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[Teem-commit] teem/src/ell GNUmakefile,1.12,1.13

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

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23166

Modified Files:
	GNUmakefile 
Log Message:
little tool to help make diagrams of the eigenwheel

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/GNUmakefile,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** GNUmakefile	7 Jan 2004 15:34:29 -0000	1.12
--- GNUmakefile	29 Mar 2004 21:15:16 -0000	1.13
***************
*** 48,52 ****
  $(L).PRIVATE_HEADERS =
  $(L).OBJS = cubicEll.o eigen.o miscEll.o vecEll.o mat.o quat.o genmat.o
! $(L).TESTS = test/sort3 test/invert test/tq
  ####
  ####
--- 48,52 ----
  $(L).PRIVATE_HEADERS =
  $(L).OBJS = cubicEll.o eigen.o miscEll.o vecEll.o mat.o quat.o genmat.o
! $(L).TESTS = test/sort3 test/invert test/tq test/wheel
  ####
  ####

[Teem-commit] teem/src/mite ray.c,1.20,1.21

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

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12467

Modified Files:
	ray.c 
Log Message:
fixed bug in setting of Z depth

Index: ray.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/ray.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** ray.c	4 Mar 2004 14:04:08 -0000	1.20
--- ray.c	25 Mar 2004 03:13:33 -0000	1.21
***************
*** 39,43 ****
    mtt->RR = mtt->GG = mtt->BB = 0.0;
    mtt->TT = 1.0;
!   mtt->ZZ = -1.0;
    ELL_3V_SCALE(mtt->V, -1, rayDirWorld);
  
--- 39,43 ----
    mtt->RR = mtt->GG = mtt->BB = 0.0;
    mtt->TT = 1.0;
!   mtt->ZZ = AIR_NAN;
    ELL_3V_SCALE(mtt->V, -1, rayDirWorld);
  
***************
*** 225,229 ****
  
    /* set Z if it hasn't been set already */
!   if (1-mtt->TT >= muu->opacMatters && mtt->ZZ < 0) {
      mtt->ZZ = rayT;
    }
--- 225,229 ----
  
    /* set Z if it hasn't been set already */
!   if (1-mtt->TT >= muu->opacMatters && !AIR_EXISTS(mtt->ZZ)) {
      mtt->ZZ = rayT;
    }
***************
*** 245,249 ****
  	       A, mtt->ZZ);
    } else {
!     ELL_5V_SET(imgData + 5*idx, 0, 0, 0, 0, -1);
    }
    return 0;
--- 245,249 ----
  	       A, mtt->ZZ);
    } else {
!     ELL_5V_SET(imgData + 5*idx, 0, 0, 0, 0, AIR_NAN);
    }
    return 0;

[Teem-commit] teem/src/ell cubicEll.c,1.7,1.8

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

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12380

Modified Files:
	cubicEll.c 
Log Message:
renamed variables to be consistent with gage and thesis text

Index: cubicEll.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/cubicEll.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** cubicEll.c	19 Feb 2004 06:45:11 -0000	1.7
--- cubicEll.c	25 Mar 2004 03:12:52 -0000	1.8
***************
*** 44,64 ****
  ell_cubic(double root[3], double A, double B, double C, int newton) {
    char me[]="ell_cubic";
!   double epsilon = 1.0E-11, sq_A, p, q, cb_p, D, sqrt_D, der,
!     u, v, x, phi, t, sub;
  
!   sub = 1.0/3.0*A;
!   sq_A = A*A;
!   p = 1.0/3.0*(-1.0/3.0*sq_A + B);
!   q = 1.0/2.0*(2.0/27.0*A*sq_A - 1.0/3.0*A*B + C);
!   cb_p = p*p*p;
!   D = q*q + cb_p;
    if (D < -epsilon) {
      /* three distinct roots- this is the most common case, it has 
         been tested the most, its code should go first */
!     phi = 1.0/3.0*acos(-q/sqrt(-cb_p));
!     t = 2*sqrt(-p);
!     root[0] = t*cos(phi) - sub;
!     root[1] = t*cos(phi + 2*AIR_PI/3.0) - sub;
!     root[2] = t*cos(phi - 2*AIR_PI/3.0) - sub;
      /*
      if (!AIR_EXISTS(root[0])) {
--- 44,64 ----
  ell_cubic(double root[3], double A, double B, double C, int newton) {
    char me[]="ell_cubic";
!   double epsilon = 1.0E-11, AA, Q, R, QQQ, D, sqrt_D, der,
!     u, v, x, theta, t, sub;
  
!   sub = A/3.0;
!   AA = A*A;
!   Q = (AA/3.0 - B)/3.0;
!   R = (-2.0*A*AA/27.0 + A*B/3.0 - C)/2.0;
!   QQQ = Q*Q*Q;
!   D = R*R - QQQ;
    if (D < -epsilon) {
      /* three distinct roots- this is the most common case, it has 
         been tested the most, its code should go first */
!     theta = acos(R/sqrt(QQQ))/3.0;
!     t = 2*sqrt(Q);
!     root[0] = t*cos(theta) - sub;
!     root[1] = t*cos(theta + 2*AIR_PI/3.0) - sub;
!     root[2] = t*cos(theta - 2*AIR_PI/3.0) - sub;
      /*
      if (!AIR_EXISTS(root[0])) {
***************
*** 72,77 ****
      /* one real solution, except maybe also a "rescued" double root */
      sqrt_D = sqrt(D);
!     u = airCbrt(sqrt_D-q);
!     v = -airCbrt(sqrt_D+q);
      x = u+v - sub;
      if (!newton) {
--- 72,77 ----
      /* one real solution, except maybe also a "rescued" double root */
      sqrt_D = sqrt(D);
!     u = airCbrt(sqrt_D+R);
!     v = -airCbrt(sqrt_D-R);
      x = u+v - sub;
      if (!newton) {
***************
*** 115,121 ****
    else {
      /* else D is in the interval [-epsilon, +epsilon] */
!     if (q < -epsilon || q > epsilon) {
        /* one double root and one single root */
!       u = airCbrt(-q);
        root[0] = 2*u - sub;
        root[1] = -u - sub;
--- 115,121 ----
    else {
      /* else D is in the interval [-epsilon, +epsilon] */
!     if (R < -epsilon || epsilon < R) {
        /* one double root and one single root */
!       u = airCbrt(R);
        root[0] = 2*u - sub;
        root[1] = -u - sub;

[Teem-commit] teem/src/coil coil.h,1.2,1.3 coreCoil.c,1.3,1.4 enumsCoil.c,1.2,1.3 methodsCoil.c,1.3,1.4 realmethods.c,1.3,1.4 scalarCoil.c,1.2,1.3 tensorCoil.c,1.2,1.3

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

Update of /cvsroot/teem/teem/src/coil
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12209

Modified Files:
	coil.h coreCoil.c enumsCoil.c methodsCoil.c realmethods.c 
	scalarCoil.c tensorCoil.c 
Log Message:
some new stuff

Index: coil.h
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/coil.h,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** coil.h	24 Mar 2004 06:48:50 -0000	1.2
--- coil.h	25 Mar 2004 03:11:50 -0000	1.3
***************
*** 204,207 ****
--- 204,208 ----
  /* scalarCoil.c */
  TEEM_API const coilKind *coilKindScalar;
+ TEEM_API const coilKind *coilKindArray[COIL_KIND_TYPE_MAX+1];
  
  /* tensorCoil.c */

Index: tensorCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/tensorCoil.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** tensorCoil.c	24 Mar 2004 06:48:50 -0000	1.2
--- tensorCoil.c	25 Mar 2004 03:11:50 -0000	1.3
***************
*** 21,24 ****
--- 21,45 ----
  
  void
+ _coilKind7TensorTangents(coil_t traceGrad[6],
+ 			 coil_t varianceGrad[6],
+ 			 coil_t skewGrad[6],
+ 			 coil_t rot0Grad[6],
+ 			 coil_t rot1Grad[6],
+ 			 coil_t rot2Grad[6],
+ 			 coil_t tensor[7]) {
+   /*
+   coil_t a, b, c, d, e, f;
+ 
+   a = tensor[1];
+   b = tensor[2];
+   c = tensor[3];
+   d = tensor[4];
+   e = tensor[5];
+   f = tensor[6];
+   ELL_6V_SET(traceGrad, 1, 0, 0, 1, 0, 1);
+   */
+ }
+ 
+ void
  _coilKind7TensorFilterTesting(coil_t *delta, coil_t **iv3, 
  			      double spacing[3],
***************
*** 33,45 ****
  }
  
  void
  _coilKind7TensorFilterHomogeneous(coil_t *delta, coil_t **iv3, 
  				  double spacing[3],
  				  double parm[COIL_PARMS_NUM]) {
!   
  }
  
  void
! _coilKindTensorUpdate(coil_t *val, coil_t *delta) {
    
    val[0] += delta[0]; /* WARNING: this could change confidence! */
--- 54,97 ----
  }
  
+ /*
+ **  x ----> X
+ **   \   [0][ 0]-[06]  [1][ 0]  [2][ 0]
+ **  |  \   [0][ 7]-[13]  [1][ 7]  [2][ 7]
+ **  |    Y   [0][14]-[20]  [1][14]  [2][14]
+ **  |
+ **  |    [0][21]-[27]  [1][21]  [2][21]
+ **  Z      [0][28]-[34]  [1][28]  [2][28]
+ **           [0][35]-[41]  [1][35]  [2][35]
+ **  
+ **       [0][42]-[48]  [1][42]  [2][42]
+ **         [0][49]-[55]  [1][49]  [2][49]
+ **           [0][56]-[62]  [1][56]  [2][56]
+ */
+ 
+ #define LAPL(iv3, vi, rspX, rspY, rspZ) \
+   (  rspX*(iv3[0][vi + 7*4] - 2*iv3[1][vi + 7*4] + iv3[2][vi + 7*4]) \
+    + rspY*(iv3[1][vi + 7*3] - 2*iv3[1][vi + 7*4] + iv3[1][vi + 7*5]) \
+    + rspZ*(iv3[1][vi + 7*1] - 2*iv3[1][vi + 7*4] + iv3[1][vi + 7*7]))
+ 
  void
  _coilKind7TensorFilterHomogeneous(coil_t *delta, coil_t **iv3, 
  				  double spacing[3],
  				  double parm[COIL_PARMS_NUM]) {
!   coil_t rspX, rspY, rspZ;
! 
!   rspX = 1.0/(spacing[0]*spacing[0]);
!   rspY = 1.0/(spacing[1]*spacing[1]);
!   rspZ = 1.0/(spacing[2]*spacing[2]);
!   delta[0] = 0;
!   delta[1] = parm[0]*LAPL(iv3, 1, rspX, rspY, rspZ);
!   delta[2] = parm[0]*LAPL(iv3, 2, rspX, rspY, rspZ);
!   delta[3] = parm[0]*LAPL(iv3, 3, rspX, rspY, rspZ);
!   delta[4] = parm[0]*LAPL(iv3, 4, rspX, rspY, rspZ);
!   delta[5] = parm[0]*LAPL(iv3, 5, rspX, rspY, rspZ);
!   delta[6] = parm[0]*LAPL(iv3, 6, rspX, rspY, rspZ);
  }
  
  void
! _coilKind7TensorUpdate(coil_t *val, coil_t *delta) {
    
    val[0] += delta[0]; /* WARNING: this could change confidence! */
***************
*** 53,57 ****
  
  const coilKind
! _coilKindTensor = {
    "tensor",
    7,
--- 105,109 ----
  
  const coilKind
! _coilKind7Tensor = {
    "tensor",
    7,
***************
*** 62,68 ****
     NULL,
     NULL},
!   _coilKindTensorUpdate
  };
  
  const coilKind *
! coilKindTensor = &_coilKindTensor;
--- 114,120 ----
     NULL,
     NULL},
!   _coilKind7TensorUpdate
  };
  
  const coilKind *
! coilKind7Tensor = &_coilKind7Tensor;

Index: scalarCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/scalarCoil.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** scalarCoil.c	24 Mar 2004 06:48:50 -0000	1.2
--- scalarCoil.c	25 Mar 2004 03:11:50 -0000	1.3
***************
*** 20,23 ****
--- 20,38 ----
  #include "coil.h"
  
+ /*
+ **  x ----> X
+ **   \   [0][0]  [1][0]  [2][0]
+ **  |  \   [0][1]  [1][1]  [2][1]
+ **  |    Y   [0][2]  [1][2]  [2][2]
+ **  |
+ **  |    [0][3]  [1][3]  [2][3]
+ **  Z      [0][4]  [1][4]  [2][4]
+ **           [0][5]  [1][5]  [2][5]
+ **  
+ **       [0][6]  [1][6]  [2][6]
+ **         [0][7]  [1][7]  [2][7]
+ **           [0][8]  [1][8]  [2][8]
+ */
+ 
  coil_t
  _coilLaplacian3(coil_t **iv3, double spacing[3]) {
***************
*** 43,72 ****
  }
  
- /*
- **  x ----> X
- **   \   [0][0]  [1][0]  [2][0]
- **  |  \   [0][1]  [1][1]  [2][1]
- **  |    Y   [0][2]  [1][2]  [2][2]
- **  |
- **  |    [0][3]  [1][3]  [2][3]
- **  Z      [0][4]  [1][4]  [2][4]
- **           [0][5]  [1][5]  [2][5]
- **  
- **       [0][6]  [1][6]  [2][6]
- **         [0][7]  [1][7]  [2][7]
- **           [0][8]  [1][8]  [2][8]
- */
- 
  void
! _coilKindScalarFilterPeronaMalik(coil_t *delta, coil_t **i,
! 				 double spacing[3],
! 				 double parm[COIL_PARMS_NUM]) {
!   coil_t forwX[3], backX[3], forwY[3], backY[3], forwZ[3], backZ[3], 
!     KK, rspX, rspY, rspZ;
! 
!   /* reciprocals of spacings in X, Y, and Z */
!   rspX = 1.0/spacing[0];
!   rspY = 1.0/spacing[1];
!   rspZ = 1.0/spacing[2];
  
    /* gradients at forward and backward X */
--- 58,67 ----
  }
  
  void
! _coilKindScalar3x3x3Gradients(coil_t *forwX, coil_t *backX,
! 			      coil_t *forwY, coil_t *backY,
! 			      coil_t *forwZ, coil_t *backZ,
! 			      coil_t **i,
! 			      coil_t rspX, coil_t rspY, coil_t rspZ) {
  
    /* gradients at forward and backward X */
***************
*** 94,113 ****
    backZ[2] = rspZ*(i[1][4] - i[1][1]);
  
    /* compute fluxes */
    KK = parm[1]*parm[1];
!   /*
!   forwX[0] *= 1.0/(1.0 + ELL_3V_DOT(forwX, forwX)/KK);
!   forwY[1] *= 1.0/(1.0 + ELL_3V_DOT(forwY, forwY)/KK);
!   forwZ[2] *= 1.0/(1.0 + ELL_3V_DOT(forwZ, forwZ)/KK);
!   backX[0] *= 1.0/(1.0 + ELL_3V_DOT(backX, backX)/KK);
!   backY[1] *= 1.0/(1.0 + ELL_3V_DOT(backY, backY)/KK);
!   backZ[2] *= 1.0/(1.0 + ELL_3V_DOT(backZ, backZ)/KK);
!   */
!   forwX[0] *= exp(-0.5*ELL_3V_DOT(forwX, forwX)/KK);
!   forwY[1] *= exp(-0.5*ELL_3V_DOT(forwY, forwY)/KK);
!   forwZ[2] *= exp(-0.5*ELL_3V_DOT(forwZ, forwZ)/KK);
!   backX[0] *= exp(-0.5*ELL_3V_DOT(backX, backX)/KK);
!   backY[1] *= exp(-0.5*ELL_3V_DOT(backY, backY)/KK);
!   backZ[2] *= exp(-0.5*ELL_3V_DOT(backZ, backZ)/KK);
  
    delta[0] = parm[0]*(rspX*(forwX[0] - backX[0])
--- 89,129 ----
    backZ[2] = rspZ*(i[1][4] - i[1][1]);
  
+   return;
+ }
+ 
+ #define _COIL_CONDUCT(LL, KK) \
+   (exp(-0.5*(LL)/(KK)))
+ 
+ /*
+ #define _COIL_CONDUCT(vec, KK) \
+   (1.0/(1.0 + (LL)/(KK)))
+ */
+ 
+ void
+ _coilKindScalarFilterPeronaMalik(coil_t *delta, coil_t **iv3,
+ 				 double spacing[3],
+ 				 double parm[COIL_PARMS_NUM]) {
+   coil_t forwX[3], backX[3], forwY[3], backY[3], forwZ[3], backZ[3], 
+     KK, rspX, rspY, rspZ;
+ 
+   /* reciprocals of spacings in X, Y, and Z */
+   rspX = 1.0/spacing[0];
+   rspY = 1.0/spacing[1];
+   rspZ = 1.0/spacing[2];
+ 
+   _coilKindScalar3x3x3Gradients(forwX, backX,
+ 				forwY, backY,
+ 				forwZ, backZ,
+ 				iv3,
+ 				rspX, rspY, rspZ);
+   
    /* compute fluxes */
    KK = parm[1]*parm[1];
!   forwX[0] *= _COIL_CONDUCT(ELL_3V_DOT(forwX, forwX), KK);
!   forwY[1] *= _COIL_CONDUCT(ELL_3V_DOT(forwY, forwY), KK);
!   forwZ[2] *= _COIL_CONDUCT(ELL_3V_DOT(forwZ, forwZ), KK);
!   backX[0] *= _COIL_CONDUCT(ELL_3V_DOT(backX, backX), KK);
!   backY[1] *= _COIL_CONDUCT(ELL_3V_DOT(backY, backY), KK);
!   backZ[2] *= _COIL_CONDUCT(ELL_3V_DOT(backZ, backZ), KK);
  
    delta[0] = parm[0]*(rspX*(forwX[0] - backX[0])
***************
*** 117,120 ****
--- 133,179 ----
  
  void
+ _coilKindScalarFilterModifiedCurvature(coil_t *delta, coil_t **iv3,
+ 				       double spacing[3],
+ 				       double parm[COIL_PARMS_NUM]) {
+   coil_t forwX[3], backX[3], forwY[3], backY[3], forwZ[3], backZ[3],
+     grad[3], gm, eps, KK, LL, rspX, rspY, rspZ;
+ 
+   /* reciprocals of spacings in X, Y, and Z */
+   rspX = 1.0/spacing[0];
+   rspY = 1.0/spacing[1];
+   rspZ = 1.0/spacing[2];
+ 
+   _coilKindScalar3x3x3Gradients(forwX, backX,
+ 				forwY, backY,
+ 				forwZ, backZ,
+ 				iv3,
+ 				rspX, rspY, rspZ);
+   grad[0] = rspX*(iv3[2][4] - iv3[0][4]);
+   grad[1] = rspY*(iv3[1][5] - iv3[1][3]);
+   grad[2] = rspZ*(iv3[1][7] - iv3[1][1]);
+   gm = ELL_3V_LEN(grad);
+   
+   /* compute fluxes */
+   eps = 0.000001;
+   KK = parm[1]*parm[1];
+   LL = ELL_3V_DOT(forwX, forwX);
+   forwX[0] *= _COIL_CONDUCT(LL, KK)/(eps + sqrt(LL));
+   LL = ELL_3V_DOT(forwY, forwY);
+   forwY[1] *= _COIL_CONDUCT(LL, KK)/(eps + sqrt(LL));
+   LL = ELL_3V_DOT(forwZ, forwZ);
+   forwZ[2] *= _COIL_CONDUCT(LL, KK)/(eps + sqrt(LL));
+   LL = ELL_3V_DOT(backX, backX);
+   backX[0] *= _COIL_CONDUCT(LL, KK)/(eps + sqrt(LL));
+   LL = ELL_3V_DOT(backY, backY);
+   backY[1] *= _COIL_CONDUCT(LL, KK)/(eps + sqrt(LL));
+   LL = ELL_3V_DOT(backZ, backZ);
+   backZ[2] *= _COIL_CONDUCT(LL, KK)/(eps + sqrt(LL));
+   
+   delta[0] = gm*parm[0]*(rspX*(forwX[0] - backX[0])
+ 			 + rspY*(forwY[1] - backY[1])
+ 			 + rspZ*(forwZ[2] - backZ[2]));
+ }
+ 
+ void
  _coilKindScalarUpdate(coil_t *val, coil_t *delta) {
    
***************
*** 130,134 ****
     _coilKindScalarFilterHomogeneous,
     _coilKindScalarFilterPeronaMalik,
!    NULL,
     NULL},
    _coilKindScalarUpdate
--- 189,193 ----
     _coilKindScalarFilterHomogeneous,
     _coilKindScalarFilterPeronaMalik,
!    _coilKindScalarFilterModifiedCurvature,
     NULL},
    _coilKindScalarUpdate
***************
*** 137,138 ****
--- 196,209 ----
  const coilKind *
  coilKindScalar = &_coilKindScalar;
+ 
+ /* ------------------------------------------ */
+ 
+ extern const coilKind _coilKind7Tensor;
+ 
+ const coilKind*
+ coilKindArray[COIL_KIND_TYPE_MAX+1] = {
+   NULL,
+   &_coilKindScalar,
+   NULL,
+   &_coilKind7Tensor
+ };

Index: realmethods.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/realmethods.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** realmethods.c	24 Mar 2004 06:48:50 -0000	1.3
--- realmethods.c	25 Mar 2004 03:11:50 -0000	1.4
***************
*** 20,23 ****
--- 20,24 ----
  #include "coil.h"
  
+ /* ------------------------------------------ */
  const coilMethod
  _coilMethodTesting = {
***************
*** 29,32 ****
--- 30,34 ----
  coilMethodTesting = &_coilMethodTesting;
  
+ /* ------------------------------------------ */
  const coilMethod
  _coilMethodHomogeneous = {
***************
*** 38,41 ****
--- 40,44 ----
  coilMethodHomogeneous = &_coilMethodHomogeneous;
  
+ /* ------------------------------------------ */
  const coilMethod
  _coilMethodPeronaMalik = {
***************
*** 47,50 ****
--- 50,64 ----
  coilMethodPeronaMalik = &_coilMethodPeronaMalik;
  
+ /* ------------------------------------------ */
+ const coilMethod
+ _coilMethodModifiedCurvature = {
+   "modified-curvature",
+   coilMethodTypeModifiedCurvature,
+   2
+ };
+ const coilMethod*
+ coilMethodModifiedCurvature = &_coilMethodModifiedCurvature;
+ 
+ /* ------------------------------------------ */
  const coilMethod*
  coilMethodArray[COIL_METHOD_TYPE_MAX+1] = {
***************
*** 53,57 ****
    &_coilMethodHomogeneous,
    &_coilMethodPeronaMalik,
!   NULL,
    NULL
  };
--- 67,71 ----
    &_coilMethodHomogeneous,
    &_coilMethodPeronaMalik,
!   &_coilMethodModifiedCurvature,
    NULL
  };

Index: methodsCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/methodsCoil.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** methodsCoil.c	24 Mar 2004 06:48:50 -0000	1.3
--- methodsCoil.c	25 Mar 2004 03:11:50 -0000	1.4
***************
*** 191,194 ****
--- 191,195 ----
  coilOutputGet(Nrrd *nout, coilContext *cctx) {
    char me[]="coilOutputGet", err[AIR_STRLEN_MED];
+   int baseDim;
  
    if (!(nout && cctx)) {
***************
*** 196,200 ****
      biffAdd(COIL, err); return 1;
    }
!   if (nrrdSlice(nout, cctx->nvol, 0, 0)) {
      sprintf(err, "%s: trouble slicing to get output", me);
      biffMove(COIL, err, NRRD); return 1;
--- 197,202 ----
      biffAdd(COIL, err); return 1;
    }
!   baseDim = (1 == cctx->kind->valLen ? 0 : 1);
!   if (nrrdSlice(nout, cctx->nvol, baseDim, 0)) {
      sprintf(err, "%s: trouble slicing to get output", me);
      biffMove(COIL, err, NRRD); return 1;

Index: enumsCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/enumsCoil.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** enumsCoil.c	24 Mar 2004 06:48:50 -0000	1.2
--- enumsCoil.c	25 Mar 2004 03:11:50 -0000	1.3
***************
*** 93,97 ****
    "scalar",
    "3color",
!   "7tensor",
    ""
  };
--- 93,97 ----
    "scalar",
    "3color",
!   "7tensor", "tensor",
    ""
  };
***************
*** 101,105 ****
    coilKindTypeScalar,
    coilKindType3Color,
!   coilKindType7Tensor
  };
  
--- 101,105 ----
    coilKindTypeScalar,
    coilKindType3Color,
!   coilKindType7Tensor, coilKindType7Tensor
  };
  

Index: coreCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/coreCoil.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** coreCoil.c	24 Mar 2004 06:48:50 -0000	1.3
--- coreCoil.c	25 Mar 2004 03:11:50 -0000	1.4
***************
*** 89,92 ****
--- 89,104 ----
  }
  
+ void
+ _coilIv3Fill_1_7(coil_t **iv3, coil_t *here, int radius, int valLen,
+ 	     int x0, int y0, int z0, int sizeX, int sizeY, int sizeZ) {
+   int vi,          /* value index */
+     xni, yni, zni, /* neighborhood (iv3) indices */
+     xvi, yvi, zvi; /* volume indices */
+   coil_t *tmp;
+ 
+   _COIL_IV3_FILL(1, 3, 7);
+   return;
+ }
+ 
  int
  _coilThisZGet(coilTask *task, int doFilter) {
***************
*** 188,191 ****
--- 200,205 ----
      if (1 == cctx->radius && 1 == cctx->kind->valLen) {
        task->iv3Fill = _coilIv3Fill_1_1;
+     } else if (1 == cctx->radius && 7 == cctx->kind->valLen) {
+       task->iv3Fill = _coilIv3Fill_1_7;
      } else {
        task->iv3Fill = _coilIv3Fill_R_L;

[Teem-commit] teem/src/coil/test coiler.c,1.4,1.5

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

Update of /cvsroot/teem/teem/src/coil/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12209/test

Modified Files:
	coiler.c 
Log Message:
some new stuff

Index: coiler.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/test/coiler.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** coiler.c	24 Mar 2004 06:48:50 -0000	1.4
--- coiler.c	25 Mar 2004 03:11:50 -0000	1.5
***************
*** 29,33 ****
    airArray *mop;
    
!   int numIters, numThreads, methodType, _parmLen, pi, radius;
    Nrrd *nin, *nout;
    coilContext *cctx;
--- 29,33 ----
    airArray *mop;
    
!   int numIters, numThreads, methodType, kindType, _parmLen, pi, radius;
    Nrrd *nin, *nout;
    coilContext *cctx;
***************
*** 40,43 ****
--- 40,45 ----
    hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1, &numThreads, "5",
  	     "number of threads to run");
+   hestOptAdd(&hopt, "k", "kind", airTypeEnum, 1, 1, &kindType, NULL,
+ 	     "what kind of volume is input", NULL, coilKindType);
    hestOptAdd(&hopt, "m", "method", airTypeEnum, 1, 1, &methodType, "test",
  	     "what kind of filtering to perform", NULL, coilMethodType);
***************
*** 71,75 ****
    }
    if (coilContextAllSet(cctx, nin,
! 			coilKindScalar, coilMethodArray[methodType],
  			radius, numThreads, 1 /* verbose */,
  			parm)
--- 73,77 ----
    }
    if (coilContextAllSet(cctx, nin,
! 			coilKindArray[kindType], coilMethodArray[methodType],
  			radius, numThreads, 1 /* verbose */,
  			parm)

[Teem-commit] teem/src/ten tendPoint.c,1.7,1.8

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11408

Modified Files:
	tendPoint.c 
Log Message:
mathematica-friendly matrix coff list output

Index: tendPoint.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendPoint.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** tendPoint.c	7 Jan 2004 15:34:31 -0000	1.7
--- tendPoint.c	25 Mar 2004 03:06:07 -0000	1.8
***************
*** 70,73 ****
--- 70,75 ----
    fprintf(stderr, "confidence = %g\n", tdata[0]);
    fprintf(stderr, "tensor =\n");
+   fprintf(stderr, "{%.7f,%.7f,%.7f,%.7f,%.7f,%.7f} = \n",
+ 	  tdata[1], tdata[2], tdata[3], tdata[4], tdata[5], tdata[6]);
    fprintf(stderr, "% 15.7f % 15.7f % 15.7f\n", tdata[1], tdata[2], tdata[3]);
    fprintf(stderr, "% 15.7f % 15.7f % 15.7f\n", tdata[2], tdata[4], tdata[5]);

[Teem-commit] teem/src/gage vecGage.c,1.15,1.16

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

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29006

Modified Files:
	vecGage.c 
Log Message:
made the vector kind row-major compliant

Index: vecGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/vecGage.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** vecGage.c	13 Feb 2004 23:12:52 -0000	1.15
--- vecGage.c	25 Mar 2004 01:37:45 -0000	1.16
***************
*** 30,34 ****
    {gageVecDivergence,    1,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
    {gageVecCurl,          3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
!   /* HEY: if teem matrices go to row-major, these will change to sub-items */
    {gageVecGradient0,     3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
    {gageVecGradient1,     3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
--- 30,34 ----
    {gageVecDivergence,    1,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
    {gageVecCurl,          3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
!   /* HEY: these should change to sub-items!!! */
    {gageVecGradient0,     3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
    {gageVecGradient1,     3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
***************
*** 86,97 ****
    }
  
-   if (pvl->needD[1]) {
-     /* because we operated component-at-a-time, and because matrices are
-        in column order, the 1st column currently contains the three
-        derivatives of the X component; this should be the 1st row, and
-        likewise for the 2nd and 3rd column/rows.  */
-     ELL_3M_TRANSPOSE_IP(jac, tmp);
-   }
- 
    return;
  }
--- 86,89 ----
***************
*** 126,132 ****
      /* done if doV1 */
      /*
!       0:dv_x/dx  3:dv_x/dy  6:dv_x/dz
!       1:dv_y/dx  4:dv_y/dy  7:dv_y/dz
!       2:dv_z/dx  5:dv_z/dy  8:dv_z/dz
      */
      if (ctx->verbose) {
--- 118,124 ----
      /* done if doV1 */
      /*
!       0:dv_x/dx  1:dv_x/dy  2:dv_x/dz
!       3:dv_y/dx  4:dv_y/dy  5:dv_y/dz
!       6:dv_z/dx  7:dv_z/dy  8:dv_z/dz
      */
      if (ctx->verbose) {
***************
*** 145,168 ****
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurl)) {
      ELL_3V_SET(pvl->directAnswer[gageVecCurl],
! 	       jacAns[5] - jacAns[7],
! 	       jacAns[6] - jacAns[2],
! 	       jacAns[1] - jacAns[3]);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient0)) {
      ELL_3V_SET(pvl->directAnswer[gageVecGradient0],
  	       jacAns[0],
! 	       jacAns[3],
! 	       jacAns[6]);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient1)) {
      ELL_3V_SET(pvl->directAnswer[gageVecGradient1],
! 	       jacAns[1],
  	       jacAns[4],
! 	       jacAns[7]);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient2)) {
      ELL_3V_SET(pvl->directAnswer[gageVecGradient2],
! 	       jacAns[2],
! 	       jacAns[5],
  	       jacAns[8]);
    }
--- 137,160 ----
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurl)) {
      ELL_3V_SET(pvl->directAnswer[gageVecCurl],
! 	       jacAns[7] - jacAns[5],
! 	       jacAns[2] - jacAns[6],
! 	       jacAns[3] - jacAns[1]);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient0)) {
      ELL_3V_SET(pvl->directAnswer[gageVecGradient0],
  	       jacAns[0],
! 	       jacAns[1],
! 	       jacAns[2]);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient1)) {
      ELL_3V_SET(pvl->directAnswer[gageVecGradient1],
! 	       jacAns[3],
  	       jacAns[4],
! 	       jacAns[5]);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient2)) {
      ELL_3V_SET(pvl->directAnswer[gageVecGradient2],
! 	       jacAns[6],
! 	       jacAns[7],
  	       jacAns[8]);
    }

[Teem-commit] teem/src/coil coil.h,1.1,1.2 coreCoil.c,1.2,1.3 enumsCoil.c,1.1,1.2 methodsCoil.c,1.2,1.3 realmethods.c,1.2,1.3 scalarCoil.c,1.1,1.2 tensorCoil.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/coil
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15148

Modified Files:
	coil.h coreCoil.c enumsCoil.c methodsCoil.c realmethods.c 
	scalarCoil.c tensorCoil.c 
Log Message:
better load balancing, better conductance, just friggen better

Index: coil.h
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/coil.h,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** coil.h	22 Mar 2004 21:40:11 -0000	1.1
--- coil.h	24 Mar 2004 06:48:50 -0000	1.2
***************
*** 72,77 ****
    coilMethodTypeUnknown,            /* 0 */
    coilMethodTypeTesting,            /* 1: basically a no-op */
!   coilMethodTypeIsotropic,          /* 2 */
!   coilMethodTypeAnisotropic,        /* 3 */
    coilMethodTypeModifiedCurvature,  /* 4 */
    coilMethodTypeCurvatureFlow,      /* 5 */
--- 72,77 ----
    coilMethodTypeUnknown,            /* 0 */
    coilMethodTypeTesting,            /* 1: basically a no-op */
!   coilMethodTypeHomogeneous,        /* 2 */
!   coilMethodTypePeronaMalik,        /* 3 */
    coilMethodTypeModifiedCurvature,  /* 4 */
    coilMethodTypeCurvatureFlow,      /* 5 */
***************
*** 124,128 ****
  				       or something else (baseDim=1) */
                                      /* all the available methods */
!   void (*filter[COIL_METHOD_TYPE_MAX+1])(coil_t *delta, coil_t *iv3,
  					 double spacing[3],
  					 double parm[COIL_PARMS_NUM]);
--- 124,128 ----
  				       or something else (baseDim=1) */
                                      /* all the available methods */
!   void (*filter[COIL_METHOD_TYPE_MAX+1])(coil_t *delta, coil_t **iv3,
  					 double spacing[3],
  					 double parm[COIL_PARMS_NUM]);
***************
*** 140,149 ****
    struct coilContext_t *cctx;      /* parent's context */
    airThread *thread;               /* my thread */
!   int threadIdx,                   /* which thread am I */
!     startZ, endZ;                  /* my index range (inclusive) of slices */
!   coil_t *iv3;                     /* cache of local values, ordering same
! 				      as in gage: any multiple values per
! 				      voxel are the slowest axis, not the
! 				      fastest */
    void *returnPtr;                 /* for airThreadJoin */
  } coilTask;
--- 140,152 ----
    struct coilContext_t *cctx;      /* parent's context */
    airThread *thread;               /* my thread */
!   int threadIdx;                   /* which thread am I */
!   coil_t *_iv3,                    /* underlying value cache */
!     **iv3;                         /* short array of pointers into 2-D value
! 				      caches, in which the order is based on
! 				      the volume order:
! 				      values, then Y, then Z */
!                                    /* how to fill iv3 */
!   void (*iv3Fill)(coil_t **iv3, coil_t *here, int radius, int valLen,
! 		  int x0, int y0, int z0, int sizeX, int sizeY, int sizeZ);
    void *returnPtr;                 /* for airThreadJoin */
  } coilTask;
***************
*** 174,185 ****
  				      filtering result, and (2nd) the update
  				      values from the current iteration */
!   int finished;                    /* used to signal all threads to return */
    coilTask **task;                 /* dynamically allocated array of tasks */
!   airThreadBarrier *filterBarrier, /* for when filtering is done, and the
! 				      "update" values have been set */
!     *updateBarrier,                /* after the update values have been
! 				      applied to current values */
!     *finishBarrier;                /* so that thread 0 can see if filtering
  				      should go onward, and set "finished" */
  } coilContext;
  
--- 177,195 ----
  				      filtering result, and (2nd) the update
  				      values from the current iteration */
!   int finished,                    /* used to signal all threads to return */
!     nextSlice,                     /* global indicator of next slice needing
! 				      to be processed, either in filter or
! 				      in update stage.  Stage is done when
! 				      nextSlice == size[2] */
!     todoFilter, todoUpdate;        /* flags to signal which is scheduled to
! 				      come next, used as part of doling out
! 				      slices to workers */
!   airThreadMutex *nextSliceMutex;  /* mutex around nextSlice (and effectively,
! 				      also the "todo" flags above) */
    coilTask **task;                 /* dynamically allocated array of tasks */
!   airThreadBarrier *filterBarrier, /* so that thread 0 can see if filtering
  				      should go onward, and set "finished" */
+     *updateBarrier;                /* after the update values have been
+ 				      applied to current values */
  } coilContext;
  

Index: tensorCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/tensorCoil.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** tensorCoil.c	22 Mar 2004 21:40:11 -0000	1.1
--- tensorCoil.c	24 Mar 2004 06:48:50 -0000	1.2
***************
*** 21,25 ****
  
  void
! _coilKind7TensorFilterTesting(coil_t *delta, coil_t *iv3, 
  			      double spacing[3],
  			      double parm[COIL_PARMS_NUM]) {
--- 21,25 ----
  
  void
! _coilKind7TensorFilterTesting(coil_t *delta, coil_t **iv3, 
  			      double spacing[3],
  			      double parm[COIL_PARMS_NUM]) {
***************
*** 34,40 ****
  
  void
! _coilKind7TensorFilterIsotropic(coil_t *delta, coil_t *iv3, 
! 				double spacing[3],
! 				double parm[COIL_PARMS_NUM]) {
    
  }
--- 34,40 ----
  
  void
! _coilKind7TensorFilterHomogeneous(coil_t *delta, coil_t **iv3, 
! 				  double spacing[3],
! 				  double parm[COIL_PARMS_NUM]) {
    
  }
***************
*** 58,62 ****
    {NULL,
     _coilKind7TensorFilterTesting,
!    _coilKind7TensorFilterIsotropic,
     NULL,
     NULL,
--- 58,62 ----
    {NULL,
     _coilKind7TensorFilterTesting,
!    _coilKind7TensorFilterHomogeneous,
     NULL,
     NULL,

Index: scalarCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/scalarCoil.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** scalarCoil.c	22 Mar 2004 21:40:11 -0000	1.1
--- scalarCoil.c	24 Mar 2004 06:48:50 -0000	1.2
***************
*** 20,48 ****
  #include "coil.h"
  
- /*
- **  x ----> X
- **   \   0  1  2 
- **  |  \   3  4  5
- **  |    Y   6  7  8
- **  |
- **  |    9 10 11   
- **  Z      12 13 14
- **           15 16 17
- **  
- **       18 19 20
- **         21 22 23
- **           24 25 26
- */
- 
  coil_t
! _coilLaplacian3(coil_t *iv3, double spacing[3]) {
    
!   return ((iv3[12] - 2*iv3[13] + iv3[14])/(spacing[0]*spacing[0])
! 	  + (iv3[10] - 2*iv3[13] + iv3[16])/(spacing[1]*spacing[1])
! 	  + (iv3[ 4] - 2*iv3[13] + iv3[22])/(spacing[2]*spacing[2]));
  }
  
  void
! _coilKindScalarFilterTesting(coil_t *delta, coil_t *iv3, 
  			     double spacing[3],
  			     double parm[COIL_PARMS_NUM]) {
--- 20,33 ----
  #include "coil.h"
  
  coil_t
! _coilLaplacian3(coil_t **iv3, double spacing[3]) {
    
!   return (  (iv3[0][4] - 2*iv3[1][4] + iv3[2][4])/(spacing[0]*spacing[0])
! 	  + (iv3[1][3] - 2*iv3[1][4] + iv3[1][5])/(spacing[1]*spacing[1])
! 	  + (iv3[1][1] - 2*iv3[1][4] + iv3[1][7])/(spacing[2]*spacing[2]));
  }
  
  void
! _coilKindScalarFilterTesting(coil_t *delta, coil_t **iv3, 
  			     double spacing[3],
  			     double parm[COIL_PARMS_NUM]) {
***************
*** 51,61 ****
  
  void
! _coilKindScalarFilterIsotropic(coil_t *delta, coil_t *iv3,
! 			       double spacing[3],
! 			       double parm[COIL_PARMS_NUM]) {
!   coil_t lapl;
  
!   lapl = _coilLaplacian3(iv3, spacing);
!   delta[0] = parm[0]*lapl;
  }
  
--- 36,117 ----
  
  void
! _coilKindScalarFilterHomogeneous(coil_t *delta, coil_t **iv3,
! 				 double spacing[3],
! 				 double parm[COIL_PARMS_NUM]) {
!   
!   delta[0] = parm[0]*_coilLaplacian3(iv3, spacing);
! }
  
! /*
! **  x ----> X
! **   \   [0][0]  [1][0]  [2][0]
! **  |  \   [0][1]  [1][1]  [2][1]
! **  |    Y   [0][2]  [1][2]  [2][2]
! **  |
! **  |    [0][3]  [1][3]  [2][3]
! **  Z      [0][4]  [1][4]  [2][4]
! **           [0][5]  [1][5]  [2][5]
! **  
! **       [0][6]  [1][6]  [2][6]
! **         [0][7]  [1][7]  [2][7]
! **           [0][8]  [1][8]  [2][8]
! */
! 
! void
! _coilKindScalarFilterPeronaMalik(coil_t *delta, coil_t **i,
! 				 double spacing[3],
! 				 double parm[COIL_PARMS_NUM]) {
!   coil_t forwX[3], backX[3], forwY[3], backY[3], forwZ[3], backZ[3], 
!     KK, rspX, rspY, rspZ;
! 
!   /* reciprocals of spacings in X, Y, and Z */
!   rspX = 1.0/spacing[0];
!   rspY = 1.0/spacing[1];
!   rspZ = 1.0/spacing[2];
! 
!   /* gradients at forward and backward X */
!   forwX[0] = rspX*(i[2][4] - i[1][4]);
!   forwX[1] = rspY*(i[1][5] + i[2][5] - i[1][3] - i[2][3])/2;
!   forwX[2] = rspZ*(i[1][7] + i[2][7] - i[1][1] - i[2][1])/2;
!   backX[0] = rspX*(i[1][4] - i[0][4]);
!   backX[1] = rspY*(i[0][5] + i[1][5] - i[0][3] - i[1][3])/2;
!   backX[2] = rspZ*(i[0][7] + i[1][7] - i[0][1] - i[1][1])/2;
! 
!   /* gradients at forward and backward Y */
!   forwY[0] = rspX*(i[2][4] + i[2][5] - i[0][4] - i[0][5])/2;
!   forwY[1] = rspY*(i[1][5] - i[1][4]);
!   forwY[2] = rspZ*(i[1][7] + i[1][8] - i[1][1] - i[1][2])/2;
!   backY[0] = rspX*(i[2][3] + i[2][4] - i[0][3] - i[0][4])/2;
!   backY[1] = rspY*(i[1][4] - i[1][3]);
!   backY[2] = rspZ*(i[1][6] + i[1][7] - i[1][0] - i[1][1])/2;
! 
!   /* gradients at forward and backward Z */
!   forwZ[0] = rspX*(i[2][4] + i[2][7] - i[0][4] - i[0][7])/2;
!   forwZ[1] = rspY*(i[1][5] + i[1][8] - i[1][3] - i[1][6])/2;
!   forwZ[2] = rspZ*(i[1][7] - i[1][4]);
!   backZ[0] = rspX*(i[2][1] + i[2][4] - i[0][1] - i[0][4])/2;
!   backZ[1] = rspY*(i[1][2] + i[1][5] - i[1][0] - i[1][3])/2;
!   backZ[2] = rspZ*(i[1][4] - i[1][1]);
! 
!   /* compute fluxes */
!   KK = parm[1]*parm[1];
!   /*
!   forwX[0] *= 1.0/(1.0 + ELL_3V_DOT(forwX, forwX)/KK);
!   forwY[1] *= 1.0/(1.0 + ELL_3V_DOT(forwY, forwY)/KK);
!   forwZ[2] *= 1.0/(1.0 + ELL_3V_DOT(forwZ, forwZ)/KK);
!   backX[0] *= 1.0/(1.0 + ELL_3V_DOT(backX, backX)/KK);
!   backY[1] *= 1.0/(1.0 + ELL_3V_DOT(backY, backY)/KK);
!   backZ[2] *= 1.0/(1.0 + ELL_3V_DOT(backZ, backZ)/KK);
!   */
!   forwX[0] *= exp(-0.5*ELL_3V_DOT(forwX, forwX)/KK);
!   forwY[1] *= exp(-0.5*ELL_3V_DOT(forwY, forwY)/KK);
!   forwZ[2] *= exp(-0.5*ELL_3V_DOT(forwZ, forwZ)/KK);
!   backX[0] *= exp(-0.5*ELL_3V_DOT(backX, backX)/KK);
!   backY[1] *= exp(-0.5*ELL_3V_DOT(backY, backY)/KK);
!   backZ[2] *= exp(-0.5*ELL_3V_DOT(backZ, backZ)/KK);
! 
!   delta[0] = parm[0]*(rspX*(forwX[0] - backX[0])
! 		      + rspY*(forwY[1] - backY[1])
! 		      + rspZ*(forwZ[2] - backZ[2]));
  }
  
***************
*** 72,77 ****
    {NULL,
     _coilKindScalarFilterTesting,
!    _coilKindScalarFilterIsotropic,
!    NULL,
     NULL,
     NULL},
--- 128,133 ----
    {NULL,
     _coilKindScalarFilterTesting,
!    _coilKindScalarFilterHomogeneous,
!    _coilKindScalarFilterPeronaMalik,
     NULL,
     NULL},

Index: realmethods.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/realmethods.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** realmethods.c	23 Mar 2004 01:18:40 -0000	1.2
--- realmethods.c	24 Mar 2004 06:48:50 -0000	1.3
***************
*** 29,41 ****
  coilMethodTesting = &_coilMethodTesting;
  
- 
  const coilMethod
! _coilMethodIsotropic = {
!   "isotropic",
!   coilMethodTypeIsotropic,
    1
  };
  const coilMethod*
! coilMethodIsotropic = &_coilMethodIsotropic;
  
  const coilMethod*
--- 29,49 ----
  coilMethodTesting = &_coilMethodTesting;
  
  const coilMethod
! _coilMethodHomogeneous = {
!   "homogeneous",
!   coilMethodTypeHomogeneous,
    1
  };
  const coilMethod*
! coilMethodHomogeneous = &_coilMethodHomogeneous;
! 
! const coilMethod
! _coilMethodPeronaMalik = {
!   "perona-malik",
!   coilMethodTypePeronaMalik,
!   2
! };
! const coilMethod*
! coilMethodPeronaMalik = &_coilMethodPeronaMalik;
  
  const coilMethod*
***************
*** 43,48 ****
    NULL,
    &_coilMethodTesting,
!   &_coilMethodIsotropic,
!   NULL,
    NULL,
    NULL
--- 51,56 ----
    NULL,
    &_coilMethodTesting,
!   &_coilMethodHomogeneous,
!   &_coilMethodPeronaMalik,
    NULL,
    NULL

Index: methodsCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/methodsCoil.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** methodsCoil.c	23 Mar 2004 01:18:40 -0000	1.2
--- methodsCoil.c	24 Mar 2004 06:48:50 -0000	1.3
***************
*** 57,61 ****
      cctx->finished = AIR_FALSE;
      cctx->task = NULL;
!     cctx->finishBarrier = NULL;
      cctx->filterBarrier = NULL;
      cctx->updateBarrier = NULL;
--- 57,61 ----
      cctx->finished = AIR_FALSE;
      cctx->task = NULL;
!     cctx->nextSliceMutex = NULL;
      cctx->filterBarrier = NULL;
      cctx->updateBarrier = NULL;
***************
*** 207,210 ****
--- 207,211 ----
  
    if (cctx) {
+     /* thread machinery destroyed with coilFinish() */
      cctx->nvol = nrrdNuke(cctx->nvol);
      cctx = airFree(cctx);

Index: enumsCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/enumsCoil.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** enumsCoil.c	22 Mar 2004 21:40:11 -0000	1.1
--- enumsCoil.c	24 Mar 2004 06:48:50 -0000	1.2
***************
*** 24,29 ****
    "(unknown_method)",
    "testing",
!   "isotropic",
!   "anisotropic",
    "modified curvature",
    "curvature flow"
--- 24,29 ----
    "(unknown_method)",
    "testing",
!   "homogeneous",
!   "perona-malik",
    "modified curvature",
    "curvature flow"
***************
*** 34,39 ****
    "unknown_method",
    "nothing, actually, just here for testing",
!   "isotropic diffusion (Gaussian blurring)",
!   "anisotropic diffusion (Perona-Malik)",
    "modified curvature diffusion",
    "curvature flow"
--- 34,39 ----
    "unknown_method",
    "nothing, actually, just here for testing",
!   "homogenous isotropic diffusion (Gaussian blurring)",
!   "Perona-Malik",
    "modified curvature diffusion",
    "curvature flow"
***************
*** 43,48 ****
  _coilMethodTypeStrEqv[][AIR_STRLEN_SMALL] = {
    "test", "testing",
!   "iso", "isotropic",
!   "aniso", "anisotropic",
    "mcde",
    "flow", 
--- 43,48 ----
  _coilMethodTypeStrEqv[][AIR_STRLEN_SMALL] = {
    "test", "testing",
!   "homog", "homogeneous",
!   "pm", "perona-malik",
    "mcde",
    "flow", 
***************
*** 53,58 ****
  _coilMethodTypeValEqv[] = {
    coilMethodTypeTesting, coilMethodTypeTesting,
!   coilMethodTypeIsotropic, coilMethodTypeIsotropic,
!   coilMethodTypeAnisotropic, coilMethodTypeAnisotropic,
    coilMethodTypeModifiedCurvature,
    coilMethodTypeCurvatureFlow
--- 53,58 ----
  _coilMethodTypeValEqv[] = {
    coilMethodTypeTesting, coilMethodTypeTesting,
!   coilMethodTypeHomogeneous, coilMethodTypeHomogeneous,
!   coilMethodTypePeronaMalik, coilMethodTypePeronaMalik,
    coilMethodTypeModifiedCurvature,
    coilMethodTypeCurvatureFlow

Index: coreCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/coreCoil.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** coreCoil.c	23 Mar 2004 01:18:40 -0000	1.2
--- coreCoil.c	24 Mar 2004 06:48:50 -0000	1.3
***************
*** 20,58 ****
  #include "coil.h"
  
  /*
  ** 
  ** iv3 is: diam x diam x diam x valLen
  */
  void
! _coilIv3Fill(coil_t *iv3, coil_t *here, int radius, int valLen,
! 	     int x0, int y0, int z0, int sizeX, int sizeY, int sizeZ) {
    int diam, vi,    /* value index */
      xni, yni, zni, /* neighborhood (iv3) indices */
      xvi, yvi, zvi; /* volume indices */
    
-   /* this should be parameterized on both radius and valLen */
-   /* this should shuffle values within iv3 when possible */
    diam = 1 + 2*radius;
!   for (zni=0; zni<diam; zni++) {
!     zvi = AIR_CLAMP(0, zni-radius+z0, sizeZ-1) - z0;
!     for (yni=0; yni<diam; yni++) {
!       yvi = AIR_CLAMP(0, yni-radius+y0, sizeY-1) - y0;
!       for (xni=0; xni<diam; xni++) {
! 	xvi = AIR_CLAMP(0, xni-radius+x0, sizeX-1) - x0;
! 	for (vi=0; vi<valLen; vi++) {
! 	  iv3[xni + diam*(yni + diam*(zni + diam*vi))] = 
! 	    here[vi + valLen*(0 + 2*(xvi + sizeX*(yvi + sizeY*zvi)))];
! 	}
!       }
      }
    }
!   return;
  }
  
  void
  _coilProcess(coilTask *task, int doFilter) {
!   int xi, yi, zi, sizeX, sizeY, sizeZ, valLen, radius;
    coil_t *here;
!   void (*filter)(coil_t *delta, coil_t *iv3, 
  		 double spacing[3],
  		 double parm[COIL_PARMS_NUM]);
--- 20,128 ----
  #include "coil.h"
  
+ #define _COIL_IV3_FILL(radius, diam, valLen) \
+   if (0 && x0) { \
+     /* cycle through slices */ \
+     tmp = iv3[0]; \
+     for (xni=0; xni<diam-1; xni++) { \
+       iv3[xni] = iv3[xni+1]; \
+     } \
+     iv3[diam-1] = tmp; \
+     /* refill only newest one */ \
+     xni = diam-1; \
+     xvi = AIR_CLAMP(0, xni-radius+x0, sizeX-1) - x0; \
+     for (zni=0; zni<diam; zni++) { \
+       zvi = AIR_CLAMP(0, zni-radius+z0, sizeZ-1) - z0; \
+       for (yni=0; yni<diam; yni++) { \
+ 	yvi = AIR_CLAMP(0, yni-radius+y0, sizeY-1) - y0; \
+ 	for (vi=0; vi<valLen; vi++) { \
+ 	  iv3[xni][vi + valLen*(yni + diam*zni)] =  \
+ 	    here[vi + valLen*(0 + 2*(xvi + sizeX*(yvi + sizeY*zvi)))]; \
+ 	} \
+       } \
+     } \
+   } else { \
+     /* have to re-fill entire thing */ \
+     for (zni=0; zni<diam; zni++) { \
+       zvi = AIR_CLAMP(0, zni-radius+z0, sizeZ-1) - z0; \
+       for (yni=0; yni<diam; yni++) { \
+ 	yvi = AIR_CLAMP(0, yni-radius+y0, sizeY-1) - y0; \
+ 	for (xni=0; xni<diam; xni++) { \
+ 	  xvi = AIR_CLAMP(0, xni-radius+x0, sizeX-1) - x0; \
+ 	  for (vi=0; vi<valLen; vi++) { \
+ 	    iv3[xni][vi + valLen*(yni + diam*zni)] =  \
+ 	      here[vi + valLen*(0 + 2*(xvi + sizeX*(yvi + sizeY*zvi)))]; \
+ 	  } \
+ 	} \
+       } \
+     } \
+   }
+ 
  /*
  ** 
  ** iv3 is: diam x diam x diam x valLen
+ **
+ ** this should be parameterized on both radius and valLen
  */
  void
! _coilIv3Fill_R_L(coil_t **iv3, coil_t *here, int radius, int valLen,
! 		 int x0, int y0, int z0, int sizeX, int sizeY, int sizeZ) {
    int diam, vi,    /* value index */
      xni, yni, zni, /* neighborhood (iv3) indices */
      xvi, yvi, zvi; /* volume indices */
+   coil_t *tmp;
    
    diam = 1 + 2*radius;
!   _COIL_IV3_FILL(radius, diam, valLen);
!   return;
! }
! 
! void
! _coilIv3Fill_1_1(coil_t **iv3, coil_t *here, int radius, int valLen,
! 	     int x0, int y0, int z0, int sizeX, int sizeY, int sizeZ) {
!   int vi,          /* value index */
!     xni, yni, zni, /* neighborhood (iv3) indices */
!     xvi, yvi, zvi; /* volume indices */
!   coil_t *tmp;
! 
!   _COIL_IV3_FILL(1, 3, 1);
!   return;
! }
! 
! int
! _coilThisZGet(coilTask *task, int doFilter) {
!   int thisZ, *thisFlag, *thatFlag;
! 
!   if (doFilter) {
!     thisFlag = &(task->cctx->todoFilter);
!     thatFlag = &(task->cctx->todoUpdate);
!   } else {
!     thisFlag = &(task->cctx->todoUpdate);
!     thatFlag = &(task->cctx->todoFilter);
!   }
! 
!   airThreadMutexLock(task->cctx->nextSliceMutex);
!   if (task->cctx->nextSlice == task->cctx->size[2]
!       && *thisFlag) {
!     /* we're the first thread to start this phase */
!     task->cctx->nextSlice = 0;
!     *thisFlag = AIR_FALSE;
!   }
!   thisZ = task->cctx->nextSlice;
!   if (task->cctx->nextSlice < task->cctx->size[2]) {
!     task->cctx->nextSlice++;
!     if (task->cctx->nextSlice == task->cctx->size[2]) {
!       /* we just grabbed the last slice of this phase */
!       *thatFlag = AIR_TRUE;
      }
    }
!   airThreadMutexUnlock(task->cctx->nextSliceMutex);
!   return thisZ;
  }
  
  void
  _coilProcess(coilTask *task, int doFilter) {
!   int xi, yi, sizeX, sizeY, thisZ, sizeZ, valLen, radius;
    coil_t *here;
!   void (*filter)(coil_t *delta, coil_t **iv3, 
  		 double spacing[3],
  		 double parm[COIL_PARMS_NUM]);
***************
*** 64,76 ****
    radius = task->cctx->radius;
    filter = task->cctx->kind->filter[task->cctx->method->type];
-   here = (coil_t*)(task->cctx->nvol->data);
-   here += 2*valLen*sizeX*sizeY*task->startZ;
    if (doFilter) {
!     for (zi=task->startZ; zi<=task->endZ; zi++) {
        for (yi=0; yi<sizeY; yi++) {
  	for (xi=0; xi<sizeX; xi++) {
! 	  _coilIv3Fill(task->iv3, here + 0*valLen, radius, valLen,
! 		       xi, yi, zi, sizeX, sizeY, sizeZ);
! 	  filter(here + 1*valLen, task->iv3, task->cctx->spacing, task->cctx->parm);
  	  here += 2*valLen;
  	}
--- 134,150 ----
    radius = task->cctx->radius;
    filter = task->cctx->kind->filter[task->cctx->method->type];
    if (doFilter) {
!     while (1) {
!       thisZ = _coilThisZGet(task, doFilter);
!       if (thisZ == sizeZ) {
! 	break;
!       }
!       here = (coil_t*)(task->cctx->nvol->data) + 2*valLen*sizeX*sizeY*thisZ;
        for (yi=0; yi<sizeY; yi++) {
  	for (xi=0; xi<sizeX; xi++) {
! 	  task->iv3Fill(task->iv3, here + 0*valLen, radius, valLen,
! 			xi, yi, thisZ, sizeX, sizeY, sizeZ);
! 	  filter(here + 1*valLen, task->iv3,
! 		 task->cctx->spacing, task->cctx->parm);
  	  here += 2*valLen;
  	}
***************
*** 78,82 ****
      }
    } else {
!     for (zi=task->startZ; zi<=task->endZ; zi++) {
        for (yi=0; yi<sizeY; yi++) {
  	for (xi=0; xi<sizeX; xi++) {
--- 152,161 ----
      }
    } else {
!     while (1) {
!       thisZ = _coilThisZGet(task, doFilter);
!       if (thisZ == sizeZ) {
! 	break;
!       }
!       here = (coil_t*)(task->cctx->nvol->data) + 2*valLen*sizeX*sizeY*thisZ;
        for (yi=0; yi<sizeY; yi++) {
  	for (xi=0; xi<sizeX; xi++) {
***************
*** 91,97 ****
  
  coilTask *
! _coilTaskNew(coilContext *cctx, int threadIdx, int sizeZ) {
    coilTask *task;
!   int len, diam;
  
    len = cctx->kind->valLen;
--- 170,176 ----
  
  coilTask *
! _coilTaskNew(coilContext *cctx, int threadIdx) {
    coilTask *task;
!   int len, diam, xi;
  
    len = cctx->kind->valLen;
***************
*** 101,108 ****
      task->cctx = cctx;
      task->thread = airThreadNew();
-     task->startZ = threadIdx*sizeZ/cctx->numThreads;
-     task->endZ = (threadIdx+1)*sizeZ/cctx->numThreads - 1;
      task->threadIdx = threadIdx;
!     task->iv3 = (coil_t*)calloc(len*diam*diam*diam, sizeof(coil_t));
      task->returnPtr = NULL;
    }
--- 180,194 ----
      task->cctx = cctx;
      task->thread = airThreadNew();
      task->threadIdx = threadIdx;
!     task->_iv3 = (coil_t*)calloc(len*diam*diam*diam, sizeof(coil_t));
!     task->iv3 = (coil_t**)calloc(diam, sizeof(coil_t*));
!     for (xi=0; xi<diam; xi++) {
!       task->iv3[xi] = task->_iv3 + xi*len*diam*diam;
!     }
!     if (1 == cctx->radius && 1 == cctx->kind->valLen) {
!       task->iv3Fill = _coilIv3Fill_1_1;
!     } else {
!       task->iv3Fill = _coilIv3Fill_R_L;
!     }
      task->returnPtr = NULL;
    }
***************
*** 115,118 ****
--- 201,205 ----
    if (task) {
      task->thread = airThreadNix(task->thread);
+     task->_iv3 = airFree(task->_iv3);
      task->iv3 = airFree(task->iv3);
      free(task);
***************
*** 130,161 ****
    while (1) {
      /* wait until parent has set cctx->finished */
!     if (task->cctx->verbose) {
        fprintf(stderr, "%s(%d): waiting to check finished\n",
  	      me, task->threadIdx);
      }
!     airThreadBarrierWait(task->cctx->finishBarrier);
      if (task->cctx->finished) {
!       if (task->cctx->verbose) {
  	fprintf(stderr, "%s(%d): done!\n", me, task->threadIdx);
        }
        break;
      }
!     /* else there's work */
  
      /* first: filter */
!     if (task->cctx->verbose) {
        fprintf(stderr, "%s(%d): filtering ... \n",
  	      me, task->threadIdx);
      }
      _coilProcess(task, AIR_TRUE);
-     airThreadBarrierWait(task->cctx->filterBarrier);
  
      /* second: update */
!     if (task->cctx->verbose) {
        fprintf(stderr, "%s(%d): updating ... \n",
  	      me, task->threadIdx);
      }
      _coilProcess(task, AIR_FALSE);
!     airThreadBarrierWait(task->cctx->updateBarrier);
    }
  
--- 217,248 ----
    while (1) {
      /* wait until parent has set cctx->finished */
!     if (task->cctx->verbose > 1) {
        fprintf(stderr, "%s(%d): waiting to check finished\n",
  	      me, task->threadIdx);
      }
!     airThreadBarrierWait(task->cctx->filterBarrier);
      if (task->cctx->finished) {
!       if (task->cctx->verbose > 1) {
  	fprintf(stderr, "%s(%d): done!\n", me, task->threadIdx);
        }
        break;
      }
!     /* else there's work to do ... */
  
      /* first: filter */
!     if (task->cctx->verbose > 1) {
        fprintf(stderr, "%s(%d): filtering ... \n",
  	      me, task->threadIdx);
      }
      _coilProcess(task, AIR_TRUE);
  
      /* second: update */
!     airThreadBarrierWait(task->cctx->updateBarrier);
!     if (task->cctx->verbose > 1) {
        fprintf(stderr, "%s(%d): updating ... \n",
  	      me, task->threadIdx);
      }
      _coilProcess(task, AIR_FALSE);
! 
    }
  
***************
*** 182,186 ****
    cctx->task[0] = NULL;
    for (tidx=0; tidx<cctx->numThreads; tidx++) {
!     cctx->task[tidx] = _coilTaskNew(cctx, tidx, cctx->size[2]);
      if (!(cctx->task[tidx])) {
        sprintf(err, "%s: couldn't allocate task %d", me, tidx);
--- 269,273 ----
    cctx->task[0] = NULL;
    for (tidx=0; tidx<cctx->numThreads; tidx++) {
!     cctx->task[tidx] = _coilTaskNew(cctx, tidx);
      if (!(cctx->task[tidx])) {
        sprintf(err, "%s: couldn't allocate task %d", me, tidx);
***************
*** 191,213 ****
    cctx->finished = AIR_FALSE;
    if (cctx->numThreads > 1) {
!     cctx->finishBarrier = airThreadBarrierNew(cctx->numThreads);
      cctx->filterBarrier = airThreadBarrierNew(cctx->numThreads);
      cctx->updateBarrier = airThreadBarrierNew(cctx->numThreads);
    }
  
-   /* start threads 1 and up running (they won't get far) */
-   if (cctx->verbose) {
-     fprintf(stderr, "%s: parent doing slices Z=[%d,%d]\n", me, 
- 	    cctx->task[0]->startZ, cctx->task[0]->endZ);
-   }
-   for (tidx=1; tidx<cctx->numThreads; tidx++) {
-     if (cctx->verbose) {
-       fprintf(stderr, "%s: spawning thread %d (Z=[%d,%d])\n", me, tidx,
- 	      cctx->task[tidx]->startZ, cctx->task[tidx]->endZ);
-     }
-     airThreadStart(cctx->task[tidx]->thread, _coilWorker,
- 		   (void *)(cctx->task[tidx]));
-   }
- 
    /* initialize the values in cctx->nvol */
    val = (coil_t*)(cctx->nvol->data);
--- 278,286 ----
    cctx->finished = AIR_FALSE;
    if (cctx->numThreads > 1) {
!     cctx->nextSliceMutex = airThreadMutexNew();
      cctx->filterBarrier = airThreadBarrierNew(cctx->numThreads);
      cctx->updateBarrier = airThreadBarrierNew(cctx->numThreads);
    }
  
    /* initialize the values in cctx->nvol */
    val = (coil_t*)(cctx->nvol->data);
***************
*** 226,243 ****
    }
    
!   return 0;
! }
! 
! int
! _coilPause(int huge) {
!   int i, j, num;
!   
!   num = 0;
!   for (i=1; i<huge; i++) {
!     for (j=0; j<huge; j++) {
!       num *= i;
      }
    }
!   return num;
  }
  
--- 299,317 ----
    }
    
!   /* start threads 1 and up running; they'll all hit filterBarrier  */
!   for (tidx=1; tidx<cctx->numThreads; tidx++) {
!     if (cctx->verbose > 1) {
!       fprintf(stderr, "%s: spawning thread %d\n", me, tidx);
      }
+     airThreadStart(cctx->task[tidx]->thread, _coilWorker,
+ 		   (void *)(cctx->task[tidx]));
    }
! 
!   /* set things as though we've just finished an update phase */
!   cctx->nextSlice = cctx->size[2];
!   cctx->todoFilter = AIR_TRUE;
!   cctx->todoUpdate = AIR_FALSE;
!   
!   return 0;
  }
  
***************
*** 253,256 ****
--- 327,331 ----
    char me[]="coilIterate", err[AIR_STRLEN_MED];
    int iter;
+   double time0, time1;
  
    if (!cctx) {
***************
*** 259,288 ****
    }
    
    for (iter=0; iter<numIterations; iter++) {
      if (cctx->verbose) {
!       fprintf(stderr, "%s: starting iter %d\n", me, iter);
      }
      cctx->finished = AIR_FALSE;
      if (cctx->numThreads > 1) {
!       airThreadBarrierWait(cctx->finishBarrier);
      }
      
      /* first: filter */
!     if (cctx->verbose) {
        fprintf(stderr, "%s: filtering ... \n", me);
      }
      _coilProcess(cctx->task[0], AIR_TRUE);
-     if (cctx->numThreads > 1) {
-       airThreadBarrierWait(cctx->filterBarrier);
-     }
  
      /* second: update */
!     if (cctx->verbose) {
        fprintf(stderr, "%s: updating ... \n", me);
      }
-     _coilProcess(cctx->task[0], AIR_FALSE);
      if (cctx->numThreads > 1) {
        airThreadBarrierWait(cctx->updateBarrier);
      }
    }
    return 0;
--- 334,368 ----
    }
    
+   time0 = airTime();
    for (iter=0; iter<numIterations; iter++) {
      if (cctx->verbose) {
!       fprintf(stderr, "%s: starting iter %d (of %d)\n", me, iter, 
! 	      numIterations);
      }
      cctx->finished = AIR_FALSE;
      if (cctx->numThreads > 1) {
!       airThreadBarrierWait(cctx->filterBarrier);
      }
      
      /* first: filter */
!     if (cctx->verbose > 1) {
        fprintf(stderr, "%s: filtering ... \n", me);
      }
      _coilProcess(cctx->task[0], AIR_TRUE);
  
      /* second: update */
!     if (cctx->verbose > 1) {
        fprintf(stderr, "%s: updating ... \n", me);
      }
      if (cctx->numThreads > 1) {
        airThreadBarrierWait(cctx->updateBarrier);
      }
+     _coilProcess(cctx->task[0], AIR_FALSE);
+ 
+   }
+   time1 = airTime();
+   if (cctx->verbose) {
+     fprintf(stderr, "%s: elapsed time = %g (%g/iter)\n", me,
+ 	    time1 - time0, (time1 - time0)/numIterations);
    }
    return 0;
***************
*** 299,308 ****
    }
  
!   if (cctx->verbose) {
      fprintf(stderr, "%s: finishing workers\n", me);
    }
    cctx->finished = AIR_TRUE;
    if (cctx->numThreads > 1) {
!     airThreadBarrierWait(cctx->finishBarrier);
    }
    for (tidx=1; tidx<cctx->numThreads; tidx++) {
--- 379,388 ----
    }
  
!   if (cctx->verbose > 1) {
      fprintf(stderr, "%s: finishing workers\n", me);
    }
    cctx->finished = AIR_TRUE;
    if (cctx->numThreads > 1) {
!     airThreadBarrierWait(cctx->filterBarrier);
    }
    for (tidx=1; tidx<cctx->numThreads; tidx++) {
***************
*** 315,318 ****
--- 395,404 ----
    cctx->task = airFree(cctx->task);
  
+   if (cctx->numThreads > 1) {
+     cctx->nextSliceMutex = airThreadMutexNix(cctx->nextSliceMutex);
+     cctx->filterBarrier = airThreadBarrierNix(cctx->filterBarrier);
+     cctx->updateBarrier = airThreadBarrierNix(cctx->updateBarrier);
+   }
+ 
    return 0;
  }

[Teem-commit] teem/src/coil/test coiler.c,1.3,1.4

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

Update of /cvsroot/teem/teem/src/coil/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15148/test

Modified Files:
	coiler.c 
Log Message:
better load balancing, better conductance, just friggen better

Index: coiler.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/test/coiler.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** coiler.c	23 Mar 2004 01:18:40 -0000	1.3
--- coiler.c	24 Mar 2004 06:48:50 -0000	1.4
***************
*** 72,76 ****
    if (coilContextAllSet(cctx, nin,
  			coilKindScalar, coilMethodArray[methodType],
! 			radius, numThreads, AIR_TRUE,
  			parm)
        || coilStart(cctx)
--- 72,76 ----
    if (coilContextAllSet(cctx, nin,
  			coilKindScalar, coilMethodArray[methodType],
! 			radius, numThreads, 1 /* verbose */,
  			parm)
        || coilStart(cctx)

[Teem-commit] teem/src/coil coreCoil.c,1.1,1.2 methodsCoil.c,1.1,1.2 realmethods.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/coil
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17006

Modified Files:
	coreCoil.c methodsCoil.c realmethods.c 
Log Message:
we now have a revolutionary new way to do isotropic blurring!

Index: realmethods.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/realmethods.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** realmethods.c	22 Mar 2004 21:40:11 -0000	1.1
--- realmethods.c	23 Mar 2004 01:18:40 -0000	1.2
***************
*** 34,38 ****
    "isotropic",
    coilMethodTypeIsotropic,
!   0
  };
  const coilMethod*
--- 34,38 ----
    "isotropic",
    coilMethodTypeIsotropic,
!   1
  };
  const coilMethod*

Index: coreCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/coreCoil.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** coreCoil.c	22 Mar 2004 21:40:11 -0000	1.1
--- coreCoil.c	23 Mar 2004 01:18:40 -0000	1.2
***************
*** 35,46 ****
    diam = 1 + 2*radius;
    for (zni=0; zni<diam; zni++) {
!     zvi = AIR_CLAMP(0, zni-radius+z0, sizeZ-1);
      for (yni=0; yni<diam; yni++) {
!       yvi = AIR_CLAMP(0, yni-radius+y0, sizeY-1);
        for (xni=0; xni<diam; xni++) {
! 	xvi = AIR_CLAMP(0, xni-radius+x0, sizeX-1);
  	for (vi=0; vi<valLen; vi++) {
  	  iv3[xni + diam*(yni + diam*(zni + diam*vi))] = 
! 	    here[vi + valLen*(xvi + sizeX*(yvi + sizeY*zvi))];
  	}
        }
--- 35,46 ----
    diam = 1 + 2*radius;
    for (zni=0; zni<diam; zni++) {
!     zvi = AIR_CLAMP(0, zni-radius+z0, sizeZ-1) - z0;
      for (yni=0; yni<diam; yni++) {
!       yvi = AIR_CLAMP(0, yni-radius+y0, sizeY-1) - y0;
        for (xni=0; xni<diam; xni++) {
! 	xvi = AIR_CLAMP(0, xni-radius+x0, sizeX-1) - x0;
  	for (vi=0; vi<valLen; vi++) {
  	  iv3[xni + diam*(yni + diam*(zni + diam*vi))] = 
! 	    here[vi + valLen*(0 + 2*(xvi + sizeX*(yvi + sizeY*zvi)))];
  	}
        }
***************
*** 51,57 ****
  
  void
! _coilProcess(coilTask *task, int filter) {
    int xi, yi, zi, sizeX, sizeY, sizeZ, valLen, radius;
    coil_t *here;
    
    sizeX = task->cctx->size[0];
--- 51,60 ----
  
  void
! _coilProcess(coilTask *task, int doFilter) {
    int xi, yi, zi, sizeX, sizeY, sizeZ, valLen, radius;
    coil_t *here;
+   void (*filter)(coil_t *delta, coil_t *iv3, 
+ 		 double spacing[3],
+ 		 double parm[COIL_PARMS_NUM]);
    
    sizeX = task->cctx->size[0];
***************
*** 60,72 ****
    valLen = task->cctx->kind->valLen;
    radius = task->cctx->radius;
    here = (coil_t*)(task->cctx->nvol->data);
    here += 2*valLen*sizeX*sizeY*task->startZ;
!   if (filter) {
      for (zi=task->startZ; zi<=task->endZ; zi++) {
        for (yi=0; yi<sizeY; yi++) {
  	for (xi=0; xi<sizeX; xi++) {
! 	  _coilIv3Fill(task->iv3, here, radius, valLen,
  		       xi, yi, zi, sizeX, sizeY, sizeZ);
! 	  /* filter */
  	  here += 2*valLen;
  	}
--- 63,76 ----
    valLen = task->cctx->kind->valLen;
    radius = task->cctx->radius;
+   filter = task->cctx->kind->filter[task->cctx->method->type];
    here = (coil_t*)(task->cctx->nvol->data);
    here += 2*valLen*sizeX*sizeY*task->startZ;
!   if (doFilter) {
      for (zi=task->startZ; zi<=task->endZ; zi++) {
        for (yi=0; yi<sizeY; yi++) {
  	for (xi=0; xi<sizeX; xi++) {
! 	  _coilIv3Fill(task->iv3, here + 0*valLen, radius, valLen,
  		       xi, yi, zi, sizeX, sizeY, sizeZ);
! 	  filter(here + 1*valLen, task->iv3, task->cctx->spacing, task->cctx->parm);
  	  here += 2*valLen;
  	}
***************
*** 186,192 ****
    
    cctx->finished = AIR_FALSE;
!   cctx->finishBarrier = airThreadBarrierNew(cctx->numThreads);
!   cctx->filterBarrier = airThreadBarrierNew(cctx->numThreads);
!   cctx->updateBarrier = airThreadBarrierNew(cctx->numThreads);
  
    /* start threads 1 and up running (they won't get far) */
--- 190,198 ----
    
    cctx->finished = AIR_FALSE;
!   if (cctx->numThreads > 1) {
!     cctx->finishBarrier = airThreadBarrierNew(cctx->numThreads);
!     cctx->filterBarrier = airThreadBarrierNew(cctx->numThreads);
!     cctx->updateBarrier = airThreadBarrierNew(cctx->numThreads);
!   }
  
    /* start threads 1 and up running (they won't get far) */
***************
*** 258,262 ****
      }
      cctx->finished = AIR_FALSE;
!     airThreadBarrierWait(cctx->finishBarrier);
      
      /* first: filter */
--- 264,270 ----
      }
      cctx->finished = AIR_FALSE;
!     if (cctx->numThreads > 1) {
!       airThreadBarrierWait(cctx->finishBarrier);
!     }
      
      /* first: filter */
***************
*** 265,269 ****
      }
      _coilProcess(cctx->task[0], AIR_TRUE);
!     airThreadBarrierWait(cctx->filterBarrier);
  
      /* second: update */
--- 273,279 ----
      }
      _coilProcess(cctx->task[0], AIR_TRUE);
!     if (cctx->numThreads > 1) {
!       airThreadBarrierWait(cctx->filterBarrier);
!     }
  
      /* second: update */
***************
*** 272,276 ****
      }
      _coilProcess(cctx->task[0], AIR_FALSE);
!     airThreadBarrierWait(cctx->updateBarrier);
    }
    return 0;
--- 282,288 ----
      }
      _coilProcess(cctx->task[0], AIR_FALSE);
!     if (cctx->numThreads > 1) {
!       airThreadBarrierWait(cctx->updateBarrier);
!     }
    }
    return 0;
***************
*** 291,300 ****
    }
    cctx->finished = AIR_TRUE;
!   airThreadBarrierWait(cctx->finishBarrier);
    for (tidx=1; tidx<cctx->numThreads; tidx++) {
      airThreadJoin(cctx->task[tidx]->thread, &(cctx->task[tidx]->returnPtr));
      cctx->task[tidx]->thread = airThreadNix(cctx->task[tidx]->thread);
    }
    cctx->task[0]->thread = airThreadNix(cctx->task[0]->thread);
  
    return 0;
--- 303,317 ----
    }
    cctx->finished = AIR_TRUE;
!   if (cctx->numThreads > 1) {
!     airThreadBarrierWait(cctx->finishBarrier);
!   }
    for (tidx=1; tidx<cctx->numThreads; tidx++) {
      airThreadJoin(cctx->task[tidx]->thread, &(cctx->task[tidx]->returnPtr));
      cctx->task[tidx]->thread = airThreadNix(cctx->task[tidx]->thread);
+     cctx->task[tidx] = _coilTaskNix(cctx->task[tidx]);
    }
    cctx->task[0]->thread = airThreadNix(cctx->task[0]->thread);
+   cctx->task[0] = _coilTaskNix(cctx->task[0]);
+   cctx->task = airFree(cctx->task);
  
    return 0;

Index: methodsCoil.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/methodsCoil.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** methodsCoil.c	22 Mar 2004 21:40:11 -0000	1.1
--- methodsCoil.c	23 Mar 2004 01:18:40 -0000	1.2
***************
*** 74,77 ****
--- 74,78 ----
    airArray *mop;
    
+   cctx->verbose = verbose;
    if (!( cctx && nin && kind && method )) {
      sprintf(err, "%s: got NULL pointer", me);
***************
*** 147,150 ****
--- 148,155 ----
    }
    ELL_3V_SET(cctx->spacing, xsp, ysp, zsp);
+   if (cctx->verbose) {
+     fprintf(stderr, "%s: spacings: %g %g %g\n", me, 
+ 	    cctx->spacing[0], cctx->spacing[1], cctx->spacing[2]);
+   }
    
    /* allocate nvol */
***************
*** 166,170 ****
    cctx->radius = radius;
    cctx->numThreads = numThreads;
-   cctx->verbose = verbose;
  
    airMopOkay(mop);
--- 171,174 ----

[Teem-commit] teem/src/coil/test coiler.c,1.2,1.3

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

Update of /cvsroot/teem/teem/src/coil/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17006/test

Modified Files:
	coiler.c 
Log Message:
we now have a revolutionary new way to do isotropic blurring!

Index: coiler.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/test/coiler.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** coiler.c	22 Mar 2004 21:50:12 -0000	1.2
--- coiler.c	23 Mar 2004 01:18:40 -0000	1.3
***************
*** 29,36 ****
    airArray *mop;
    
!   int numIters, numThreads, methodType;
    Nrrd *nin, *nout;
    coilContext *cctx;
!   double parm[COIL_PARMS_NUM];
    
    mop = airMopNew();
--- 29,36 ----
    airArray *mop;
    
!   int numIters, numThreads, methodType, _parmLen, pi, radius;
    Nrrd *nin, *nout;
    coilContext *cctx;
!   double *_parm, parm[COIL_PARMS_NUM];
    
    mop = airMopNew();
***************
*** 42,45 ****
--- 42,49 ----
    hestOptAdd(&hopt, "m", "method", airTypeEnum, 1, 1, &methodType, "test",
  	     "what kind of filtering to perform", NULL, coilMethodType);
+   hestOptAdd(&hopt, "p", "parms", airTypeDouble, 1, -1, &_parm, NULL,
+ 	     "all the parameters required for filtering method", &_parmLen);
+   hestOptAdd(&hopt, "r", "radius", airTypeInt, 1, 1, &radius, "1",
+ 	     "radius of filtering neighborhood");
    hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &(nin), "",
  	     "input volume to filter", NULL, NULL, nrrdHestNrrd);
***************
*** 56,62 ****
    airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
    
    if (coilContextAllSet(cctx, nin,
  			coilKindScalar, coilMethodArray[methodType],
! 			3, numThreads, AIR_TRUE,
  			parm)
        || coilStart(cctx)
--- 60,76 ----
    airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
    
+   if (_parmLen != coilMethodArray[methodType]->numParm) {
+     fprintf(stderr, "%s: %s method wants %d parms, but got %d\n", me, 
+ 	    coilMethodArray[methodType]->name,
+ 	    coilMethodArray[methodType]->numParm, _parmLen);
+     airMopError(mop); 
+     return 1;
+   }
+   for (pi=0; pi<_parmLen; pi++) {
+     parm[pi] = _parm[pi];
+   }
    if (coilContextAllSet(cctx, nin,
  			coilKindScalar, coilMethodArray[methodType],
! 			radius, numThreads, AIR_TRUE,
  			parm)
        || coilStart(cctx)

[Teem-commit] teem/src/coil/test coiler.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/coil/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5016/test

Modified Files:
	coiler.c 
Log Message:
debugging ...

Index: coiler.c
===================================================================
RCS file: /cvsroot/teem/teem/src/coil/test/coiler.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** coiler.c	22 Mar 2004 21:40:11 -0000	1.1
--- coiler.c	22 Mar 2004 21:50:12 -0000	1.2
***************
*** 31,38 ****
    int numIters, numThreads, methodType;
    Nrrd *nin, *nout;
-   mop = airMopNew();
    coilContext *cctx;
    double parm[COIL_PARMS_NUM];
    
    me = argv[0];
    hestOptAdd(&hopt, "iter", "# iters", airTypeInt, 1, 1, &numIters, "5",
--- 31,38 ----
    int numIters, numThreads, methodType;
    Nrrd *nin, *nout;
    coilContext *cctx;
    double parm[COIL_PARMS_NUM];
    
+   mop = airMopNew();
    me = argv[0];
    hestOptAdd(&hopt, "iter", "# iters", airTypeInt, 1, 1, &numIters, "5",

[Teem-commit] teem/src GNUmakefile,1.52,1.53

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

Update of /cvsroot/teem/teem/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4904

Modified Files:
	GNUmakefile 
Log Message:
added coil to teem lib list

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/GNUmakefile,v
retrieving revision 1.52
retrieving revision 1.53
diff -C2 -d -r1.52 -r1.53
*** GNUmakefile	26 Feb 2004 06:27:32 -0000	1.52
--- GNUmakefile	22 Mar 2004 21:49:54 -0000	1.53
***************
*** 96,102 ****
  ## {R}NUM/LIBS: used for craziness below
  ##
! LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten mite
! NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E   F
! RNUMS = F   E    D    C    B    A    9    8    7    6    5    4     3    2    1   0
  #LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten
  #NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E  
--- 96,102 ----
  ## {R}NUM/LIBS: used for craziness below
  ##
! LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten mite coil
! NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E   F    G
! RNUMS = G   F   E    D    C    B    A    9    8    7    6    5    4     3    2    1   0
  #LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten
  #NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E  

[Teem-commit] teem/src/coil coil.h,NONE,1.1 GNUmakefile,NONE,1.1 coreCoil.c,NONE,1.1 defaultsCoil.c,NONE,1.1 enumsCoil.c,NONE,1.1 methodsCoil.c,NONE,1.1 realmethods.c,NONE,1.1 scalarCoil.c,NONE,1.1 tensorCoil.c,NONE,1.1

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

Update of /cvsroot/teem/teem/src/coil
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3054

Added Files:
	coil.h GNUmakefile coreCoil.c defaultsCoil.c enumsCoil.c 
	methodsCoil.c realmethods.c scalarCoil.c tensorCoil.c 
Log Message:
this is the last teem library that Gordon will write while he does not have a PhD

--- NEW FILE: defaultsCoil.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

const char *
coilBiffKey = "coil";

int
coilDefaultRadius = 1;

--- NEW FILE: GNUmakefile ---
#
# teem: Gordon Kindlmann's research software
# Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
#

#### Library name
####
####
L := coil
####
####
####

# boilerplate: default targets and include tricks
TEEM_ROOT ?= ../..
TEEM_SRC ?= ..
ifeq (,$(DEF_TARGETS))
DEF_TARGETS = true
dev     : $(L)/dev
install : $(L)/install
clean   : $(L)/clean
clobber : $(L)/clobber
include ../GNUmakefile
endif
ifeq (,$($(L).SEEN))
$(L).SEEN := true

#### Describe library here
#### (ell for macros)
####
$(L).NEED = ten gage ell nrrd biff air
$(L).PUBLIC_HEADERS = coil.h
$(L).PRIVATE_HEADERS = 
$(L).OBJS = defaultsCoil.o enumsCoil.o scalarCoil.o tensorCoil.o \
            realmethods.o methodsCoil.o coreCoil.o
$(L).TESTS = test/coiler
####
####
####

# boilerplate: declare rules for this library
include $(TEEM_SRC)/make/template.mk
endif
ifeq (,$(INCLUDED))
  include $(TEEM_SRC)/bin/GNUmakefile
endif

--- NEW FILE: coil.h ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#ifndef COIL_HAS_BEEN_INCLUDED
#define COIL_HAS_BEEN_INCLUDED

#include <teem/air.h>
#include <teem/biff.h>
#include <teem/ell.h>
#include <teem/nrrd.h>
#include <teem/gage.h>
#include <teem/ten.h>

#ifdef __cplusplus
extern "C" {
#endif

#define COIL coilBiffKey

/*
******** coil_t
** 
** this is the very crude means by which you can control the type
** of values that coil works with: "float" or "double".  It is an
** unfortunate but greatly simplifying restriction that this type
** is used for all kinds of volumes, and all methods of filtering
**
** So: choose double by defining TEEM_COIL_TYPE_DOUBLE and float
** otherwise.
*/

#ifdef TEEM_COIL_TYPE_DOUBLE
typedef double coil_t;
#define coil_nrrdType nrrdTypeDouble
#define COIL_TYPE_FLOAT 0
#else
typedef float coil_t;
#define coil_nrrdType nrrdTypeFloat
#define COIL_TYPE_FLOAT 1
#endif

/*
******** #define COIL_PARMS_NUM
**
** maximum number of parameters that may be needed by any coil-driven
** filtering method
*/
#define COIL_PARMS_NUM 5

/*
******** coilMethodType* enum
**
** enumerated possibilities for different filtering methods
*/
enum {
  coilMethodTypeUnknown,            /* 0 */
  coilMethodTypeTesting,            /* 1: basically a no-op */
  coilMethodTypeIsotropic,          /* 2 */
  coilMethodTypeAnisotropic,        /* 3 */
  coilMethodTypeModifiedCurvature,  /* 4 */
  coilMethodTypeCurvatureFlow,      /* 5 */
  coilMethodTypeLast
};
#define COIL_METHOD_TYPE_MAX           5

/*
******** coilMethod struct
**
** someday, there will be total orthogonality between kind and method.
** until then, this will have only a portion of the things relating to
** running one method, regardless of kind
*/
typedef struct {
  char name[AIR_STRLEN_SMALL];
  int type;                         /* from coilMethodType* enum */
  int numParm;                      /* number of parameters we need */
} coilMethod;

/*
******** coilKindType* enum
**
** enumerated possibilities for different kinds
*/
enum {
  coilKindTypeUnknown,              /* 0 */
  coilKindTypeScalar,               /* 1 */
  coilKindType3Color,               /* 2 */
  coilKindType7Tensor,              /* 3 */
  coilKindTypeLast
};
#define COIL_KIND_TYPE_MAX             3

/*
******** coilKind struct
**
** yes, there is some redunancy with the gageKind, but the the main
** reason is that its significantly easier to implement meaningful
** per-sample filtering of various quantities, than it is to do
** gage-style convolution-based measurements at arbitrary locations.
** So, there will probably be significantly more coilKinds than
** there are gageKinds.  The two kind systems may play closer together
** at some point in the future where appropriate.
*/
typedef struct {
  char name[AIR_STRLEN_SMALL];      /* short identifying string for kind */
  int valLen;                       /* number of scalars per data point
				       1 for plain scalars (baseDim=0),
				       or something else (baseDim=1) */
                                    /* all the available methods */
  void (*filter[COIL_METHOD_TYPE_MAX+1])(coil_t *delta, coil_t *iv3,
					 double spacing[3],
					 double parm[COIL_PARMS_NUM]);
  void (*update)(coil_t *val, coil_t *delta); /* how to apply update */
} coilKind;

struct coilContext_t;

/*
******** coilTask
**
** passed to all worker threads
*/
typedef struct {
  struct coilContext_t *cctx;      /* parent's context */
  airThread *thread;               /* my thread */
  int threadIdx,                   /* which thread am I */
    startZ, endZ;                  /* my index range (inclusive) of slices */
  coil_t *iv3;                     /* cache of local values, ordering same
				      as in gage: any multiple values per
				      voxel are the slowest axis, not the
				      fastest */
  void *returnPtr;                 /* for airThreadJoin */
} coilTask;

/*
******** coilContext struct
**
** bag of stuff relating to filtering one volume
*/
typedef struct coilContext_t {
  /* ---------- input */
  const Nrrd *nin;                 /* input volume, converted to coil_t nvol */
  const coilKind *kind;            /* what kind of volume is nin */
  const coilMethod *method;        /* what method of filtering to use */
  int radius,                      /* how big a neighborhood to look at when
				      doing filtering (use 1 for 3x3x3 size) */
    numThreads,                    /* number of threads to enlist */
    verbose;                       /* blah blah blah */
  double parm[COIL_PARMS_NUM];     /* all the parameters used to control the 
				      action of the filtering.  The timestep is
				      probably the first value. */
  /* ---------- internal */
  int size[3];                     /* size of volume */
  double spacing[3];               /* sample spacings we'll use- we perhaps 
				      should be using a gageShape, but this is
				      actually all we really need... */
  Nrrd *nvol;                      /* an interleaved volume of (1st) the last
				      filtering result, and (2nd) the update
				      values from the current iteration */
  int finished;                    /* used to signal all threads to return */
  coilTask **task;                 /* dynamically allocated array of tasks */
  airThreadBarrier *filterBarrier, /* for when filtering is done, and the
				      "update" values have been set */
    *updateBarrier,                /* after the update values have been
				      applied to current values */
    *finishBarrier;                /* so that thread 0 can see if filtering
				      should go onward, and set "finished" */
} coilContext;

/* defaultsCoil.c */
TEEM_API const char *coilBiffKey;
TEEM_API int coilDefaultRadius;

/* enumsCoil.c */
TEEM_API airEnum *coilMethodType;
TEEM_API airEnum *coilKindType;

/* scalarCoil.c */
TEEM_API const coilKind *coilKindScalar;

/* tensorCoil.c */
TEEM_API const coilKind *coilKindTensor;

/* realmethods.c */
TEEM_API const coilMethod *coilMethodTesting;
TEEM_API const coilMethod *coilMethodIsotropic;
TEEM_API const coilMethod *coilMethodArray[COIL_METHOD_TYPE_MAX+1];

/* methodsCoil.c (sorry, confusing name!) */
TEEM_API coilContext *coilContextNew();
TEEM_API int coilVolumeCheck(const Nrrd *nin, const coilKind *kind);
TEEM_API int coilContextAllSet(coilContext *cctx, const Nrrd *nin,
			       const coilKind *kind, const coilMethod *method,
			       int radius, int numThreads, int verbose,
			       double parm[COIL_PARMS_NUM]);
TEEM_API int coilOutputGet(Nrrd *nout, coilContext *cctx);
TEEM_API coilContext *coilContextNix(coilContext *cctx);

/* coreCoil.c */
TEEM_API int coilStart(coilContext *cctx);
TEEM_API int coilIterate(coilContext *cctx, int numIterations);
TEEM_API int coilFinish(coilContext *cctx);

#ifdef __cplusplus
}
#endif

#endif /* COIL_HAS_BEEN_INCLUDED */

--- NEW FILE: tensorCoil.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

void
_coilKind7TensorFilterTesting(coil_t *delta, coil_t *iv3, 
			      double spacing[3],
			      double parm[COIL_PARMS_NUM]) {
  delta[0] = 0;
  delta[1] = 0;
  delta[2] = 0;
  delta[3] = 0;
  delta[4] = 0;
  delta[5] = 0;
  delta[6] = 0;
}

void
_coilKind7TensorFilterIsotropic(coil_t *delta, coil_t *iv3, 
				double spacing[3],
				double parm[COIL_PARMS_NUM]) {
  
}

void
_coilKindTensorUpdate(coil_t *val, coil_t *delta) {
  
  val[0] += delta[0]; /* WARNING: this could change confidence! */
  val[1] += delta[1];
  val[2] += delta[2];
  val[3] += delta[3];
  val[4] += delta[4];
  val[5] += delta[5];
  val[6] += delta[6];
}

const coilKind
_coilKindTensor = {
  "tensor",
  7,
  {NULL,
   _coilKind7TensorFilterTesting,
   _coilKind7TensorFilterIsotropic,
   NULL,
   NULL,
   NULL},
  _coilKindTensorUpdate
};

const coilKind *
coilKindTensor = &_coilKindTensor;

--- NEW FILE: scalarCoil.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

/*
**  x ----> X
**   \   0  1  2 
**  |  \   3  4  5
**  |    Y   6  7  8
**  |
**  |    9 10 11   
**  Z      12 13 14
**           15 16 17
**  
**       18 19 20
**         21 22 23
**           24 25 26
*/

coil_t
_coilLaplacian3(coil_t *iv3, double spacing[3]) {
  
  return ((iv3[12] - 2*iv3[13] + iv3[14])/(spacing[0]*spacing[0])
	  + (iv3[10] - 2*iv3[13] + iv3[16])/(spacing[1]*spacing[1])
	  + (iv3[ 4] - 2*iv3[13] + iv3[22])/(spacing[2]*spacing[2]));
}

void
_coilKindScalarFilterTesting(coil_t *delta, coil_t *iv3, 
			     double spacing[3],
			     double parm[COIL_PARMS_NUM]) {
  delta[0] = 0;
}

void
_coilKindScalarFilterIsotropic(coil_t *delta, coil_t *iv3,
			       double spacing[3],
			       double parm[COIL_PARMS_NUM]) {
  coil_t lapl;

  lapl = _coilLaplacian3(iv3, spacing);
  delta[0] = parm[0]*lapl;
}

void
_coilKindScalarUpdate(coil_t *val, coil_t *delta) {
  
  val[0] += delta[0];
}

const coilKind
_coilKindScalar = {
  "scalar",
  1,
  {NULL,
   _coilKindScalarFilterTesting,
   _coilKindScalarFilterIsotropic,
   NULL,
   NULL,
   NULL},
  _coilKindScalarUpdate
};

const coilKind *
coilKindScalar = &_coilKindScalar;

--- NEW FILE: realmethods.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

const coilMethod
_coilMethodTesting = {
  "testing",
  coilMethodTypeTesting,
  0
};
const coilMethod*
coilMethodTesting = &_coilMethodTesting;


const coilMethod
_coilMethodIsotropic = {
  "isotropic",
  coilMethodTypeIsotropic,
  0
};
const coilMethod*
coilMethodIsotropic = &_coilMethodIsotropic;

const coilMethod*
coilMethodArray[COIL_METHOD_TYPE_MAX+1] = {
  NULL,
  &_coilMethodTesting,
  &_coilMethodIsotropic,
  NULL,
  NULL,
  NULL
};

--- NEW FILE: coreCoil.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

/*
** 
** iv3 is: diam x diam x diam x valLen
*/
void
_coilIv3Fill(coil_t *iv3, coil_t *here, int radius, int valLen,
	     int x0, int y0, int z0, int sizeX, int sizeY, int sizeZ) {
  int diam, vi,    /* value index */
    xni, yni, zni, /* neighborhood (iv3) indices */
    xvi, yvi, zvi; /* volume indices */
  
  /* this should be parameterized on both radius and valLen */
  /* this should shuffle values within iv3 when possible */
  diam = 1 + 2*radius;
  for (zni=0; zni<diam; zni++) {
    zvi = AIR_CLAMP(0, zni-radius+z0, sizeZ-1);
    for (yni=0; yni<diam; yni++) {
      yvi = AIR_CLAMP(0, yni-radius+y0, sizeY-1);
      for (xni=0; xni<diam; xni++) {
	xvi = AIR_CLAMP(0, xni-radius+x0, sizeX-1);
	for (vi=0; vi<valLen; vi++) {
	  iv3[xni + diam*(yni + diam*(zni + diam*vi))] = 
	    here[vi + valLen*(xvi + sizeX*(yvi + sizeY*zvi))];
	}
      }
    }
  }
  return;
}

void
_coilProcess(coilTask *task, int filter) {
  int xi, yi, zi, sizeX, sizeY, sizeZ, valLen, radius;
  coil_t *here;
  
  sizeX = task->cctx->size[0];
  sizeY = task->cctx->size[1];
  sizeZ = task->cctx->size[2];
  valLen = task->cctx->kind->valLen;
  radius = task->cctx->radius;
  here = (coil_t*)(task->cctx->nvol->data);
  here += 2*valLen*sizeX*sizeY*task->startZ;
  if (filter) {
    for (zi=task->startZ; zi<=task->endZ; zi++) {
      for (yi=0; yi<sizeY; yi++) {
	for (xi=0; xi<sizeX; xi++) {
	  _coilIv3Fill(task->iv3, here, radius, valLen,
		       xi, yi, zi, sizeX, sizeY, sizeZ);
	  /* filter */
	  here += 2*valLen;
	}
      }
    }
  } else {
    for (zi=task->startZ; zi<=task->endZ; zi++) {
      for (yi=0; yi<sizeY; yi++) {
	for (xi=0; xi<sizeX; xi++) {
	  task->cctx->kind->update(here + 0*valLen, here + 1*valLen);
	  here += 2*valLen;
	}
      }
    }
  }
  return;
}

coilTask *
_coilTaskNew(coilContext *cctx, int threadIdx, int sizeZ) {
  coilTask *task;
  int len, diam;

  len = cctx->kind->valLen;
  diam = 1 + 2*cctx->radius;
  task = (coilTask *)calloc(1, sizeof(coilTask));
  if (task) {
    task->cctx = cctx;
    task->thread = airThreadNew();
    task->startZ = threadIdx*sizeZ/cctx->numThreads;
    task->endZ = (threadIdx+1)*sizeZ/cctx->numThreads - 1;
    task->threadIdx = threadIdx;
    task->iv3 = (coil_t*)calloc(len*diam*diam*diam, sizeof(coil_t));
    task->returnPtr = NULL;
  }
  return task;
}

coilTask *
_coilTaskNix(coilTask *task) {

  if (task) {
    task->thread = airThreadNix(task->thread);
    task->iv3 = airFree(task->iv3);
    free(task);
  }
  return NULL;
}

void *
_coilWorker(void *_task) {
  char me[]="_coilWorker";
  coilTask *task;

  task = (coilTask *)_task;

  while (1) {
    /* wait until parent has set cctx->finished */
    if (task->cctx->verbose) {
      fprintf(stderr, "%s(%d): waiting to check finished\n",
	      me, task->threadIdx);
    }
    airThreadBarrierWait(task->cctx->finishBarrier);
    if (task->cctx->finished) {
      if (task->cctx->verbose) {
	fprintf(stderr, "%s(%d): done!\n", me, task->threadIdx);
      }
      break;
    }
    /* else there's work */

    /* first: filter */
    if (task->cctx->verbose) {
      fprintf(stderr, "%s(%d): filtering ... \n",
	      me, task->threadIdx);
    }
    _coilProcess(task, AIR_TRUE);
    airThreadBarrierWait(task->cctx->filterBarrier);

    /* second: update */
    if (task->cctx->verbose) {
      fprintf(stderr, "%s(%d): updating ... \n",
	      me, task->threadIdx);
    }
    _coilProcess(task, AIR_FALSE);
    airThreadBarrierWait(task->cctx->updateBarrier);
  }

  return _task;
}

int
coilStart(coilContext *cctx) {
  char me[]="coilStart", err[AIR_STRLEN_MED];
  int tidx, elIdx, valIdx, valLen;
  coil_t (*lup)(const void*, size_t), *val;

  if (!cctx) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(COIL, err); return 1;
  }
  cctx->task = (coilTask **)calloc(cctx->numThreads, sizeof(coilTask *));
  if (!(cctx->task)) {
    sprintf(err, "%s: couldn't allocate array of tasks", me);
    biffAdd(COIL, err); return 1;
  }
  
  /* we create tasks for ALL threads, including me, thread 0 */
  cctx->task[0] = NULL;
  for (tidx=0; tidx<cctx->numThreads; tidx++) {
    cctx->task[tidx] = _coilTaskNew(cctx, tidx, cctx->size[2]);
    if (!(cctx->task[tidx])) {
      sprintf(err, "%s: couldn't allocate task %d", me, tidx);
      biffAdd(COIL, err); return 1;
    }
  }
  
  cctx->finished = AIR_FALSE;
  cctx->finishBarrier = airThreadBarrierNew(cctx->numThreads);
  cctx->filterBarrier = airThreadBarrierNew(cctx->numThreads);
  cctx->updateBarrier = airThreadBarrierNew(cctx->numThreads);

  /* start threads 1 and up running (they won't get far) */
  if (cctx->verbose) {
    fprintf(stderr, "%s: parent doing slices Z=[%d,%d]\n", me, 
	    cctx->task[0]->startZ, cctx->task[0]->endZ);
  }
  for (tidx=1; tidx<cctx->numThreads; tidx++) {
    if (cctx->verbose) {
      fprintf(stderr, "%s: spawning thread %d (Z=[%d,%d])\n", me, tidx,
	      cctx->task[tidx]->startZ, cctx->task[tidx]->endZ);
    }
    airThreadStart(cctx->task[tidx]->thread, _coilWorker,
		   (void *)(cctx->task[tidx]));
  }

  /* initialize the values in cctx->nvol */
  val = (coil_t*)(cctx->nvol->data);
  valLen = cctx->kind->valLen;
#if COIL_TYPE_FLOAT
  lup = nrrdFLookup[cctx->nin->type];
#else
  lup = nrrdDLookup[cctx->nin->type];
#endif
  for (elIdx=0; elIdx<cctx->size[0]*cctx->size[1]*cctx->size[2]; elIdx++) {
    for (valIdx=0; valIdx<valLen; valIdx++) {
      val[valIdx + 0*valLen] = lup(cctx->nin->data, valIdx + valLen*elIdx);
      val[valIdx + 1*valLen] = 0;
    }
    val += 2*valLen;
  }
  
  return 0;
}

int
_coilPause(int huge) {
  int i, j, num;
  
  num = 0;
  for (i=1; i<huge; i++) {
    for (j=0; j<huge; j++) {
      num *= i;
    }
  }
  return num;
}

/*
******** coilIterate
**
** (documentation)
**
** NB: this implements the body of thread 0
*/
int
coilIterate(coilContext *cctx, int numIterations) {
  char me[]="coilIterate", err[AIR_STRLEN_MED];
  int iter;

  if (!cctx) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(COIL, err); return 1;
  }
  
  for (iter=0; iter<numIterations; iter++) {
    if (cctx->verbose) {
      fprintf(stderr, "%s: starting iter %d\n", me, iter);
    }
    cctx->finished = AIR_FALSE;
    airThreadBarrierWait(cctx->finishBarrier);
    
    /* first: filter */
    if (cctx->verbose) {
      fprintf(stderr, "%s: filtering ... \n", me);
    }
    _coilProcess(cctx->task[0], AIR_TRUE);
    airThreadBarrierWait(cctx->filterBarrier);

    /* second: update */
    if (cctx->verbose) {
      fprintf(stderr, "%s: updating ... \n", me);
    }
    _coilProcess(cctx->task[0], AIR_FALSE);
    airThreadBarrierWait(cctx->updateBarrier);
  }
  return 0;
}

int
coilFinish(coilContext *cctx) {
  char me[]="coilFinish", err[AIR_STRLEN_MED];
  int tidx;

  if (!cctx) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(COIL, err); return 1;
  }

  if (cctx->verbose) {
    fprintf(stderr, "%s: finishing workers\n", me);
  }
  cctx->finished = AIR_TRUE;
  airThreadBarrierWait(cctx->finishBarrier);
  for (tidx=1; tidx<cctx->numThreads; tidx++) {
    airThreadJoin(cctx->task[tidx]->thread, &(cctx->task[tidx]->returnPtr));
    cctx->task[tidx]->thread = airThreadNix(cctx->task[tidx]->thread);
  }
  cctx->task[0]->thread = airThreadNix(cctx->task[0]->thread);

  return 0;
}

--- NEW FILE: enumsCoil.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

char
_coilMethodTypeStr[COIL_METHOD_TYPE_MAX+1][AIR_STRLEN_SMALL] = {
  "(unknown_method)",
  "testing",
  "isotropic",
  "anisotropic",
  "modified curvature",
  "curvature flow"
};

char
_coilMethodTypeDesc[COIL_METHOD_TYPE_MAX+1][AIR_STRLEN_MED] = {
  "unknown_method",
  "nothing, actually, just here for testing",
  "isotropic diffusion (Gaussian blurring)",
  "anisotropic diffusion (Perona-Malik)",
  "modified curvature diffusion",
  "curvature flow"
};

char
_coilMethodTypeStrEqv[][AIR_STRLEN_SMALL] = {
  "test", "testing",
  "iso", "isotropic",
  "aniso", "anisotropic",
  "mcde",
  "flow", 
  ""
};

int
_coilMethodTypeValEqv[] = {
  coilMethodTypeTesting, coilMethodTypeTesting,
  coilMethodTypeIsotropic, coilMethodTypeIsotropic,
  coilMethodTypeAnisotropic, coilMethodTypeAnisotropic,
  coilMethodTypeModifiedCurvature,
  coilMethodTypeCurvatureFlow
};

airEnum
_coilMethodType = {
  "method",
  COIL_METHOD_TYPE_MAX,
  _coilMethodTypeStr,  NULL,
  _coilMethodTypeDesc,
  _coilMethodTypeStrEqv, _coilMethodTypeValEqv,
  AIR_FALSE
};
airEnum *
coilMethodType = &_coilMethodType;

/* -------------------------------------------------- */

char
_coilKindTypeStr[COIL_KIND_TYPE_MAX+1][AIR_STRLEN_SMALL] = {
  "(unknown_kind)",
  "scalar",
  "3color",
  "7tensor"
};

char
_coilKindTypeDesc[COIL_KIND_TYPE_MAX+1][AIR_STRLEN_MED] = {
  "unknown_kind",
  "plain old scalar quantities",
  "3-component color",
  "ten-style 7-valued tensor"
};

char
_coilKindTypeStrEqv[][AIR_STRLEN_SMALL] = {
  "scalar",
  "3color",
  "7tensor",
  ""
};

int
_coilKindTypeValEqv[] = {
  coilKindTypeScalar,
  coilKindType3Color,
  coilKindType7Tensor
};

airEnum
_coilKindType = {
  "kind",
  COIL_KIND_TYPE_MAX,
  _coilKindTypeStr,  NULL,
  _coilKindTypeDesc,
  _coilKindTypeStrEqv, _coilKindTypeValEqv,
  AIR_FALSE
};
airEnum *
coilKindType = &_coilKindType;

--- NEW FILE: methodsCoil.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

#include "coil.h"

int
coilVolumeCheck(const Nrrd *nin, const coilKind *kind) {
  char me[]="coilVolumeCheck", err[AIR_STRLEN_MED];
  int baseDim;
  
  if (!(nin && kind)) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(COIL, err); return 1;
  }
  if (nrrdTypeBlock == nin->type) {
    sprintf(err, "%s: can only operate on scalar types, not %s", me,
	    airEnumStr(nrrdType, nrrdTypeBlock));
    biffAdd(COIL, err); return 1;
  }
  baseDim = (1 == kind->valLen ? 0 : 1);
  if (3 + baseDim != nin->dim) {
    sprintf(err, "%s: dim of input must be 3+%d (3 + baseDim), not %d", 
	    me, baseDim, nin->dim);
    biffAdd(COIL, err); return 1;
  }

  return 0;
}

coilContext *
coilContextNew() {
  coilContext *cctx;
  
  cctx = (coilContext *)calloc(1, sizeof(coilContext));
  if (cctx) {
    cctx->nin = NULL;
    cctx->radius = coilDefaultRadius;
    cctx->numThreads = 1;
    ELL_3V_SET(cctx->spacing, AIR_NAN, AIR_NAN, AIR_NAN);
    cctx->nvol = NULL;
    cctx->finished = AIR_FALSE;
    cctx->task = NULL;
    cctx->finishBarrier = NULL;
    cctx->filterBarrier = NULL;
    cctx->updateBarrier = NULL;
  }
  return cctx;
}

int
coilContextAllSet(coilContext *cctx, const Nrrd *nin,
		  const coilKind *kind, const coilMethod *method,
		  int radius, int numThreads, int verbose,
		  double parm[COIL_PARMS_NUM]) {
  char me[]="coilContextAllSet", err[AIR_STRLEN_MED];
  int size[NRRD_DIM_MAX], sx, sy, sz, someExist, allExist, baseDim, pi;
  double xsp, ysp, zsp;
  airArray *mop;
  
  if (!( cctx && nin && kind && method )) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(COIL, err); return 1;
  }
  if (coilVolumeCheck(nin, kind)) {
    sprintf(err, "%s: input volume not usable as %s", me, kind->name);
    biffAdd(COIL, err); return 1;
  }
  if (!( radius >= 1 && numThreads >= 1 )) {
    sprintf(err, "%s: radius (%d) not >= 1 or numThreads (%d) not >= 1", me,
	    radius, numThreads);
    biffAdd(COIL, err); return 1;
  }
  if (!( AIR_IN_OP(coilMethodTypeUnknown, method->type,
		   coilMethodTypeLast) )) {
    sprintf(err, "%s: method->type %d not valid", me, method->type);
    biffAdd(COIL, err); return 1;
  }
  
  if (!kind->filter[method->type]) {
    sprintf(err, "%s: sorry, %s filtering not available on %s kind",
	    me, method->name, kind->name);
    biffAdd(COIL, err); return 1;
  }

  /* warn if we can't do the multiple threads user wants */
  if (numThreads > 1 && !airThreadCapable && airThreadNoopWarning) {
    fprintf(stderr, "%s: WARNING: this teem not thread capable: using 1 "
	    "thread, not %d\n", me, numThreads);
    numThreads = 1;
  }
  
  mop = airMopNew();

  /* set parms */
  for (pi=0; pi<method->numParm; pi++) {
    if (!AIR_EXISTS(parm[pi])) {
      sprintf(err, "%s: parm[%d] (need %d) doesn't exist",
	      me, pi, method->numParm);
      biffAdd(COIL, err); airMopError(mop); return 1;
    }
    cctx->parm[pi] = parm[pi];
  }

  /* set sizes and spacings */
  baseDim = (1 == kind->valLen ? 0 : 1);
  sx = nin->axis[0 + baseDim].size;
  sy = nin->axis[1 + baseDim].size;
  sz = nin->axis[2 + baseDim].size;
  if (sz < numThreads) {
    fprintf(stderr, "%s: wanted %d threads but volume only has %d slices, "
	    "using %d threads instead\n", me, numThreads, sz, sz);
    numThreads = sz;
  }
  ELL_3V_SET(cctx->size, sx, sy, sz);
  xsp = nin->axis[0 + baseDim].spacing;
  ysp = nin->axis[1 + baseDim].spacing;
  zsp = nin->axis[2 + baseDim].spacing;
  someExist = AIR_EXISTS(xsp) || AIR_EXISTS(ysp) || AIR_EXISTS(zsp);
  allExist = AIR_EXISTS(xsp) && AIR_EXISTS(ysp) && AIR_EXISTS(zsp);
  if (!( someExist )) {
    fprintf(stderr, "%s: WARNING: assuming unit spacing for all axes\n", me);
    xsp = 1;
    ysp = 1;
    zsp = 1;
  } else {
    if ( !allExist ) {
      sprintf(err, "%s: spacings (%g,%g,%g) not uniformly existant", 
	      me, xsp, ysp, zsp);
      biffAdd(COIL, err); airMopError(mop); return 1;
    }
  }
  ELL_3V_SET(cctx->spacing, xsp, ysp, zsp);
  
  /* allocate nvol */
  if (0 == baseDim) {
    ELL_4V_SET(size, 2, sx, sy, sz);
  } else {
    ELL_5V_SET(size, kind->valLen, 2, sx, sy, sz);
  }
  cctx->nvol = nrrdNew();
  if (nrrdMaybeAlloc_nva(cctx->nvol, coil_nrrdType, 4 + baseDim, size)) {
    sprintf(err, "%s: couldn't allocate internal processing volume", me);
    biffMove(COIL, err, NRRD); airMopError(mop); return 1;
  }
  airMopAdd(mop, cctx->nvol, (airMopper)nrrdNuke, airMopOnError);
  
  cctx->nin = nin;
  cctx->kind = kind;
  cctx->method = method;
  cctx->radius = radius;
  cctx->numThreads = numThreads;
  cctx->verbose = verbose;

  airMopOkay(mop);
  return 0;
}

/*
******** coilOutputGet
**
** slice the present intermediate volume to get an output.  
**
** No, this does not do quantization or rounding to match the input 
** type (of cctx->nin).  The reason is that after filtering, it is often
** the case that subtle differences in values emerge, and it may be
** reckless to dump them back into the limited type or value range
** that they started with.  That sort of operation should be under
** explicit user control.
*/
int
coilOutputGet(Nrrd *nout, coilContext *cctx) {
  char me[]="coilOutputGet", err[AIR_STRLEN_MED];

  if (!(nout && cctx)) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(COIL, err); return 1;
  }
  if (nrrdSlice(nout, cctx->nvol, 0, 0)) {
    sprintf(err, "%s: trouble slicing to get output", me);
    biffMove(COIL, err, NRRD); return 1;
  }
  return 0;
}

coilContext *
coilContextNix(coilContext *cctx) {

  if (cctx) {
    cctx->nvol = nrrdNuke(cctx->nvol);
    cctx = airFree(cctx);
  }
  return NULL;
}

[Teem-commit] teem/src/coil/test coiler.c,NONE,1.1

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

Update of /cvsroot/teem/teem/src/coil/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3054/test

Added Files:
	coiler.c 
Log Message:
this is the last teem library that Gordon will write while he does not have a PhD

--- NEW FILE: coiler.c ---
/*
  teem: Gordon Kindlmann's research software
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/


#include "../coil.h"

char *info = ("Test program for coil library.");

int
main(int argc, char *argv[]) {
  char *me, *err, *outS;
  hestOpt *hopt=NULL;
  airArray *mop;
  
  int numIters, numThreads, methodType;
  Nrrd *nin, *nout;
  mop = airMopNew();
  coilContext *cctx;
  double parm[COIL_PARMS_NUM];
  
  me = argv[0];
  hestOptAdd(&hopt, "iter", "# iters", airTypeInt, 1, 1, &numIters, "5",
	     "number of iterations to do processing for");
  hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1, &numThreads, "5",
	     "number of threads to run");
  hestOptAdd(&hopt, "m", "method", airTypeEnum, 1, 1, &methodType, "test",
	     "what kind of filtering to perform", NULL, coilMethodType);
  hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &(nin), "",
	     "input volume to filter", NULL, NULL, nrrdHestNrrd);
  hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
	     "output file to save filtering result into");
  hestParseOrDie(hopt, argc-1, argv+1, NULL,
		 me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
  airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
  airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);

  cctx = coilContextNew();
  airMopAdd(mop, cctx, (airMopper)coilContextNix, airMopAlways);
  nout = nrrdNew();
  airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
  
  if (coilContextAllSet(cctx, nin,
			coilKindScalar, coilMethodArray[methodType],
			3, numThreads, AIR_TRUE,
			parm)
      || coilStart(cctx)
      || coilIterate(cctx, numIters)
      || coilFinish(cctx)
      || coilOutputGet(nout, cctx)) {
    airMopAdd(mop, err = biffGetDone(COIL), airFree, airMopAlways);
    fprintf(stderr, "%s: trouble with coil:\n%s\n", me, err);
    airMopError(mop); 
    return 1;
  }
  if (nrrdSave(outS, nout, NULL)) {
    airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
    fprintf(stderr, "%s: couldn't save output:\n%s\n", me, err);
    airMopError(mop); 
    return 1;
  }
  airMopOkay(mop);
  return 0;
}

[Teem-commit] teem/src/coil/test - New directory

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

Update of /cvsroot/teem/teem/src/coil/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2670/test

Log Message:
Directory /cvsroot/teem/teem/src/coil/test added to the repository

[Teem-commit] teem/src/coil - New directory

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

Update of /cvsroot/teem/teem/src/coil
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2489/coil

Log Message:
Directory /cvsroot/teem/teem/src/coil added to the repository

[Teem-commit] teem/src/nrrd nrrd.h,1.134,1.135 write.c,1.88,1.89

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26704

Modified Files:
	nrrd.h write.c 
Log Message:
these functions did not meet standard teem naming conventions

Index: nrrd.h
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/nrrd.h,v
retrieving revision 1.134
retrieving revision 1.135
diff -C2 -d -r1.134 -r1.135
*** nrrd.h	26 Feb 2004 20:59:45 -0000	1.134
--- nrrd.h	15 Mar 2004 03:07:41 -0000	1.135
***************
*** 602,612 ****
  /* write.c */
  TEEM_API int nrrdIoStateSet(NrrdIoState *io, int parm, int value);
! TEEM_API int nrrdIoStateSetEncoding(NrrdIoState *io,
  				    const NrrdEncoding *encoding);
! TEEM_API int nrrdIoStateSetFormat(NrrdIoState *io, 
  				  const NrrdFormat *format);
  TEEM_API int nrrdIoStateGet(NrrdIoState *io, int parm);
! TEEM_API const NrrdEncoding *nrrdIoStateGetEncoding(NrrdIoState *io);
! TEEM_API const NrrdFormat *nrrdIoStateBetFormat(NrrdIoState *io);
  TEEM_API int nrrdSave(const char *filename, const Nrrd *nrrd, NrrdIoState *io);
  TEEM_API int nrrdWrite(FILE *file, const Nrrd *nrrd, NrrdIoState *io);
--- 602,612 ----
  /* write.c */
  TEEM_API int nrrdIoStateSet(NrrdIoState *io, int parm, int value);
! TEEM_API int nrrdIoStateEncodingSet(NrrdIoState *io,
  				    const NrrdEncoding *encoding);
! TEEM_API int nrrdIoStateFormatSet(NrrdIoState *io, 
  				  const NrrdFormat *format);
  TEEM_API int nrrdIoStateGet(NrrdIoState *io, int parm);
! TEEM_API const NrrdEncoding *nrrdIoStateEncodingGet(NrrdIoState *io);
! TEEM_API const NrrdFormat *nrrdIoStateFormatGet(NrrdIoState *io);
  TEEM_API int nrrdSave(const char *filename, const Nrrd *nrrd, NrrdIoState *io);
  TEEM_API int nrrdWrite(FILE *file, const Nrrd *nrrd, NrrdIoState *io);

Index: write.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/write.c,v
retrieving revision 1.88
retrieving revision 1.89
diff -C2 -d -r1.88 -r1.89
*** write.c	7 Jan 2004 15:34:30 -0000	1.88
--- write.c	15 Mar 2004 03:07:41 -0000	1.89
***************
*** 96,101 ****
  
  int
! nrrdIoStateSetEncoding (NrrdIoState *nio, const NrrdEncoding *encoding) {
!   char me[]="nrrdIoStateSetEncoding", err[AIR_STRLEN_MED];
  
    if (!( nio && encoding )) {
--- 96,101 ----
  
  int
! nrrdIoStateEncodingSet (NrrdIoState *nio, const NrrdEncoding *encoding) {
!   char me[]="nrrdIoStateEncodingSet", err[AIR_STRLEN_MED];
  
    if (!( nio && encoding )) {
***************
*** 117,122 ****
  
  int
! nrrdIoStateSetFormat (NrrdIoState *nio, const NrrdFormat *format) {
!   char me[]="nrrdIoStateSetFormat", err[AIR_STRLEN_MED];
  
    if (!( nio && format )) {
--- 117,122 ----
  
  int
! nrrdIoStateFormatSet (NrrdIoState *nio, const NrrdFormat *format) {
!   char me[]="nrrdIoStateFormatSet", err[AIR_STRLEN_MED];
  
    if (!( nio && format )) {
***************
*** 191,195 ****
  */
  const NrrdEncoding *
! nrrdIoStateGetEncoding (NrrdIoState *nio) {
  
    return nio ? nio->encoding : nrrdEncodingUnknown;
--- 191,195 ----
  */
  const NrrdEncoding *
! nrrdIoStateEncodingGet (NrrdIoState *nio) {
  
    return nio ? nio->encoding : nrrdEncodingUnknown;
***************
*** 200,204 ****
  */
  const NrrdFormat *
! nrrdIoStateGetFormat (NrrdIoState *nio) {
  
    return nio ? nio->format : nrrdFormatUnknown;
--- 200,204 ----
  */
  const NrrdFormat *
! nrrdIoStateFormatGet (NrrdIoState *nio) {
  
    return nio ? nio->format : nrrdFormatUnknown;

[Teem-commit] teem/src/bin mrender.c,1.32,1.33 talkweb.c,1.7,1.8

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

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

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

Index: mrender.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/mrender.c,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** mrender.c	19 Feb 2004 11:15:13 -0000	1.32
--- mrender.c	13 Mar 2004 20:03:08 -0000	1.33
***************
*** 125,129 ****
    if (uu) {
      airMopOkay(uu->mrmop);
!     AIR_FREE(uu);
    }
    return NULL;
--- 125,129 ----
    if (uu) {
      airMopOkay(uu->mrmop);
!     uu = airFree(uu);
    }
    return NULL;
***************
*** 301,305 ****
  mrendThreadEnd(mrendThread *tt, mrendRender *rr, mrendUser *uu) {
    
!   AIR_FREE(tt->val);
  
    return 0;
--- 301,305 ----
  mrendThreadEnd(mrendThread *tt, mrendRender *rr, mrendUser *uu) {
    
!   tt->val = airFree(tt->val);
  
    return 0;
***************
*** 333,337 ****
    newLen = AIR_ROUNDUP(rayLen/tt->rayStep) + 1;
    if (!tt->val || newLen > tt->valLen) {
!     AIR_FREE(tt->val);
      tt->valLen = newLen;
      tt->val = (float*)calloc(newLen, sizeof(float));
--- 333,337 ----
    newLen = AIR_ROUNDUP(rayLen/tt->rayStep) + 1;
    if (!tt->val || newLen > tt->valLen) {
!     tt->val = airFree(tt->val);
      tt->valLen = newLen;
      tt->val = (float*)calloc(newLen, sizeof(float));

Index: talkweb.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/talkweb.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** talkweb.c	7 Jan 2004 15:34:28 -0000	1.7
--- talkweb.c	13 Mar 2004 20:03:08 -0000	1.8
***************
*** 78,85 ****
  tkwbSlideNix(tkwbSlide *slide) {
  
!   AIR_FREE(slide->title);
!   AIR_FREE(slide->image);
!   AIR_FREE(slide->text);
!   AIR_FREE(slide);
    return NULL;
  }
--- 78,85 ----
  tkwbSlideNix(tkwbSlide *slide) {
  
!   slide->title = airFree(slide->title);
!   slide->image = airFree(slide->image);
!   slide->text = airFree(slide->text);
!   slide = airFree(slide);
    return NULL;
  }

[Teem-commit] teem/src/air air.h,1.39,1.40 string.c,1.7,1.8

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

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

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

Index: air.h
===================================================================
RCS file: /cvsroot/teem/teem/src/air/air.h,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** air.h	19 Feb 2004 06:45:11 -0000	1.39
--- air.h	13 Mar 2004 20:03:08 -0000	1.40
***************
*** 621,633 ****
  
  /*
- ******** AIR_FREE, AIR_FCLOSE
- **
- ** just to help you set all pointers to free'd data and fclose'd files to NULL
- */
- #define AIR_FREE(x) (x) = airFree((x))
- #define AIR_FCLOSE(f) (f) = airFclose((f))
- 
- 
- /*
  ******** AIR_IN_OP(a,b,c), AIR_IN_CL(a,b,c)
  **
--- 621,624 ----

Index: string.c
===================================================================
RCS file: /cvsroot/teem/teem/src/air/string.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** string.c	7 Jan 2004 15:34:27 -0000	1.7
--- string.c	13 Mar 2004 20:03:08 -0000	1.8
***************
*** 132,136 ****
        t = airStrtok(NULL, ct, &l);
      }
!     AIR_FREE(s);
    }
    return n;
--- 132,136 ----
        t = airStrtok(NULL, ct, &l);
      }
!     s = airFree(s);
    }
    return n;

[Teem-commit] teem/src/nrrd axis.c,1.5,1.6 formatNRRD.c,1.5,1.6 formatPNG.c,1.5,1.6 gzio.c,1.15,1.16 histogram.c,1.48,1.49 keyvalue.c,1.7,1.8 measure.c,1.46,1.47 methodsNrrd.c,1.39,1.40 read.c,1.87,1.88 reorder.c,1.55,1.56 resampleNrrd.c,1.19,1.20 simple.c,1.59,1.60

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

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

Modified Files:
	axis.c formatNRRD.c formatPNG.c gzio.c histogram.c keyvalue.c 
	measure.c methodsNrrd.c read.c reorder.c resampleNrrd.c 
	simple.c 
Log Message:
killed off AIR_FREE and AIR_FCLOSE macros- they were just way too cute for their own good

Index: axis.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/axis.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** axis.c	7 Jan 2004 15:34:30 -0000	1.5
--- axis.c	13 Mar 2004 20:03:10 -0000	1.6
***************
*** 30,35 ****
      axis->spacing = AIR_NAN;
      axis->min = axis->max = AIR_NAN;
!     AIR_FREE(axis->label);
!     AIR_FREE(axis->unit);
      axis->center = nrrdCenterUnknown;
    }
--- 30,35 ----
      axis->spacing = AIR_NAN;
      axis->min = axis->max = AIR_NAN;
!     axis->label = airFree(axis->label);
!     axis->unit = airFree(axis->unit);
      axis->center = nrrdCenterUnknown;
    }
***************
*** 53,59 ****
  
    if (axis) {
!     AIR_FREE(axis->label);
!     AIR_FREE(axis->unit);
!     AIR_FREE(axis);
    }
    return NULL;
--- 53,59 ----
  
    if (axis) {
!     axis->label = airFree(axis->label);
!     axis->unit = airFree(axis->unit);
!     axis = airFree(axis);
    }
    return NULL;
***************
*** 83,87 ****
    if (!(NRRD_AXIS_INFO_LABEL_BIT & bitflag)) {
      if (dest->label != src->label) {
!       AIR_FREE(dest->label);
        dest->label = airStrdup(src->label);
      }
--- 83,87 ----
    if (!(NRRD_AXIS_INFO_LABEL_BIT & bitflag)) {
      if (dest->label != src->label) {
!       dest->label = airFree(dest->label);
        dest->label = airStrdup(src->label);
      }
***************
*** 89,93 ****
    if (!(NRRD_AXIS_INFO_UNIT_BIT & bitflag)) {
      if (dest->unit != src->unit) {
!       AIR_FREE(dest->unit);
        dest->unit = airStrdup(src->unit);
      }
--- 89,93 ----
    if (!(NRRD_AXIS_INFO_UNIT_BIT & bitflag)) {
      if (dest->unit != src->unit) {
!       dest->unit = airFree(dest->unit);
        dest->unit = airStrdup(src->unit);
      }
***************
*** 185,193 ****
        break;
      case nrrdAxisInfoLabel:
!       AIR_FREE(nrrd->axis[d].label);
        nrrd->axis[d].label = airStrdup(info.CP[d]);
        break;
      case nrrdAxisInfoUnit:
!       AIR_FREE(nrrd->axis[d].unit);
        nrrd->axis[d].unit = airStrdup(info.CP[d]);
        break;
--- 185,193 ----
        break;
      case nrrdAxisInfoLabel:
!       nrrd->axis[d].label = airFree(nrrd->axis[d].label);
        nrrd->axis[d].label = airStrdup(info.CP[d]);
        break;
      case nrrdAxisInfoUnit:
!       nrrd->axis[d].unit = airFree(nrrd->axis[d].unit);
        nrrd->axis[d].unit = airStrdup(info.CP[d]);
        break;

Index: formatNRRD.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/formatNRRD.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** formatNRRD.c	7 Jan 2004 15:34:30 -0000	1.5
--- formatNRRD.c	13 Mar 2004 20:03:10 -0000	1.6
***************
*** 285,289 ****
    } else {
      if (nio->detachedHeader) {
!       AIR_FCLOSE(nio->dataFile);
        /* fprintf(stderr, "!%s: nio->dataFile = %p\n", me, nio->dataFile); */
      } else {
--- 285,289 ----
    } else {
      if (nio->detachedHeader) {
!       nio->dataFile = airFclose(nio->dataFile);
        /* fprintf(stderr, "!%s: nio->dataFile = %p\n", me, nio->dataFile); */
      } else {
***************
*** 380,384 ****
      }
      if (nio->detachedHeader) {
!       AIR_FCLOSE(nio->dataFile);
      } else {
        nio->dataFile = NULL;
--- 380,384 ----
      }
      if (nio->detachedHeader) {
!       nio->dataFile = airFclose(nio->dataFile);
      } else {
        nio->dataFile = NULL;

Index: formatPNG.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/formatPNG.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** formatPNG.c	7 Jan 2004 15:34:30 -0000	1.5
--- formatPNG.c	13 Mar 2004 20:03:10 -0000	1.6
***************
*** 311,315 ****
  	 descriptor did NOT come from a line of text as read by
  	 _nrrdOneLine */
!       AIR_FREE(nio->line);
        nio->line = airStrdup(txt[i].text);
        ret = _nrrdReadNrrdParseField(nrrd, nio, AIR_FALSE);
--- 311,315 ----
  	 descriptor did NOT come from a line of text as read by
  	 _nrrdOneLine */
!       nio->line = airFree(nio->line);
        nio->line = airStrdup(txt[i].text);
        ret = _nrrdReadNrrdParseField(nrrd, nio, AIR_FALSE);
***************
*** 366,370 ****
    png_read_end(png, info);
    /* clean up */
!   AIR_FREE(row);
    png_destroy_read_struct(&png, &info, NULL);
  
--- 366,370 ----
    png_read_end(png, info);
    /* clean up */
!   row = airFree(row);
    png_destroy_read_struct(&png, &info, NULL);
  
***************
*** 515,521 ****
    /* clean up */
    for (i=0; i<numtxt; i++) {
!     AIR_FREE(txt[i].text);
    }
!   AIR_FREE(row);
    png_destroy_write_struct(&png, &info);
  
--- 515,521 ----
    /* clean up */
    for (i=0; i<numtxt; i++) {
!     txt[i].text = airFree(txt[i].text);
    }
!   row = airFree(row);
    png_destroy_write_struct(&png, &info);
  

Index: gzio.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/gzio.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** gzio.c	7 Jan 2004 15:34:30 -0000	1.15
--- gzio.c	13 Mar 2004 20:03:10 -0000	1.16
***************
*** 556,560 ****
      return 1;
    }
!   AIR_FREE(s->msg);
    if (s->stream.state != NULL) {
      if (s->mode == 'w') {
--- 556,560 ----
      return 1;
    }
!   s->msg = airFree(s->msg);
    if (s->stream.state != NULL) {
      if (s->mode == 'w') {
***************
*** 573,579 ****
      biffAdd(NRRD, err);
    }
!   AIR_FREE(s->inbuf);
!   AIR_FREE(s->outbuf);
!   AIR_FREE(s);
    return error != Z_OK;
  }
--- 573,579 ----
      biffAdd(NRRD, err);
    }
!   s->inbuf = airFree(s->inbuf);
!   s->outbuf = airFree(s->outbuf);
!   s = airFree(s);
    return error != Z_OK;
  }

Index: histogram.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/histogram.c,v
retrieving revision 1.48
retrieving revision 1.49
diff -C2 -d -r1.48 -r1.49
*** histogram.c	7 Jan 2004 15:34:30 -0000	1.48
--- histogram.c	13 Mar 2004 20:03:10 -0000	1.49
***************
*** 138,142 ****
      biffAdd(NRRD, err); airMopError(mop); return 1;
    }
!   AIR_FREE(nout->axis[0].label);
    nout->axis[0].label = airStrdup(nout->content);
  
--- 138,142 ----
      biffAdd(NRRD, err); airMopError(mop); return 1;
    }
!   nout->axis[0].label = airFree(nout->axis[0].label);
    nout->axis[0].label = airStrdup(nout->content);
  
***************
*** 188,192 ****
    nout->axis[0].center = nout->axis[1].center = nrrdCenterCell;
    nout->axis[0].label = airStrdup(nin->axis[0].label);
!   AIR_FREE(nout->axis[1].label);
    nrrdPeripheralInit(nout);
    pgmData = nout->data;
--- 188,192 ----
    nout->axis[0].center = nout->axis[1].center = nrrdCenterCell;
    nout->axis[0].label = airStrdup(nin->axis[0].label);
!   nout->axis[1].label = airFree(nout->axis[1].label);
    nrrdPeripheralInit(nout);
    pgmData = nout->data;
***************
*** 506,510 ****
        }
      } else {
!       AIR_FREE(nout->axis[d].label);
        totalContentStrlen += 2;
      }
--- 506,510 ----
        }
      } else {
!       nout->axis[d].label = airFree(nout->axis[d].label);
        totalContentStrlen += 2;
      }

Index: keyvalue.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/keyvalue.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** keyvalue.c	13 Feb 2004 03:40:58 -0000	1.7
--- keyvalue.c	13 Mar 2004 20:03:10 -0000	1.8
***************
*** 93,98 ****
    nk = nrrd->kvpArr->len;
    for (ki=0; ki<nk; ki++) {
!     AIR_FREE(nrrd->kvp[0 + 2*ki]);
!     AIR_FREE(nrrd->kvp[1 + 2*ki]);
    }
    airArraySetLen(nrrd->kvpArr, 0);
--- 93,98 ----
    nk = nrrd->kvpArr->len;
    for (ki=0; ki<nk; ki++) {
!     nrrd->kvp[0 + 2*ki] = airFree(nrrd->kvp[0 + 2*ki]);
!     nrrd->kvp[1 + 2*ki] = airFree(nrrd->kvp[1 + 2*ki]);
    }
    airArraySetLen(nrrd->kvpArr, 0);
***************
*** 113,118 ****
      return 0;
    }
!   AIR_FREE(nrrd->kvp[0 + 2*ki]);
!   AIR_FREE(nrrd->kvp[1 + 2*ki]);
    nk = nrrd->kvpArr->len;
    for (; ki<nk-1; ki++) {
--- 113,118 ----
      return 0;
    }
!   nrrd->kvp[0 + 2*ki] = airFree(nrrd->kvp[0 + 2*ki]);
!   nrrd->kvp[1 + 2*ki] = airFree(nrrd->kvp[1 + 2*ki]);
    nk = nrrd->kvpArr->len;
    for (; ki<nk-1; ki++) {
***************
*** 144,148 ****
    }
    if (-1 != (ki = _nrrdKeyValueIdxFind(nrrd, key))) {
!     AIR_FREE(nrrd->kvp[1 + 2*ki]);
      nrrd->kvp[1 + 2*ki] = airStrdup(value);
    } else {
--- 144,148 ----
    }
    if (-1 != (ki = _nrrdKeyValueIdxFind(nrrd, key))) {
!     nrrd->kvp[1 + 2*ki] = airFree(nrrd->kvp[1 + 2*ki]);
      nrrd->kvp[1 + 2*ki] = airStrdup(value);
    } else {

Index: measure.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/measure.c,v
retrieving revision 1.46
retrieving revision 1.47
diff -C2 -d -r1.46 -r1.47
*** measure.c	7 Jan 2004 15:34:30 -0000	1.46
--- measure.c	13 Mar 2004 20:03:10 -0000	1.47
***************
*** 878,882 ****
    nrrdPeripheralInit(nout);
  
!   AIR_FREE(_line);
    return 0;
  }
--- 878,882 ----
    nrrdPeripheralInit(nout);
  
!   _line = airFree(_line);
    return 0;
  }

Index: methodsNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/methodsNrrd.c,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** methodsNrrd.c	16 Jan 2004 17:35:12 -0000	1.39
--- methodsNrrd.c	13 Mar 2004 20:03:10 -0000	1.40
***************
*** 28,35 ****
  
    if (nio) {
!     AIR_FREE(nio->path);
!     AIR_FREE(nio->base);
!     AIR_FREE(nio->dataFN);
!     AIR_FREE(nio->line);
      nio->lineLen = 0;
      nio->pos = 0;
--- 28,35 ----
  
    if (nio) {
!     nio->path = airFree(nio->path);
!     nio->base = airFree(nio->base);
!     nio->dataFN = airFree(nio->dataFN);
!     nio->line = airFree(nio->line);
      nio->lineLen = 0;
      nio->pos = 0;
***************
*** 77,86 ****
  NrrdIoState *
  nrrdIoStateNix (NrrdIoState *nio) {
! 
!   AIR_FREE(nio->path);
!   AIR_FREE(nio->base);
!   AIR_FREE(nio->dataFN);
!   AIR_FREE(nio->line);
!   AIR_FREE(nio);
    /* the NrrdIoState never owned nio->oldData; we don't free it */
    return NULL;
--- 77,86 ----
  NrrdIoState *
  nrrdIoStateNix (NrrdIoState *nio) {
!   
!   nio->path = airFree(nio->path);
!   nio->base = airFree(nio->base);
!   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;
***************
*** 126,130 ****
  nrrdResampleInfoNix (NrrdResampleInfo *info) {
    
!   AIR_FREE(info);
    return NULL;
  }
--- 126,130 ----
  nrrdResampleInfoNix (NrrdResampleInfo *info) {
    
!   info = airFree(info);
    return NULL;
  }
***************
*** 150,154 ****
  nrrdKernelSpecNix (NrrdKernelSpec *ksp) {
  
!   AIR_FREE(ksp);
    return NULL;
  }
--- 150,154 ----
  nrrdKernelSpecNix (NrrdKernelSpec *ksp) {
  
!   ksp = airFree(ksp);
    return NULL;
  }
***************
*** 200,204 ****
  
    if (nrrd) {
!     AIR_FREE(nrrd->data);
      nrrd->type = nrrdTypeUnknown;
      nrrd->dim = 0;
--- 200,204 ----
  
    if (nrrd) {
!     nrrd->data = airFree(nrrd->data);
      nrrd->type = nrrdTypeUnknown;
      nrrd->dim = 0;
***************
*** 208,212 ****
      }
      
!     AIR_FREE(nrrd->content);
      nrrd->blockSize = 0;
      nrrd->oldMin = nrrd->oldMax = AIR_NAN;
--- 208,212 ----
      }
      
!     nrrd->content = airFree(nrrd->content);
      nrrd->blockSize = 0;
      nrrd->oldMin = nrrd->oldMax = AIR_NAN;
***************
*** 284,291 ****
    
    if (nrrd) {
!     AIR_FREE(nrrd->content);
      /* HEY: this is a symptom of some stupidity, no? */
      for (i=0; i<NRRD_DIM_MAX; i++) {
!       AIR_FREE(nrrd->axis[i].label);
      }
      nrrdCommentClear(nrrd);
--- 284,291 ----
    
    if (nrrd) {
!     nrrd->content = airFree(nrrd->content);
      /* HEY: this is a symptom of some stupidity, no? */
      for (i=0; i<NRRD_DIM_MAX; i++) {
!       nrrd->axis[i].label = airFree(nrrd->axis[i].label);
      }
      nrrdCommentClear(nrrd);
***************
*** 293,297 ****
      nrrdKeyValueClear(nrrd);
      nrrd->kvpArr = airArrayNix(nrrd->kvpArr);
!     AIR_FREE(nrrd);
    }
    return NULL;
--- 293,297 ----
      nrrdKeyValueClear(nrrd);
      nrrd->kvpArr = airArrayNix(nrrd->kvpArr);
!     nrrd = airFree(nrrd);
    }
    return NULL;
***************
*** 309,313 ****
    
    if (nrrd) {
!     AIR_FREE(nrrd->data);
      nrrdInit(nrrd);
    }
--- 309,313 ----
    
    if (nrrd) {
!     nrrd->data = airFree(nrrd->data);
      nrrdInit(nrrd);
    }
***************
*** 482,486 ****
  
    /* HEY: shouldn't this be handled with nrrdPeripheralCopy() */
!   AIR_FREE(nout->content);
    nout->content = airStrdup(nin->content);
    if (nin->content && !nout->content) {
--- 482,486 ----
  
    /* HEY: shouldn't this be handled with nrrdPeripheralCopy() */
!   nout->content = airFree(nout->content);
    nout->content = airStrdup(nin->content);
    if (nin->content && !nout->content) {
***************
*** 553,557 ****
  
    nrrd->type = type;
!   AIR_FREE(nrrd->data);
    nrrd->dim = dim;
    if (_nrrdSizeCheck(dim, size, AIR_TRUE)) {
--- 553,557 ----
  
    nrrd->type = type;
!   nrrd->data = airFree(nrrd->data);
    nrrd->dim = dim;
    if (_nrrdSizeCheck(dim, size, AIR_TRUE)) {

Index: read.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/read.c,v
retrieving revision 1.87
retrieving revision 1.88
diff -C2 -d -r1.87 -r1.88
*** read.c	13 Feb 2004 03:40:58 -0000	1.87
--- read.c	13 Mar 2004 20:03:10 -0000	1.88
***************
*** 137,141 ****
      memset(nrrd->data, 0, needDataSize);
    } else {
!     AIR_FREE(nrrd->data);
      nrrd->data = calloc(nrrdElementNumber(nrrd), nrrdElementSize(nrrd));
      if (!nrrd->data) {
--- 137,141 ----
      memset(nrrd->data, 0, needDataSize);
    } else {
!     nrrd->data = airFree(nrrd->data);
      nrrd->data = calloc(nrrdElementNumber(nrrd), nrrdElementSize(nrrd));
      if (!nrrd->data) {
***************
*** 312,316 ****
    /* free prior memory if we didn't end up using it */
    if (nio->oldData != nrrd->data) {
!     AIR_FREE(nio->oldData);
      nio->oldDataSize = 0;
    }
--- 312,316 ----
    /* free prior memory if we didn't end up using it */
    if (nio->oldData != nrrd->data) {
!     nio->oldData = airFree(nio->oldData);
      nio->oldDataSize = 0;
    }
***************
*** 336,343 ****
    
    if (dirP) {
!     AIR_FREE(*dirP);
    }
    if (baseP) {
!     AIR_FREE(*baseP);
    }
    where = strrchr(name, '/');
--- 336,343 ----
    
    if (dirP) {
!     *dirP = airFree(*dirP);
    }
    if (baseP) {
!     *baseP = airFree(*baseP);
    }
    where = strrchr(name, '/');

Index: reorder.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/reorder.c,v
retrieving revision 1.55
retrieving revision 1.56
diff -C2 -d -r1.55 -r1.56
*** reorder.c	7 Jan 2004 15:34:30 -0000	1.55
--- reorder.c	13 Mar 2004 20:03:10 -0000	1.56
***************
*** 435,439 ****
    nout->axis[axis].min = nin->axis[axis].max;
    nout->axis[axis].max = nin->axis[axis].min;
!   AIR_FREE(perm);
    return 0;
  }
--- 435,439 ----
    nout->axis[axis].min = nin->axis[axis].max;
    nout->axis[axis].max = nin->axis[axis].min;
!   perm = airFree(perm);
    return 0;
  }

Index: resampleNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/resampleNrrd.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** resampleNrrd.c	7 Jan 2004 15:34:30 -0000	1.19
--- resampleNrrd.c	13 Mar 2004 20:03:10 -0000	1.20
***************
*** 673,677 ****
        } else {
  	airMopSub(mop, array[pass-1], airFree);
! 	AIR_FREE(array[pass-1]);
  	/*
  	printf("%s: pass %d: freeing array[%d]\n", me, pass, pass-1);
--- 673,677 ----
        } else {
  	airMopSub(mop, array[pass-1], airFree);
! 	array[pass-1] = airFree(array[pass-1]);
  	/*
  	printf("%s: pass %d: freeing array[%d]\n", me, pass, pass-1);
***************
*** 770,776 ****
      airMopSub(mop, index, airFree);
      airMopSub(mop, inVec, airFree);
!     AIR_FREE(weight);
!     AIR_FREE(index);
!     AIR_FREE(inVec);
    }
  
--- 770,776 ----
      airMopSub(mop, index, airFree);
      airMopSub(mop, inVec, airFree);
!     weight = airFree(weight);
!     index = airFree(index);
!     inVec = airFree(inVec);
    }
  
***************
*** 778,782 ****
    if (passes > 1) {
      airMopSub(mop, array[passes-1], airFree);
!     AIR_FREE(array[passes-1]);
      /*
      printf("%s: now freeing array[%d]\n", me, passes-1);
--- 778,782 ----
    if (passes > 1) {
      airMopSub(mop, array[passes-1], airFree);
!     array[passes-1] = airFree(array[passes-1]);
      /*
      printf("%s: now freeing array[%d]\n", me, passes-1);

Index: simple.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/simple.c,v
retrieving revision 1.59
retrieving revision 1.60
diff -C2 -d -r1.59 -r1.60
*** simple.c	7 Jan 2004 15:34:30 -0000	1.59
--- simple.c	13 Mar 2004 20:03:10 -0000	1.60
***************
*** 118,122 ****
      biffAdd(NRRD, err); return 1;
    }
!   AIR_FREE(nout->content);
  
    /* we are currently praying that this won't overflow the "buff" array */
--- 118,122 ----
      biffAdd(NRRD, err); return 1;
    }
!   nout->content = airFree(nout->content);
  
    /* we are currently praying that this won't overflow the "buff" array */
***************
*** 134,142 ****
    if (!nout->content) {
      sprintf(err, "%s: couln't alloc output content!", me);
!     biffAdd(NRRD, err); AIR_FREE(buff); return 1;
    }
    sprintf(nout->content, "%s(%s%s%s)", func, content,
  	  airStrlen(buff) ? "," : "", buff);
!   AIR_FREE(buff);
    return 0;
  }
--- 134,142 ----
    if (!nout->content) {
      sprintf(err, "%s: couln't alloc output content!", me);
!     biffAdd(NRRD, err); buff = airFree(buff); return 1;
    }
    sprintf(nout->content, "%s(%s%s%s)", func, content,
  	  airStrlen(buff) ? "," : "", buff);
!   buff = airFree(buff);
    return 0;
  }
***************
*** 184,188 ****
    if (nrrdStateDisableContent) {
      /* we kill content always */
!     AIR_FREE(nout->content);
      return 0;
    }
--- 184,188 ----
    if (nrrdStateDisableContent) {
      /* we kill content always */
!     nout->content = airFree(nout->content);
      return 0;
    }
***************
*** 190,194 ****
      /* there's no input content, and we're not supposed to invent any
         content, so after freeing nout's content we're done */
!     AIR_FREE(nout->content);
      return 0;
    }
--- 190,194 ----
      /* there's no input content, and we're not supposed to invent any
         content, so after freeing nout's content we're done */
!     nout->content = airFree(nout->content);
      return 0;
    }

[Teem-commit] teem/src/unrrdu axinfo.c,1.3,1.4 axinsert.c,1.4,1.5 flotsam.c,1.16,1.17 join.c,1.22,1.23 make.c,1.48,1.49

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

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

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

Index: axinfo.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/axinfo.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** axinfo.c	7 Jan 2004 15:34:31 -0000	1.3
--- axinfo.c	13 Mar 2004 20:03:11 -0000	1.4
***************
*** 81,85 ****
    
    if (strlen(label)) {
!     AIR_FREE(nout->axis[axis].label);
      nout->axis[axis].label = airStrdup(label);
    }
--- 81,85 ----
    
    if (strlen(label)) {
!     nout->axis[axis].label = airFree(nout->axis[axis].label);
      nout->axis[axis].label = airStrdup(label);
    }

Index: axinsert.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/axinsert.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** axinsert.c	7 Jan 2004 15:34:31 -0000	1.4
--- axinsert.c	13 Mar 2004 20:03:11 -0000	1.5
***************
*** 59,63 ****
    }
    if (strlen(label)) {
!     AIR_FREE(nout->axis[axis].label);
      nout->axis[axis].label = airStrdup(label);
    }
--- 59,63 ----
    }
    if (strlen(label)) {
!     nout->axis[axis].label = airFree(nout->axis[axis].label);
      nout->axis[axis].label = airStrdup(label);
    }

Index: flotsam.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/flotsam.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** flotsam.c	7 Jan 2004 15:34:31 -0000	1.16
--- flotsam.c	13 Mar 2004 20:03:11 -0000	1.17
***************
*** 324,328 ****
    file = _file;
    if (stdin != file) {
!     AIR_FCLOSE(file);
    }
    return NULL;
--- 324,328 ----
    file = _file;
    if (stdin != file) {
!     file = airFclose(file);
    }
    return NULL;

Index: join.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/join.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** join.c	7 Jan 2004 15:34:31 -0000	1.22
--- join.c	13 Mar 2004 20:03:11 -0000	1.23
***************
*** 81,85 ****
    }
    if (strlen(label)) {
!     AIR_FREE(nout->axis[axis].label);
      nout->axis[axis].label = airStrdup(label);
    }
--- 81,85 ----
    }
    if (strlen(label)) {
!     nout->axis[axis].label = airFree(nout->axis[axis].label);
      nout->axis[axis].label = airStrdup(label);
    }

Index: make.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/make.c,v
retrieving revision 1.48
retrieving revision 1.49
diff -C2 -d -r1.48 -r1.49
*** make.c	7 Jan 2004 15:34:31 -0000	1.48
--- make.c	13 Mar 2004 20:03:11 -0000	1.49
***************
*** 58,74 ****
    if (nrrdLineSkip(nio)) {
      sprintf(err, "%s: couldn't skip lines", me);
!     AIR_FCLOSE(nio->dataFile); biffMove(me, err, NRRD); return 1;
    }
    if (!nio->encoding->isCompression) {
      if (nrrdByteSkip(nrrd, nio)) {
        sprintf(err, "%s: couldn't skip bytes", me);
!       AIR_FCLOSE(nio->dataFile); biffMove(me, err, NRRD); return 1;
      }
    }
    if (nio->encoding->read(nrrd, nio)) {
      sprintf(err, "%s: error reading data", me);
!     AIR_FCLOSE(nio->dataFile); biffMove(me, err, NRRD); return 1;
    }
!   AIR_FCLOSE(nio->dataFile);
    return 0;
  }
--- 58,77 ----
    if (nrrdLineSkip(nio)) {
      sprintf(err, "%s: couldn't skip lines", me);
!     nio->dataFile = airFclose(nio->dataFile);
!     biffMove(me, err, NRRD); return 1;
    }
    if (!nio->encoding->isCompression) {
      if (nrrdByteSkip(nrrd, nio)) {
        sprintf(err, "%s: couldn't skip bytes", me);
!       nio->dataFile = airFclose(nio->dataFile);
!       biffMove(me, err, NRRD); return 1;
      }
    }
    if (nio->encoding->read(nrrd, nio)) {
      sprintf(err, "%s: error reading data", me);
!     nio->dataFile = airFclose(nio->dataFile);
!     biffMove(me, err, NRRD); return 1;
    }
!   nio->dataFile = airFclose(nio->dataFile);
    return 0;
  }

[Teem-commit] teem/src/moss methodsMoss.c,1.8,1.9 sampler.c,1.10,1.11

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

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

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

Index: methodsMoss.c
===================================================================
RCS file: /cvsroot/teem/teem/src/moss/methodsMoss.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** methodsMoss.c	7 Jan 2004 15:34:30 -0000	1.8
--- methodsMoss.c	13 Mar 2004 20:03:10 -0000	1.9
***************
*** 75,83 ****
  
    if (smplr) {
!     AIR_FREE(smplr->ivc);
!     AIR_FREE(smplr->xFslw);
!     AIR_FREE(smplr->yFslw);
!     AIR_FREE(smplr->xIdx);
!     AIR_FREE(smplr->yIdx);
      smplr->fdiam = 0;
      smplr->ncol = 0;
--- 75,83 ----
  
    if (smplr) {
!     smplr->ivc = airFree(smplr->ivc);
!     smplr->xFslw = airFree(smplr->xFslw);
!     smplr->yFslw = airFree(smplr->yFslw);
!     smplr->xIdx = airFree(smplr->xIdx);
!     smplr->yIdx = airFree(smplr->yIdx);
      smplr->fdiam = 0;
      smplr->ncol = 0;
***************
*** 91,95 ****
    if (smplr) {
      mossSamplerEmpty(smplr);
!     AIR_FREE(smplr->bg);
      free(smplr);
    }
--- 91,95 ----
    if (smplr) {
      mossSamplerEmpty(smplr);
!     smplr->bg = airFree(smplr->bg);
      free(smplr);
    }

Index: sampler.c
===================================================================
RCS file: /cvsroot/teem/teem/src/moss/sampler.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** sampler.c	16 Jan 2004 17:40:14 -0000	1.10
--- sampler.c	13 Mar 2004 20:03:10 -0000	1.11
***************
*** 37,41 ****
    smplr->flag[mossFlagImage] = AIR_TRUE;
    ncol = MOSS_NCOL(image);
!   AIR_FREE(smplr->bg);
    smplr->bg = (float*)calloc(ncol, sizeof(float));
    if (bg) {
--- 37,41 ----
    smplr->flag[mossFlagImage] = AIR_TRUE;
    ncol = MOSS_NCOL(image);
!   smplr->bg = airFree(smplr->bg);
    smplr->bg = (float*)calloc(ncol, sizeof(float));
    if (bg) {

[Teem-commit] teem/src/ten bimod.c,1.7,1.8 epireg.c,1.27,1.28 tendEval.c,1.14,1.15 tendEvec.c,1.15,1.16 tensor.c,1.28,1.29

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

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

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

Index: bimod.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/bimod.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** bimod.c	7 Mar 2004 00:46:42 -0000	1.7
--- bimod.c	13 Mar 2004 20:03:11 -0000	1.8
***************
*** 47,53 ****
  
    if (biparm) {
!     AIR_FREE(biparm->histo);
!     AIR_FREE(biparm->pp1);
!     AIR_FREE(biparm->pp2);
    }
    return airFree(biparm);
--- 47,53 ----
  
    if (biparm) {
!     biparm->histo = airFree(biparm->histo);
!     biparm->pp1 = airFree(biparm->pp1);
!     biparm->pp2 = airFree(biparm->pp2);
    }
    return airFree(biparm);

Index: epireg.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/epireg.c,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** epireg.c	8 Mar 2004 14:41:24 -0000	1.27
--- epireg.c	13 Mar 2004 20:03:11 -0000	1.28
***************
*** 588,601 ****
  		     gB[1] - pxfr[SCALE]*gA[1],
  		     gB[2] - pxfr[SCALE]*gA[2],
! 		     gB[0] - pxfr[SCALE]*gA[0],
! 		     gB[1] - pxfr[SCALE]*gA[1],
! 		     gB[2] - pxfr[SCALE]*gA[2],
! 		     gB[0] - pxfr[SCALE]*gA[0],
! 		     gB[1] - pxfr[SCALE]*gA[1],
! 		     gB[2] - pxfr[SCALE]*gA[2]);
! 		     /*
! 		     gB[0]*gB[0] - pxfr[SCALE]*gA[0]*gA[0],
! 		     gB[1]*gB[1] - pxfr[SCALE]*gA[1]*gA[1],
! 		     gB[2]*gB[2] - pxfr[SCALE]*gA[2]*gA[2],
  		     gB[0]*gB[1] - pxfr[SCALE]*gA[0]*gA[1],
  		     gB[0]*gB[2] - pxfr[SCALE]*gA[0]*gA[2],
--- 588,597 ----
  		     gB[1] - pxfr[SCALE]*gA[1],
  		     gB[2] - pxfr[SCALE]*gA[2],
! 		     gB[0]*gB[0]*gB[0] - pxfr[SCALE]*gA[0]*gA[0]*gA[0],
! 		     gB[1]*gB[1]*gB[1] - pxfr[SCALE]*gA[1]*gA[1]*gA[1],
! 		     gB[2]*gB[2]*gB[2] - pxfr[SCALE]*gA[2]*gA[2]*gA[2],
! 		     gB[0]*gB[1]*gB[2] - pxfr[SCALE]*gA[0]*gA[1]*gA[2],
! 		     1, 1);
! 	  /*
  		     gB[0]*gB[1] - pxfr[SCALE]*gA[0]*gA[1],
  		     gB[0]*gB[2] - pxfr[SCALE]*gA[0]*gA[2],
***************
*** 624,630 ****
      }
    }
- 
-   /* ------ find Hx, Hy, Hz per slice */
    vec = (double *)(nvec->data);
    for (z=0; z<sz; z++) {
      if (nrrdHasNonExist(nmat[z])) {
--- 620,626 ----
      }
    }
    vec = (double *)(nvec->data);
+ 
+   /* ------ find Sx, Sy, Sz per slice */
    for (z=0; z<sz; z++) {
      if (nrrdHasNonExist(nmat[z])) {
***************
*** 638,647 ****
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
! 	vec[ri] = pxfr[SHEAR];
  	ri += 1;
        }
      }
      if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Hx, Hy, Hz",
  	      me, z);
        biffMove(TEN, err, ELL); airMopError(mop); return 1;
--- 634,643 ----
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
! 	vec[ri] = pxfr[SCALE] - 1;
  	ri += 1;
        }
      }
      if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Sx, Sy, Sz",
  	      me, z);
        biffMove(TEN, err, ELL); airMopError(mop); return 1;
***************
*** 649,659 ****
      ans = (double *)(nans->data);
      if (1 == order) {
!       ELL_3V_COPY(hst + 0*3, ans);
      } else {
!       ELL_9V_COPY(hst + 0*9, ans);
      }
    }
  
!   /* ------ find Sx, Sy, Sz per slice */
    for (z=0; z<sz; z++) {
      if (nrrdHasNonExist(nmat[z])) {
--- 645,655 ----
      ans = (double *)(nans->data);
      if (1 == order) {
!       ELL_3V_COPY(hst + 1*3, ans);
      } else {
!       ELL_9V_COPY(hst + 1*9, ans);
      }
    }
  
!   /* ------ find Hx, Hy, Hz per slice */
    for (z=0; z<sz; z++) {
      if (nrrdHasNonExist(nmat[z])) {
***************
*** 667,676 ****
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
! 	vec[ri] = pxfr[SCALE] - 1;
  	ri += 1;
        }
      }
      if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Sx, Sy, Sz",
  	      me, z);
        biffMove(TEN, err, ELL); airMopError(mop); return 1;
--- 663,672 ----
  	if (A == B) continue;
  	pxfr = (double *)(npxfr->data) + 0 + 5*(z + sz*(A + ninLen*B));
! 	vec[ri] = pxfr[SHEAR];
  	ri += 1;
        }
      }
      if (ell_Nm_mul(nans, ninv[z], nvec)) {
!       sprintf(err, "%s: trouble estimating model (slice %d): Hx, Hy, Hz",
  	      me, z);
        biffMove(TEN, err, ELL); airMopError(mop); return 1;
***************
*** 678,684 ****
      ans = (double *)(nans->data);
      if (1 == order) {
!       ELL_3V_COPY(hst + 1*3, ans);
      } else {
!       ELL_9V_COPY(hst + 1*9, ans);
      }
    }
--- 674,680 ----
      ans = (double *)(nans->data);
      if (1 == order) {
!       ELL_3V_COPY(hst + 0*3, ans);
      } else {
!       ELL_9V_COPY(hst + 0*9, ans);
      }
    }
***************
*** 829,833 ****
  		 int reference, int ni, int zi,
  		 Nrrd *npxfr, Nrrd *nhst, Nrrd *ngrad) {
!   double *xfr, *hst, *_grad, grad[9]; /* big enough for 2nd order */
    int sz, ninLen;
  
--- 825,829 ----
  		 int reference, int ni, int zi,
  		 Nrrd *npxfr, Nrrd *nhst, Nrrd *ngrad) {
!   double *xfr, *hst, *_g, grad[9]; /* big enough for 2nd order */
    int sz, ninLen;
  
***************
*** 843,860 ****
      /* we use the estimated H,S,T vectors to determine distortion
         as a function of gradient direction, and then invert this */
!     _grad = (double*)(ngrad->data) + 0 + 3*ni;
      if (1 == order) {
        hst = (double*)(nhst->data) + 0 + 9*zi;
!       *hhP = ELL_3V_DOT(_grad, hst + 0*3);
!       *ssP = 1 + ELL_3V_DOT(_grad, hst + 1*3);
!       *ttP = ELL_3V_DOT(_grad, hst + 2*3);
      } else {
        hst = (double*)(nhst->data) + 0 + 27*zi;
!       ELL_9V_SET(grad, _grad[0], _grad[1], _grad[2],
! 		 _grad[0], _grad[1], _grad[2],
! 		 _grad[0], _grad[1], _grad[2]);
  		 /*
! 		 _grad[0]*_grad[0], _grad[1]*_grad[1], _grad[2]*_grad[2],
! 		 _grad[0]*_grad[1], _grad[0]*_grad[2], _grad[1]*_grad[2]);
  		 */
        *hhP = ELL_9V_DOT(grad, hst + 0*9);
--- 839,856 ----
      /* we use the estimated H,S,T vectors to determine distortion
         as a function of gradient direction, and then invert this */
!     _g = (double*)(ngrad->data) + 0 + 3*ni;
      if (1 == order) {
        hst = (double*)(nhst->data) + 0 + 9*zi;
!       *hhP = ELL_3V_DOT(_g, hst + 0*3);
!       *ssP = 1 + ELL_3V_DOT(_g, hst + 1*3);
!       *ttP = ELL_3V_DOT(_g, hst + 2*3);
      } else {
        hst = (double*)(nhst->data) + 0 + 27*zi;
!       ELL_9V_SET(grad, _g[0], _g[1], _g[2],
! 		 _g[0]*_g[0]*_g[0], _g[1]*_g[1]*_g[1], _g[2]*_g[2]*_g[2],
! 		 _g[0]*_g[1]*_g[2],
! 		 0, 0);
  		 /*
! 		 _g[0]*_g[1], _g[0]*_g[2], _g[1]*_g[2]);
  		 */
        *hhP = ELL_9V_DOT(grad, hst + 0*9);

Index: tendEval.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendEval.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** tendEval.c	7 Jan 2004 15:34:31 -0000	1.14
--- tendEval.c	13 Mar 2004 20:03:11 -0000	1.15
***************
*** 113,117 ****
    }
    if (1 != compLen) {
!     AIR_FREE(nout->axis[0].label);
    }
  
--- 113,117 ----
    }
    if (1 != compLen) {
!     nout->axis[0].label = airFree(nout->axis[0].label);
    }
  

Index: tendEvec.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendEvec.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** tendEvec.c	7 Jan 2004 15:34:31 -0000	1.15
--- tendEvec.c	13 Mar 2004 20:03:11 -0000	1.16
***************
*** 110,114 ****
      airMopError(mop); return 1;
    }
!   AIR_FREE(nout->axis[0].label);
  
    if (nrrdSave(outS, nout, NULL)) {
--- 110,114 ----
      airMopError(mop); return 1;
    }
!   nout->axis[0].label = airFree(nout->axis[0].label);
  
    if (nrrdSave(outS, nout, NULL)) {

Index: tensor.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tensor.c,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** tensor.c	1 Mar 2004 21:59:03 -0000	1.28
--- tensor.c	13 Mar 2004 20:03:11 -0000	1.29
***************
*** 110,114 ****
      biffMove(TEN, err, NRRD); return 1;
    }
!   AIR_FREE(nout->axis[0].label);
    nout->axis[0].label = airStrdup("matrix");
  
--- 110,114 ----
      biffMove(TEN, err, NRRD); return 1;
    }
!   nout->axis[0].label = airFree(nout->axis[0].label);
    nout->axis[0].label = airStrdup("matrix");
  
***************
*** 172,176 ****
      biffMove(TEN, err, NRRD); return 1;
    }
!   AIR_FREE(tseven->axis[0].label);
    tseven->axis[0].label = airStrdup("tensor");
  
--- 172,176 ----
      biffMove(TEN, err, NRRD); return 1;
    }
!   tseven->axis[0].label = airFree(tseven->axis[0].label);
    tseven->axis[0].label = airStrdup("tensor");
  
***************
*** 389,393 ****
      biffMove(TEN, err, NRRD); return 1;
    }
!   AIR_FREE(nout->axis[0].label);
    nout->axis[0].label = airStrdup("tensor");
  
--- 389,393 ----
      biffMove(TEN, err, NRRD); return 1;
    }
!   nout->axis[0].label = airFree(nout->axis[0].label);
    nout->axis[0].label = airStrdup("tensor");
  

[Teem-commit] teem/src/limn splineMethods.c,1.4,1.5

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

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

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

Index: splineMethods.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/splineMethods.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** splineMethods.c	7 Jan 2004 15:34:30 -0000	1.4
--- splineMethods.c	13 Mar 2004 20:03:10 -0000	1.5
***************
*** 214,219 ****
    if (spline) {
      spline->ncpt = nrrdNuke(spline->ncpt);
!     AIR_FREE(spline->time);
!     AIR_FREE(spline);
    }
    return NULL;
--- 214,219 ----
    if (spline) {
      spline->ncpt = nrrdNuke(spline->ncpt);
!     spline->time = airFree(spline->time);
!     spline = airFree(spline);
    }
    return NULL;