],
+       locEval[3], locEvec[9];
+     int didEigen=0;
+     
+     TEN_T_COPY(copyT, tenAns);
+     tenShapeGradients_d(meanGrad, 
+ 			varGrad, &varNorm,
+ 			skewGrad, &skewNorm,
+ 			locEval, locEvec, &didEigen,
+ 			copyT);
+     vecTmp[0] = TEN_T_DOT(meanGrad, gradDdXYZ + 0*7);
+     vecTmp[1] = TEN_T_DOT(meanGrad, gradDdXYZ + 1*7);
+     vecTmp[2] = TEN_T_DOT(meanGrad, gradDdXYZ + 2*7);
+     ELL_3V_COPY(pvl->directAnswer[tenGageShapeGrads] + 0*3, vecTmp);
+     vecTmp[0] = TEN_T_DOT(varGrad, gradDdXYZ + 0*7);
+     vecTmp[1] = TEN_T_DOT(varGrad, gradDdXYZ + 1*7);
+     vecTmp[2] = TEN_T_DOT(varGrad, gradDdXYZ + 2*7);
+     ELL_3V_COPY(pvl->directAnswer[tenGageShapeGrads] + 1*3, vecTmp);
+     vecTmp[0] = TEN_T_DOT(skewGrad, gradDdXYZ + 0*7);
+     vecTmp[1] = TEN_T_DOT(skewGrad, gradDdXYZ + 1*7);
+     vecTmp[2] = TEN_T_DOT(skewGrad, gradDdXYZ + 2*7);
+     ELL_3V_COPY(pvl->directAnswer[tenGageShapeGrads] + 2*3, vecTmp);
+     pvl->directAnswer[tenGageShapeGradMags][0] = 1;
+     pvl->directAnswer[tenGageShapeGradMags][1] = varNorm;
+     pvl->directAnswer[tenGageShapeGradMags][2] = skewNorm;
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvalGrads)) {
+     double matOut[9], tenOut[9];
+     int evi;
+ 
+     for (evi=0; evi<=2; evi++) {
+       ELL_3MV_OUTER(matOut, evecAns + evi*3, evecAns + evi*3);
+       TEN_M2T(tenOut, matOut);
+       vecTmp[0] = TEN_T_DOT(tenOut, gradDdXYZ + 0*7);
+       vecTmp[1] = TEN_T_DOT(tenOut, gradDdXYZ + 1*7);
+       vecTmp[2] = TEN_T_DOT(tenOut, gradDdXYZ + 2*7);
+       ELL_3V_COPY(pvl->directAnswer[tenGageEvalGrads] + evi*3, vecTmp);
+     }
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRotTans)
+       || GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRotTanMags)) {
+     double ups1[7], ups2[7], ups3[7], 
+       ups1Mag, ups2Mag, ups3Mag,
+       eval[3], evec[9], copyT[7];
+ 
+     TEN_T_COPY(copyT, tenAns);
+     ELL_3V_COPY(eval, evalAns);
+     ELL_9V_COPY(evec, evecAns);
+     tenRotationTangents_d(ups1, &ups1Mag,
+ 			  ups2, &ups2Mag,
+ 			  ups3, &ups3Mag,
+ 			  eval, evec, copyT);
+     vecTmp[0] = TEN_T_DOT(ups1, gradDdXYZ + 0*7);
+     vecTmp[1] = TEN_T_DOT(ups1, gradDdXYZ + 1*7);
+     vecTmp[2] = TEN_T_DOT(ups1, gradDdXYZ + 2*7);
+     ELL_3V_COPY(pvl->directAnswer[tenGageRotTans] + 0*3, vecTmp);
+     vecTmp[0] = TEN_T_DOT(ups2, gradDdXYZ + 0*7);
+     vecTmp[1] = TEN_T_DOT(ups2, gradDdXYZ + 1*7);
+     vecTmp[2] = TEN_T_DOT(ups2, gradDdXYZ + 2*7);
+     ELL_3V_COPY(pvl->directAnswer[tenGageRotTans] + 1*3, vecTmp);
+     vecTmp[0] = TEN_T_DOT(ups3, gradDdXYZ + 0*7);
+     vecTmp[1] = TEN_T_DOT(ups3, gradDdXYZ + 1*7);
+     vecTmp[2] = TEN_T_DOT(ups3, gradDdXYZ + 2*7);
+     ELL_3V_COPY(pvl->directAnswer[tenGageRotTans] + 2*3, vecTmp);
+     pvl->directAnswer[tenGageRotTanMags][0] = ups1Mag;
+     pvl->directAnswer[tenGageRotTanMags][1] = ups2Mag;
+     pvl->directAnswer[tenGageRotTanMags][2] = ups3Mag;
+   }
    /* --- Aniso --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageAniso)) {

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.86
retrieving revision 1.87
diff -C2 -d -r1.86 -r1.87
*** ten.h	13 May 2004 15:30:40 -0000	1.86
--- ten.h	23 Jun 2004 01:46:41 -0000	1.87
***************
*** 182,186 ****
    tenGageEvec2,         /* 17: "evec2", minor eigenvectors of tensor: GT[3] */
  
!   tenGageTensorGrad,    /* 18: "tg, all tensor component gradients, starting
  			       with the confidence gradient: GT[21] */
  
--- 182,186 ----
    tenGageEvec2,         /* 17: "evec2", minor eigenvectors of tensor: GT[3] */
  
!   tenGageTensorGrad,    /* 18: "tg", all tensor component gradients, starting
  			       with the confidence gradient: GT[21] */
  
***************
*** 217,224 ****
    tenGageThetaNormal,   /* 42: "thn", normalized gradient of Th: GT[3] */
  
!   tenGageAniso,         /* 43: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  43
  
  /*
--- 217,234 ----
    tenGageThetaNormal,   /* 42: "thn", normalized gradient of Th: GT[3] */
  
!   tenGageShapeGrads,    /* 43, "shgs", projections of tensor gradient onto the
! 			       normalized shape gradients: eigenvalue 
! 				ean, variance, skew, in that order: GT[9]  */
!   tenGageShapeGradMags, /* 44: "shgms", what the tensor-valued shape gradients
! 			       where to be normalized by: GT[3] */
!   tenGageRotTans,       /* 45: "rts", projections of the tensor gradient onto
! 			       non-normalized rotation tangents: GT[9] */
!   tenGageRotTanMags,    /* 46: "rtms", lengths of rotation tangents: GT[3] */
!   tenGageEvalGrads,     /* 47: "evgs", projections of tensor gradient onto
! 			       gradients of eigenvalues: GT[9] */
!   tenGageAniso,         /* 48: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  48
  
  /*
***************
*** 443,446 ****
--- 453,467 ----
  TEEM_API int tenMake(Nrrd *nout, Nrrd *nconf, Nrrd *neval, Nrrd *nevec);
  TEEM_API int tenSlice(Nrrd *nout, Nrrd *nten, int axis, int pos, int dim);
+ TEEM_API void tenShapeGradients_d(double mean[7],
+ 				  double var[7], double *varNorm,
+ 				  double skew[7], double *skewNorm,
+ 				  double eval[3], double evec[9],
+ 				  int *didEigen,
+ 				  double ten[7]);
+ TEEM_API void tenRotationTangents_d(double ups1[7], double *ups1Mag,
+ 				    double ups2[7], double *ups2Mag,
+ 				    double ups3[7], double *ups3Mag,
+ 				    double eval[3], double evec[9],
+ 				    double ten[7]);
  
  /* chan.c */

Index: tendGlyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendGlyph.c,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** tendGlyph.c	26 May 2004 02:02:24 -0000	1.31
--- tendGlyph.c	23 Jun 2004 01:46:41 -0000	1.32
***************
*** 127,131 ****
    cam = limnCameraNew();
    airMopAdd(mop, cam, (airMopper)limnCameraNix, airMopAlways);
!   glyph = limnObjectNew(100, AIR_TRUE);
    airMopAdd(mop, glyph, (airMopper)limnObjectNix, airMopAlways);
    scene = echoSceneNew();
--- 127,131 ----
    cam = limnCameraNew();
    airMopAdd(mop, cam, (airMopper)limnCameraNix, airMopAlways);
!   glyph = limnObjectNew(1000, AIR_TRUE);
    airMopAdd(mop, glyph, (airMopper)limnObjectNix, airMopAlways);
    scene = echoSceneNew();

[Teem-commit] teem/src/ten/test tt.c,1.14,1.15

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

Update of /cvsroot/teem/teem/src/ten/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8676/test

Modified Files:
	tt.c 
Log Message:
phd-related hacking

Index: tt.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/test/tt.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** tt.c	7 May 2004 19:13:34 -0000	1.14
--- tt.c	23 Jun 2004 01:46:41 -0000	1.15
***************
*** 43,46 ****
--- 43,47 ----
  	       AIR_AFFINE(0.0, 0.9, 1.0, mean, cp),
  	       AIR_AFFINE(0.0, 0.9, 1.0, mean, cs));
+     ELL_3V_SET(xyz, cl, cp, cs);
    } else {
      if (1 == version) {

[Teem-commit] teem/src/make darwin.mk,1.10,1.11

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

Update of /cvsroot/teem/teem/src/make
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8517/make

Modified Files:
	darwin.mk 
Log Message:
dynamic libraries seem to basically work

Index: darwin.mk
===================================================================
RCS file: /cvsroot/teem/teem/src/make/darwin.mk,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** darwin.mk	26 May 2004 11:09:35 -0000	1.10
--- darwin.mk	23 Jun 2004 01:45:36 -0000	1.11
***************
*** 19,23 ****
  #
  
- # we'll figure out shared libraries eventually...
  TEEM_SHEXT = dylib
  
--- 19,22 ----
***************
*** 29,33 ****
  
  OPT_CFLAG ?= -O2
! STATIC_CFLAG =
  SHARED_CFLAG =
  SHARED_LDFLAG = -dynamic -dynamiclib -fno-common
--- 28,32 ----
  
  OPT_CFLAG ?= -O2
! STATIC_CFLAG = -Wl,-prebind
  SHARED_CFLAG =
  SHARED_LDFLAG = -dynamic -dynamiclib -fno-common
***************
*** 39,49 ****
  ifeq ($(SUBARCH),64)
    TEEM_32BIT = 0
-   ARCH_CFLAG = -Wall
-   ARCH_LDFLAG =
  else
    ifeq ($(SUBARCH),32)
      TEEM_32BIT = 1
-     ARCH_CFLAG = -Wall
-     ARCH_LDFLAG = 
    else
      $(error darwin sub-architecture "$(SUBARCH)" not recognized)
--- 38,44 ----

[Teem-commit] teem/src/ell/test wheel.c,1.2,1.3

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

Update of /cvsroot/teem/teem/src/ell/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8427/ell/test

Modified Files:
	wheel.c 
Log Message:
changed defaults

Index: wheel.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/test/wheel.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** wheel.c	11 Apr 2004 15:06:35 -0000	1.2
--- wheel.c	23 Jun 2004 01:45:05 -0000	1.3
***************
*** 316,324 ****
  
    /* circle */
!   wheelWidth(&wps, 4);
    wheelCircle(&wps, geom[0], 0, geom[1]);
  
    /* spokes */
!   wheelWidth(&wps, 2);
    wheelLine(&wps, geom[0], 0, xroot[0], yroot[0]);
    wheelLine(&wps, geom[0], 0, xroot[1], yroot[1]);
--- 316,324 ----
  
    /* circle */
!   wheelWidth(&wps, 3);
    wheelCircle(&wps, geom[0], 0, geom[1]);
  
    /* spokes */
!   wheelWidth(&wps, 4);
    wheelLine(&wps, geom[0], 0, xroot[0], yroot[0]);
    wheelLine(&wps, geom[0], 0, xroot[1], yroot[1]);

[Teem-commit] teem/src/nrrd nrrdEnums.h,1.46,1.47 measure.c,1.47,1.48

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8204

Modified Files:
	nrrdEnums.h measure.c 
Log Message:
added skew measurement

Index: measure.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/measure.c,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** measure.c	13 Mar 2004 20:03:10 -0000	1.47
--- measure.c	23 Jun 2004 01:43:46 -0000	1.48
***************
*** 394,397 ****
--- 394,459 ----
  }
  
+ void
+ _nrrdMeasureSkew(void *ans, int ansType,
+ 		 const void *line, int lineType, int len, 
+ 		 double axmin, double axmax) {
+   double val, diff, mean, vari, third;
+   int i, count;
+   
+   /* we don't try to do any one-pass short-cuts */
+ 
+   /* find the mean */
+   mean = 0;
+   if (nrrdTypeIsIntegral[lineType]) {
+     count = len;
+     for (i=0; i<len; i++) {
+       val = nrrdDLookup[lineType](line, i);
+       mean += val;
+     }
+   } else {
+     count = 0;
+     for (i=0; i<len; i++) {
+       val = nrrdDLookup[lineType](line, i);
+       if (AIR_EXISTS(val)) {
+ 	count++;
+ 	mean += val;
+       }
+     }
+   }
+   if (0 == count) {
+     nrrdDStore[ansType](ans, AIR_NAN);
+     return;
+   }
+   mean /= count;
+ 
+   /* find the variance and third moment */
+   vari = third = 0;
+   if (nrrdTypeIsIntegral[lineType]) {
+     for (i=0; i<len; i++) {
+       diff = nrrdDLookup[lineType](line, i) - mean;
+       vari += diff*diff;
+       third += diff*diff*diff;
+     }
+   } else {
+     for (i=0; i<len; i++) {
+       val = nrrdDLookup[lineType](line, i);
+       if (AIR_EXISTS(val)) {
+ 	diff = val - mean;
+ 	vari += diff*diff;
+ 	third += diff*diff*diff;
+       }
+     }
+   }
+   if (0 == vari) {
+     /* why not have an existant value ... */
+     nrrdDStore[ansType](ans, 0);
+     return;
+   }
+   vari /= count;
+   third /= count;
+ 
+   nrrdDStore[ansType](ans, third/(vari*sqrt(vari)));
+ }
+ 
  /*
  ** one thing which ALL the _nrrdMeasureHisto measures assume is that,
***************
*** 700,703 ****
--- 762,766 ----
    _nrrdMeasureVariance,
    _nrrdMeasureSD,
+   _nrrdMeasureSkew,
    _nrrdMeasureHistoMin,
    _nrrdMeasureHistoMax,
***************
*** 739,742 ****
--- 802,806 ----
    case nrrdMeasureVariance:
    case nrrdMeasureSD:
+   case nrrdMeasureSkew:
      type = nrrdStateMeasureType;
      break;

Index: nrrdEnums.h
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/nrrdEnums.h,v
retrieving revision 1.46
retrieving revision 1.47
diff -C2 -d -r1.46 -r1.47
*** nrrdEnums.h	9 Apr 2004 19:47:26 -0000	1.46
--- nrrdEnums.h	23 Jun 2004 01:43:46 -0000	1.47
***************
*** 333,357 ****
    nrrdMeasureVariance,       /* 11 */
    nrrdMeasureSD,             /* 12: standard deviation */
    /* 
    ** the nrrduMeasureHisto... measures interpret the array as a
    ** histogram of some implied value distribution
    */
!   nrrdMeasureHistoMin,       /* 13 */
!   nrrdMeasureHistoMax,       /* 14 */
!   nrrdMeasureHistoMean,      /* 15 */
!   nrrdMeasureHistoMedian,    /* 16 */
!   nrrdMeasureHistoMode,      /* 17 */
!   nrrdMeasureHistoProduct,   /* 18 */
!   nrrdMeasureHistoSum,       /* 19 */
!   nrrdMeasureHistoL2,        /* 20 */
!   nrrdMeasureHistoVariance,  /* 21 */
!   nrrdMeasureHistoSD,        /* 22 */
    nrrdMeasureLast
  };
! #define NRRD_MEASURE_MAX        22
  #define NRRD_MEASURE_DESC \
     "Possibilities include:\n " \
!    "\b\bo \"min\", \"max\", \"mean\", \"median\", \"mode\", \"variance\"\n " \
!      "(self-explanatory)\n " \
     "\b\bo \"sd\": standard deviation\n " \
     "\b\bo \"product\", \"sum\": product or sum of all values\n " \
--- 333,358 ----
    nrrdMeasureVariance,       /* 11 */
    nrrdMeasureSD,             /* 12: standard deviation */
+   nrrdMeasureSkew,           /* 13: skew */
    /* 
    ** the nrrduMeasureHisto... measures interpret the array as a
    ** histogram of some implied value distribution
    */
!   nrrdMeasureHistoMin,       /* 14 */
!   nrrdMeasureHistoMax,       /* 15 */
!   nrrdMeasureHistoMean,      /* 16 */
!   nrrdMeasureHistoMedian,    /* 17 */
!   nrrdMeasureHistoMode,      /* 18 */
!   nrrdMeasureHistoProduct,   /* 19 */
!   nrrdMeasureHistoSum,       /* 20 */
!   nrrdMeasureHistoL2,        /* 21 */
!   nrrdMeasureHistoVariance,  /* 22 */
!   nrrdMeasureHistoSD,        /* 23 */
    nrrdMeasureLast
  };
! #define NRRD_MEASURE_MAX        23
  #define NRRD_MEASURE_DESC \
     "Possibilities include:\n " \
!    "\b\bo \"min\", \"max\", \"mean\", \"median\", \"mode\", \"variance\", " \
!      "\"skew\"\n (self-explanatory)\n " \
     "\b\bo \"sd\": standard deviation\n " \
     "\b\bo \"product\", \"sum\": product or sum of all values\n " \