[Teem-commit] teem/src/alan alan.h,1.16,1.17 coreAlan.c,1.21,1.22 methodsAlan.c,1.15,1.16

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

Update of /cvsroot/teem/teem/src/alan
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3128/alan

Modified Files:
	alan.h coreAlan.c methodsAlan.c 
Log Message:
converted all tabs to spaces

Index: coreAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/coreAlan.c,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** coreAlan.c	1 Aug 2004 07:29:21 -0000	1.21
--- coreAlan.c	6 Oct 2004 09:40:03 -0000	1.22
***************
*** 43,47 ****
    }
    if (!( actx->size[0] > 0 && actx->size[1] > 0
! 	 && (2 == actx->dim || actx->size[2] > 0) )) {
      sprintf(err, "%s: texture sizes invalid", me);
      biffAdd(ALAN, err); return 1;
--- 43,47 ----
    }
    if (!( actx->size[0] > 0 && actx->size[1] > 0
!          && (2 == actx->dim || actx->size[2] > 0) )) {
      sprintf(err, "%s: texture sizes invalid", me);
      biffAdd(ALAN, err); return 1;
***************
*** 73,86 ****
    if (2 == actx->dim) {
      ret = (nrrdMaybeAlloc(actx->_nlev[0], alan_nt, 3,
! 			  2, actx->size[0], actx->size[1])
! 	   || nrrdCopy(actx->_nlev[1], actx->_nlev[0])
! 	   || nrrdMaybeAlloc(actx->nparm, alan_nt, 3,
! 			     3, actx->size[0], actx->size[1]));
    } else {
      ret = (nrrdMaybeAlloc(actx->_nlev[0], alan_nt, 4,
! 			  2, actx->size[0], actx->size[1], actx->size[2])
! 	   || nrrdCopy(actx->_nlev[1], actx->_nlev[0])
! 	   || nrrdMaybeAlloc(actx->nparm, alan_nt, 4,
! 			     3, actx->size[0], actx->size[1], actx->size[2]));
    }
    if (ret) {
--- 73,86 ----
    if (2 == actx->dim) {
      ret = (nrrdMaybeAlloc(actx->_nlev[0], alan_nt, 3,
!                           2, actx->size[0], actx->size[1])
!            || nrrdCopy(actx->_nlev[1], actx->_nlev[0])
!            || nrrdMaybeAlloc(actx->nparm, alan_nt, 3,
!                              3, actx->size[0], actx->size[1]));
    } else {
      ret = (nrrdMaybeAlloc(actx->_nlev[0], alan_nt, 4,
!                           2, actx->size[0], actx->size[1], actx->size[2])
!            || nrrdCopy(actx->_nlev[1], actx->_nlev[0])
!            || nrrdMaybeAlloc(actx->nparm, alan_nt, 4,
!                              3, actx->size[0], actx->size[1], actx->size[2]));
    }
    if (ret) {
***************
*** 113,121 ****
      }
      if (!( alan_nt == nlevInit->type 
! 	   && nlevInit->dim == 1 + actx->dim
! 	   && actx->_nlev[0]->axis[0].size == nlevInit->axis[0].size
! 	   && actx->size[0] == nlevInit->axis[1].size
! 	   && actx->size[1] == nlevInit->axis[2].size 
! 	   && (2 == actx->dim || actx->size[2] == nlevInit->axis[3].size) )) {
        sprintf(err, "%s: type/size mismatch with given nlevInit", me);
        biffAdd(ALAN, err); return 1;
--- 113,121 ----
      }
      if (!( alan_nt == nlevInit->type 
!            && nlevInit->dim == 1 + actx->dim
!            && actx->_nlev[0]->axis[0].size == nlevInit->axis[0].size
!            && actx->size[0] == nlevInit->axis[1].size
!            && actx->size[1] == nlevInit->axis[2].size 
!            && (2 == actx->dim || actx->size[2] == nlevInit->axis[3].size) )) {
        sprintf(err, "%s: type/size mismatch with given nlevInit", me);
        biffAdd(ALAN, err); return 1;
***************
*** 129,137 ****
      }
      if (!( alan_nt == nparmInit->type 
! 	   && nparmInit->dim == 1 + actx->dim
! 	   && 3 == nparmInit->axis[0].size
! 	   && actx->size[0] == nparmInit->axis[1].size
! 	   && actx->size[1] == nparmInit->axis[2].size 
! 	   && (2 == actx->dim || actx->size[2] == nparmInit->axis[3].size) )) {
        sprintf(err, "%s: type/size mismatch with given nparmInit", me);
        biffAdd(ALAN, err); return 1;
--- 129,137 ----
      }
      if (!( alan_nt == nparmInit->type 
!            && nparmInit->dim == 1 + actx->dim
!            && 3 == nparmInit->axis[0].size
!            && actx->size[0] == nparmInit->axis[1].size
!            && actx->size[1] == nparmInit->axis[2].size 
!            && (2 == actx->dim || actx->size[2] == nparmInit->axis[3].size) )) {
        sprintf(err, "%s: type/size mismatch with given nparmInit", me);
        biffAdd(ALAN, err); return 1;
***************
*** 151,155 ****
      } else {
        /* NOTE: the random number stuff here is OUTSIDE the multi-threaded
! 	 segment of the program- only the init thread does this */
        lev0[0 + 2*I] = actx->initA + RAND;
        lev0[1 + 2*I] = actx->initB + RAND;
--- 151,155 ----
      } else {
        /* NOTE: the random number stuff here is OUTSIDE the multi-threaded
!          segment of the program- only the init thread does this */
        lev0[0 + 2*I] = actx->initA + RAND;
        lev0[1 + 2*I] = actx->initB + RAND;
***************
*** 176,180 ****
      if (actx->verbose && !(iter % 100)) {
        fprintf(stderr, "%s: iter = %d, averageChange = %g\n",
! 	      me, iter, actx->averageChange);
      }
    }
--- 176,180 ----
      if (actx->verbose && !(iter % 100)) {
        fprintf(stderr, "%s: iter = %d, averageChange = %g\n",
!               me, iter, actx->averageChange);
      }
    }
***************
*** 183,187 ****
      nrrdSave(fname, actx->_nlev[(iter+1) % 2], NULL);
      fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
! 	    me, iter, actx->averageChange, fname);
    }
    if (actx->frameInterval && !(iter % actx->frameInterval)) {
--- 183,187 ----
      nrrdSave(fname, actx->_nlev[(iter+1) % 2], NULL);
      fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
!             me, iter, actx->averageChange, fname);
    }
    if (actx->frameInterval && !(iter % actx->frameInterval)) {
***************
*** 189,196 ****
      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",
! 	    me, iter, actx->averageChange, fname);
      nrrdNuke(nslc);
      nrrdNuke(nimg);
--- 189,196 ----
      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",
!             me, iter, actx->averageChange, fname);
      nrrdNuke(nslc);
      nrrdNuke(nimg);
***************
*** 253,258 ****
    for (iter = 0; 
         (alanStopNot == task->actx->stop 
! 	&& (0 == task->actx->maxIteration
! 	    || iter < task->actx->maxIteration)); 
         iter++) {
  
--- 253,258 ----
    for (iter = 0; 
         (alanStopNot == task->actx->stop 
!         && (0 == task->actx->maxIteration
!             || iter < task->actx->maxIteration)); 
         iter++) {
  
***************
*** 268,412 ****
      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];
! 	  lapA = lapB = corrA = corrB = 0;
! 	  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) {
! 	      /*
! 	      **  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));
! 	      ten = tendata + 4*idx;
! 	      conf = (AIR_CLAMP(0.3, ten[0], 1) - 0.3)/0.7;
! 	      if (conf) {
! 		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);
! 		if (!(task->actx->homogAniso)) {
! 		  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 {
! 		/* no confidence; you diffuse */
! 		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;
! 	      }
! 	    } else {
! 	      /* no data; you diffuse */
! 	      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;
! 	    }
! 	  } 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)));
! 	    if (tendata) {
  
! 	      if (!(task->actx->homogAniso)) {
! 		
! 	      }
! 	    } 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);
! 	    }
! 	  }
! 	  
! 	  deltaA = deltaT*(react*conf*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*conf*task->actx->K*(A*B - B - beta)
! 			   + diffB*(lapB + corrB));
! 	  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; 
! 	}
        }
      }
--- 268,412 ----
      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];
!           lapA = lapB = corrA = corrB = 0;
!           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) {
!               /*
!               **  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));
!               ten = tendata + 4*idx;
!               conf = (AIR_CLAMP(0.3, ten[0], 1) - 0.3)/0.7;
!               if (conf) {
!                 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);
!                 if (!(task->actx->homogAniso)) {
!                   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 {
!                 /* no confidence; you diffuse */
!                 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;
!               }
!             } else {
!               /* no data; you diffuse */
!               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;
!             }
!           } 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)));
!             if (tendata) {
  
!               if (!(task->actx->homogAniso)) {
!                 
!               }
!             } 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);
!             }
!           }
!           
!           deltaA = deltaT*(react*conf*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*conf*task->actx->K*(A*B - B - beta)
!                            + diffB*(lapB + corrB));
!           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; 
!         }
        }
      }
***************
*** 418,436 ****
      if (task->actx->changeCount == task->actx->numThreads) {
        /* I must be the last thread to reach this point; all 
! 	 others must have passed the mutex unlock, and are
! 	 sitting at the barrier */
        if (alanStopNot != stop) {
! 	/* there was some problem in going from lev0 to lev1, which
! 	   we deal with now by setting actx->stop */
! 	task->actx->stop = stop;
        } else if (task->actx->averageChange < task->actx->minAverageChange) {
! 	/* we converged */
! 	task->actx->stop = alanStopConverged;
        } else {
! 	/* we keep going */
! 	_alanPerIteration(task->actx, iter);
! 	if (task->actx->perIteration) {
! 	  task->actx->perIteration(task->actx, iter);
! 	}
        }
        task->actx->averageChange = 0;
--- 418,436 ----
      if (task->actx->changeCount == task->actx->numThreads) {
        /* I must be the last thread to reach this point; all 
!          others must have passed the mutex unlock, and are
!          sitting at the barrier */
        if (alanStopNot != stop) {
!         /* there was some problem in going from lev0 to lev1, which
!            we deal with now by setting actx->stop */
!         task->actx->stop = stop;
        } else if (task->actx->averageChange < task->actx->minAverageChange) {
!         /* we converged */
!         task->actx->stop = alanStopConverged;
        } else {
!         /* we keep going */
!         _alanPerIteration(task->actx, iter);
!         if (task->actx->perIteration) {
!           task->actx->perIteration(task->actx, iter);
!         }
        }
        task->actx->averageChange = 0;
***************
*** 463,467 ****
    if (!( actx->_nlev[0] && actx->_nlev[0] )) {
      sprintf(err, "%s: _nlev[0,1] not allocated: "
! 	    "call alanUpdate + alanInit", me);
      biffAdd(ALAN, err); return 1;
    }
--- 463,467 ----
    if (!( actx->_nlev[0] && actx->_nlev[0] )) {
      sprintf(err, "%s: _nlev[0,1] not allocated: "
!             "call alanUpdate + alanInit", me);
      biffAdd(ALAN, err); return 1;
    }
***************
*** 481,485 ****
      task[tid].thread = airThreadNew();
      airThreadStart(task[tid].thread, _alanTuringWorker,
! 		   (void *)&(task[tid]));
    }
    for (tid=0; tid<actx->numThreads; tid++) {
--- 481,485 ----
      task[tid].thread = airThreadNew();
      airThreadStart(task[tid].thread, _alanTuringWorker,
!                    (void *)&(task[tid]));
    }
    for (tid=0; tid<actx->numThreads; tid++) {

Index: methodsAlan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/methodsAlan.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** methodsAlan.c	31 Jul 2004 13:26:25 -0000	1.15
--- methodsAlan.c	6 Oct 2004 09:40:03 -0000	1.16
***************
*** 146,150 ****
    if (!( sizeX >= 10 && sizeY >= 10 && sizeZ >= 10 )) {
      sprintf(err, "%s: sizes (%d,%d,%d) invalid (too small?)",
! 	    me, sizeX, sizeY, sizeZ);
      biffAdd(ALAN, err); return 1;
    }
--- 146,150 ----
    if (!( sizeX >= 10 && sizeY >= 10 && sizeZ >= 10 )) {
      sprintf(err, "%s: sizes (%d,%d,%d) invalid (too small?)",
!             me, sizeX, sizeY, sizeZ);
      biffAdd(ALAN, err); return 1;
    }
***************
*** 241,245 ****
      if (!airThreadCapable) {
        fprintf(stderr, "%s: WARNING: no multi-threading available, so 1 thread "
! 	      "will be used, not %d\n", me, parmI);
        parmI = 1;
      }
--- 241,245 ----
      if (!airThreadCapable) {
        fprintf(stderr, "%s: WARNING: no multi-threading available, so 1 thread "
!               "will be used, not %d\n", me, parmI);
        parmI = 1;
      }

Index: alan.h
===================================================================
RCS file: /cvsroot/teem/teem/src/alan/alan.h,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** alan.h	31 Jul 2004 13:26:25 -0000	1.16
--- alan.h	6 Oct 2004 09:40:03 -0000	1.17
***************
*** 111,118 ****
      deltaX,           /* size of spatial grid discretization */
      minAverageChange, /* min worthwhile "avergageChange" value (see below),
! 			 assume convergence if it falls below this */
      maxPixelChange,   /* maximum allowed change in the first morphogen (on
! 			 any single pixels), assume unstable divergence if 
! 			 this is exceeded */
      alpha, beta,      /* variables for turing */
      react,            /* additional scaling of reaction term */
--- 111,118 ----
      deltaX,           /* size of spatial grid discretization */
      minAverageChange, /* min worthwhile "avergageChange" value (see below),
!                          assume convergence if it falls below this */
      maxPixelChange,   /* maximum allowed change in the first morphogen (on
!                          any single pixels), assume unstable divergence if 
!                          this is exceeded */
      alpha, beta,      /* variables for turing */
      react,            /* additional scaling of reaction term */
***************
*** 122,126 ****
      randRange;        /* amplitude of noise to destabalize Turing */
    Nrrd *nten;         /* tensors guiding texture.  May have 1+3 or 1+6 values
! 			 per sample, depending on dim */
    /* if non-NULL, this is called once per iteration, at its completion */
    int (*perIteration)(struct alanContext_t *, int iter);
--- 122,126 ----
      randRange;        /* amplitude of noise to destabalize Turing */
    Nrrd *nten;         /* tensors guiding texture.  May have 1+3 or 1+6 values
!                          per sample, depending on dim */
    /* if non-NULL, this is called once per iteration, at its completion */
    int (*perIteration)(struct alanContext_t *, int iter);
***************
*** 159,163 ****
  TEEM_API int alanUpdate(alanContext *actx);
  TEEM_API int alanInit(alanContext *actx,
! 		      const Nrrd *nlevInit, const Nrrd *nparmInit);
  TEEM_API int alanPriorityParm(alanContext *actx, const Nrrd *npri);
  TEEM_API int alanRun(alanContext *actx);
--- 159,163 ----
  TEEM_API int alanUpdate(alanContext *actx);
  TEEM_API int alanInit(alanContext *actx,
!                       const Nrrd *nlevInit, const Nrrd *nparmInit);
  TEEM_API int alanPriorityParm(alanContext *actx, const Nrrd *npri);
  TEEM_API int alanRun(alanContext *actx);