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[Teem-commit] teem/src/ten aniso.c,1.29,1.30

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8015

Modified Files:
	aniso.c 
Log Message:
fixed bug to avoid NaN generation

Index: aniso.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/aniso.c,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** aniso.c	22 Apr 2004 04:49:26 -0000	1.29
--- aniso.c	22 Apr 2004 07:13:01 -0000	1.30
***************
*** 102,106 ****
    c[tenAniso_S] = e0*e0 + e1*e1 + e2*e2;
    c[tenAniso_Skew] = R/(FLT_EPSILON + sqrt(2*Q*Q*Q));
!   c[tenAniso_Th] = acos(sqrt(2)*c[tenAniso_Skew])/3;
    c[tenAniso_Cz] = ((e0 + e1)/(FLT_EPSILON + e2) 
  		    + (e1 + e2)/(FLT_EPSILON + e0) 
--- 102,106 ----
    c[tenAniso_S] = e0*e0 + e1*e1 + e2*e2;
    c[tenAniso_Skew] = R/(FLT_EPSILON + sqrt(2*Q*Q*Q));
!   c[tenAniso_Th] = acos(AIR_CLAMP(-1, sqrt(2)*c[tenAniso_Skew], 1))/3;
    c[tenAniso_Cz] = ((e0 + e1)/(FLT_EPSILON + e2) 
  		    + (e1 + e2)/(FLT_EPSILON + e0) 

[Teem-commit] teem/src/bin overrgb.c,1.12,1.13

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6356

Modified Files:
	overrgb.c 
Log Message:
added ability to do contrast and contrast fixed point

Index: overrgb.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/overrgb.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** overrgb.c	16 Jan 2004 17:52:37 -0000	1.12
--- overrgb.c	22 Apr 2004 07:01:40 -0000	1.13
***************
*** 36,39 ****
--- 36,55 ----
    "image; it will be resampled (with linear interpolation) to fit. ");
  
+ double
+ docontrast(double val, double cfp, double cpow) {
+   double v;
+ 
+   if (val < cfp) {
+     v = AIR_AFFINE(0.0, val, cfp, 0.0, 1.0);
+     v = pow(v, cpow);
+     val = AIR_AFFINE(0.0, v, 1.0, 0.0, cfp);
+   } else {
+     v = AIR_AFFINE(cfp, val, 1.0, 1.0, 0.0);
+     v = pow(v, cpow);
+     val = AIR_AFFINE(1.0, v, 0.0, cfp, 1.0);
+   }
+   return val;
+ }
+ 
  int
  main(int argc, char *argv[]) {
***************
*** 45,49 ****
      *nrgbaD;           /* rgba input as double */
    char *me, *outS, *errS;
!   double gamma, back[3], *rgbaD, r, g, b, a;
    airArray *mop;
    int E, min[3], max[3], i, rI, gI, bI, sx, sy;
--- 61,65 ----
      *nrgbaD;           /* rgba input as double */
    char *me, *outS, *errS;
!   double gamma, contr, cfp, cpow, back[3], *rgbaD, r, g, b, a;
    airArray *mop;
    int E, min[3], max[3], i, rI, gI, bI, sx, sy;
***************
*** 55,60 ****
    hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
  	     "input nrrd to composite", NULL, NULL, nrrdHestNrrd);
    hestOptAdd(&hopt, "g", "gamma", airTypeDouble, 1, 1, &gamma, "1.0",
! 	     "gamma to apply to image data");
    hestOptAdd(&hopt, "b", "background", airTypeDouble, 3, 3, back, "0 0 0",
  	     "background color to composite against; white is "
--- 71,82 ----
    hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
  	     "input nrrd to composite", NULL, NULL, nrrdHestNrrd);
+   hestOptAdd(&hopt, "c", "contrast", airTypeDouble, 1, 1, &contr, "0.0",
+ 	     "contrast to apply to RGB values, before gamma. \"0.0\" "
+ 	     "means no change, \"1.0\" means thresholding, \"-1.0\" "
+ 	     "means a complete washout.");
+   hestOptAdd(&hopt, "cfp", "fixed point", airTypeDouble, 1, 1, &cfp, "0.5",
+ 	     "component level that doesn't change with contrast");
    hestOptAdd(&hopt, "g", "gamma", airTypeDouble, 1, 1, &gamma, "1.0",
! 	     "gamma to apply to image data, after contrast");
    hestOptAdd(&hopt, "b", "background", airTypeDouble, 3, 3, back, "0 0 0",
  	     "background color to composite against; white is "
***************
*** 146,150 ****
      free(errS); return 1;
    }
!   
    outUC = (unsigned char*)nout->data;
    bgUC = nbg ? nbg->data : NULL;
--- 168,174 ----
      free(errS); return 1;
    }
! 
!   contr = AIR_CLAMP(-1, contr, 1);
!   cpow = tan(AIR_AFFINE(-1.000001, contr, 1.000001, 0, AIR_PI/2));
    outUC = (unsigned char*)nout->data;
    bgUC = nbg ? nbg->data : NULL;
***************
*** 155,158 ****
--- 179,187 ----
      b = AIR_CLAMP(0, rgbaD[2], 1);
      a = AIR_CLAMP(0, rgbaD[3], 1);
+     if (1 != cpow) {
+       r = docontrast(r, cfp, cpow);
+       g = docontrast(g, cfp, cpow);
+       b = docontrast(b, cfp, cpow);
+     }
      r = pow(r, 1.0/gamma);
      g = pow(g, 1.0/gamma);

[Teem-commit] teem/src/gage gage.h,1.65,1.66 vecGage.c,1.20,1.21

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

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8925

Modified Files:
	gage.h vecGage.c 
Log Message:
added sub-items for the individual vector components

Index: gage.h
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/gage.h,v
retrieving revision 1.65
retrieving revision 1.66
diff -C2 -d -r1.65 -r1.66
*** gage.h	11 Apr 2004 02:31:41 -0000	1.65
--- gage.h	22 Apr 2004 07:19:00 -0000	1.66
***************
*** 279,296 ****
    gageVecUnknown=-1, /* -1: nobody knows */
    gageVecVector,     /*  0: "v", component-wise-intrpolated (CWI) vec: GT[3] */
!   gageVecLength,     /*  1: "l", length of CWI vector: GT[1] */
!   gageVecNormalized, /*  2: "n", normalized CWI vector: GT[3] */
!   gageVecJacobian,   /*  3: "j", component-wise Jacobian: GT[9]
  			    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 */
!   gageVecDivergence, /*  4: "d", divergence (based on Jacobian): GT[1] */
!   gageVecCurl,       /*  5: "c", curl (based on Jacobian): GT[3] */
!   gageVecCurlNorm,   /*  6: "cm", curl magnitude: GT[1] */
!   gageVecHelicity,   /*  7: "h", helicity: vec . curl: GT[1] */
!   gageVecNormHelicity,/* 8: "nh", normalized helicity: GT[1] */
!   gageVecLambda2,    /*  9: "lmbda2", lambda2 criterion: GT[1] */
!   gageVecImaginaryPart,/* 10: "imag", imag. part of jacobian's eigenv: GT[1] */
!   gageVecHessian,    /* 11: "vh", second-order derivative: GT[27] 
  			    0:d2v_x/dxdx   1:d2v_x/dxdy   2:d2v_x/dxdz
  	                    3:d2v_x/dydx   4:d2v_x/dydy   5:d2v_x/dydz
--- 279,299 ----
    gageVecUnknown=-1, /* -1: nobody knows */
    gageVecVector,     /*  0: "v", component-wise-intrpolated (CWI) vec: GT[3] */
!   gageVecVector0,    /*  1: "v0", vector[0]: GT[1] */
!   gageVecVector1,    /*  2: "v1", vector[0]: GT[1] */
!   gageVecVector2,    /*  3: "v2", vector[0]: GT[1] */
!   gageVecLength,     /*  4: "l", length of CWI vector: GT[1] */
!   gageVecNormalized, /*  5: "n", normalized CWI vector: GT[3] */
!   gageVecJacobian,   /*  6: "j", component-wise Jacobian: GT[9]
  			    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 */
!   gageVecDivergence, /*  7: "d", divergence (based on Jacobian): GT[1] */
!   gageVecCurl,       /*  8: "c", curl (based on Jacobian): GT[3] */
!   gageVecCurlNorm,   /*  9: "cm", curl magnitude: GT[1] */
!   gageVecHelicity,   /* 10: "h", helicity: vec . curl: GT[1] */
!   gageVecNormHelicity,/*11: "nh", normalized helicity: GT[1] */
!   gageVecLambda2,    /* 12: "lmbda2", lambda2 criterion: GT[1] */
!   gageVecImaginaryPart,/* 13: "imag", imag. part of jacobian's eigenv: GT[1] */
!   gageVecHessian,    /* 14: "vh", second-order derivative: GT[27] 
  			    0:d2v_x/dxdx   1:d2v_x/dxdy   2:d2v_x/dxdz
  	                    3:d2v_x/dydx   4:d2v_x/dydy   5:d2v_x/dydz
***************
*** 299,319 ****
  			        [...]
  			   24:dv2_z/dzdx  25:d2v_z/dzdy  26:d2v_z/dzdz */
!   gageVecDivGradient,/* 12: "dg", divergence gradient: GT[3] */
!   gageVecCurlGradient,/*13: "cg", curl gradient: GT[9] */
!   gageVecCurlNormGrad,/*14: "cng", curl norm gradient: GT[3] */
!   gageVecNCurlNormGrad, /* 15: "ncng", normalized curl norm gradient: GT[3] */
!   gageVecHelGradient,/* 16: "hg", helicity gradient: GT[3] */
!   gageVecDirHelDeriv,/* 17: "dhd", directional derivative of helicity: GT[1] */ 
!   gageVecProjHelGradient, /* 18: "phg", projected helicity gradient: GT[3] */
!   gageVecGradient0,  /* 19: "g0", gradient of 1st component of vector: GT[3] */
!   gageVecGradient1,  /* 20: "g1", gradient of 2nd component of vector: GT[3] */
!   gageVecGradient2,  /* 21: "g2", gradient of 3rd component of vector: GT[3] */
!   gageVecMultiGrad,  /* 22: "mg", sum of outer products of gradients: GT[9] */
!   gageVecMGFrob,     /* 23: "mgfrob", frob norm of multi-gradient: GT[1] */
!   gageVecMGEval,     /* 24: "mgeval", eigenvalues of multi-gradient: GT[3] */
!   gageVecMGEvec,     /* 25: "mgevec", eigenvectors of multi-gradient: GT[9] */
    gageVecLast
  };
! #define GAGE_VEC_ITEM_MAX     25
  
  struct gageKind_t;       /* dumb forward declaraction, ignore */
--- 302,322 ----
  			        [...]
  			   24:dv2_z/dzdx  25:d2v_z/dzdy  26:d2v_z/dzdz */
!   gageVecDivGradient,/* 15: "dg", divergence gradient: GT[3] */
!   gageVecCurlGradient,/*16: "cg", curl gradient: GT[9] */
!   gageVecCurlNormGrad,/*17: "cng", curl norm gradient: GT[3] */
!   gageVecNCurlNormGrad, /* 18: "ncng", normalized curl norm gradient: GT[3] */
!   gageVecHelGradient,/* 19: "hg", helicity gradient: GT[3] */
!   gageVecDirHelDeriv,/* 20: "dhd", directional derivative of helicity: GT[1] */ 
!   gageVecProjHelGradient, /* 21: "phg", projected helicity gradient: GT[3] */
!   gageVecGradient0,  /* 22: "g0", gradient of 1st component of vector: GT[3] */
!   gageVecGradient1,  /* 23: "g1", gradient of 2nd component of vector: GT[3] */
!   gageVecGradient2,  /* 24: "g2", gradient of 3rd component of vector: GT[3] */
!   gageVecMultiGrad,  /* 25: "mg", sum of outer products of gradients: GT[9] */
!   gageVecMGFrob,     /* 26: "mgfrob", frob norm of multi-gradient: GT[1] */
!   gageVecMGEval,     /* 27: "mgeval", eigenvalues of multi-gradient: GT[3] */
!   gageVecMGEvec,     /* 28: "mgevec", eigenvectors of multi-gradient: GT[9] */
    gageVecLast
  };
! #define GAGE_VEC_ITEM_MAX     28
  
  struct gageKind_t;       /* dumb forward declaraction, ignore */

Index: vecGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/vecGage.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** vecGage.c	11 Apr 2004 02:31:41 -0000	1.20
--- vecGage.c	22 Apr 2004 07:19:00 -0000	1.21
***************
*** 62,65 ****
--- 62,68 ----
    /* enum value        len,deriv,  prereqs,                                             parent item, index*/
    {gageVecVector,        3,  0,  {-1, -1, -1, -1, -1},                                           -1,  -1},
+   {gageVecVector0,       1,  0,  {gageVecVector, -1, -1, -1, -1},                     gageVecVector,   0},
+   {gageVecVector1,       1,  0,  {gageVecVector, -1, -1, -1, -1},                     gageVecVector,   1},
+   {gageVecVector2,       1,  0,  {gageVecVector, -1, -1, -1, -1},                     gageVecVector,   2},
    {gageVecLength,        1,  0,  {gageVecVector, -1, -1, -1, -1},                                -1,  -1},
    {gageVecNormalized,    3,  0,  {gageVecVector, gageVecLength, -1, -1, -1},                     -1,  -1},
***************
*** 150,154 ****
    gage_t *vecAns, *normAns, *jacAns, *curlAns, *hesAns, *curlGradAns, 
           *helGradAns, *dirHelDirAns, *curlnormgradAns;
!   int asw;
  
    vecAns          = pvl->directAnswer[gageVecVector];
--- 153,157 ----
    gage_t *vecAns, *normAns, *jacAns, *curlAns, *hesAns, *curlGradAns, 
           *helGradAns, *dirHelDirAns, *curlnormgradAns;
!   /* int asw; */
  
    vecAns          = pvl->directAnswer[gageVecVector];
***************
*** 169,172 ****
--- 172,179 ----
      }
    }
+   /* done if doV 
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecVector{0,1,2})) {
+   }
+   */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecLength)) {
      pvl->directAnswer[gageVecLength][0] = ELL_3V_LEN(vecAns);
***************
*** 232,236 ****
        ELL_3M_ADD2(symm, symm, tmpMat);
        /* get eigenvalues in sorted order */
!       asw = ell_3m_eigenvalues_d(eval, symm, AIR_TRUE);
        pvl->directAnswer[gageVecLambda2][0] = eval[1];
    }
--- 239,243 ----
        ELL_3M_ADD2(symm, symm, tmpMat);
        /* get eigenvalues in sorted order */
!       /* asw = */ ell_3m_eigenvalues_d(eval, symm, AIR_TRUE);
        pvl->directAnswer[gageVecLambda2][0] = eval[1];
    }
***************
*** 383,386 ****
--- 390,396 ----
    "(unknown gageVec)",
    "vector",
+   "vector0",
+   "vector1",
+   "vector2",
    "length",
    "normalized",
***************
*** 413,416 ****
--- 423,429 ----
    "unknown gageVec query",
    "component-wise-interpolated vector",
+   "vector[0]",
+   "vector[1]",
+   "vector[2]",
    "length of vector",
    "normalized vector",
***************
*** 443,446 ****
--- 456,462 ----
    gageVecUnknown,
    gageVecVector,
+   gageVecVector0,
+   gageVecVector1,
+   gageVecVector2,
    gageVecLength,
    gageVecNormalized,
***************
*** 471,474 ****
--- 487,493 ----
  
  #define GV_V   gageVecVector
+ #define GV_V0  gageVecVector0
+ #define GV_V1  gageVecVector1
+ #define GV_V2  gageVecVector2
  #define GV_L   gageVecLength
  #define GV_N   gageVecNormalized
***************
*** 500,503 ****
--- 519,525 ----
  _gageVecStrEqv[][AIR_STRLEN_SMALL] = {
    "v", "vector", "vec",
+   "v0", "vector0", "vec0",
+   "v1", "vector1", "vec1",
+   "v2", "vector2", "vec2",
    "l", "length", "len",
    "n", "normalized", "normalized vector",
***************
*** 531,534 ****
--- 553,559 ----
  _gageVecValEqv[] = {
    GV_V, GV_V, GV_V,
+   GV_V0, GV_V0, GV_V0,
+   GV_V1, GV_V1, GV_V1,
+   GV_V2, GV_V2, GV_V2,
    GV_L, GV_L, GV_L,
    GV_N, GV_N, GV_N,

[Teem-commit] teem/src/ten enumsTen.c,1.21,1.22 ten.h,1.83,1.84 tenGage.c,1.16,1.17

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8348

Modified Files:
	enumsTen.c ten.h tenGage.c 
Log Message:
changing variable names from ...P... to ...Theta...

Index: enumsTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/enumsTen.c,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** enumsTen.c	22 Apr 2004 04:49:27 -0000	1.21
--- enumsTen.c	22 Apr 2004 07:14:54 -0000	1.22
***************
*** 189,193 ****
    tenGageFA,            /* "fa", fractional anisotropy: GT[1] */
    tenGageR,             /* "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
!   tenGageP,             /* "p", arccos(R/sqrt(Q^3)): GT[1] */
    tenGageEval,          /* "eval", all eigenvalues of tensor : GT[3] */
    tenGageEval0,         /* "eval0", major eigenvalue of tensor : GT[1] */
--- 189,193 ----
    tenGageFA,            /* "fa", fractional anisotropy: GT[1] */
    tenGageR,             /* "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
!   tenGageTheta,         /* "th", arccos(R/sqrt(Q^3))/3: GT[1] */
    tenGageEval,          /* "eval", all eigenvalues of tensor : GT[3] */
    tenGageEval0,         /* "eval0", major eigenvalue of tensor : GT[1] */
***************
*** 220,226 ****
    tenGageRGradMag,      /* "rgm", gradient magnitude of Q: GT[1] */
    tenGageRNormal,       /* "rn", normalized gradient of Q: GT[3] */
!   tenGagePGradVec,      /* "pgv", gradient vector of P: GT[3] */
!   tenGagePGradMag,      /* "pgm", gradient magnitude of P: GT[1] */
!   tenGagePNormal,       /* "pn", normalized gradient of P: GT[3] */
    tenGageAniso          /* "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
  };
--- 220,226 ----
    tenGageRGradMag,      /* "rgm", gradient magnitude of Q: GT[1] */
    tenGageRNormal,       /* "rn", normalized gradient of Q: GT[3] */
!   tenGageThetaGradVec,  /* "thgv", gradient vector of P: GT[3] */
!   tenGageThetaGradMag,  /* "thgm", gradient magnitude of P: GT[1] */
!   tenGageThetaNormal,   /* "thn", normalized gradient of P: GT[3] */
    tenGageAniso          /* "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
  };
***************
*** 237,241 ****
    "fa",
    "r",
!   "p",
    "eval",
    "eval0",
--- 237,241 ----
    "fa",
    "r",
!   "th", "theta",
    "eval",
    "eval0",
***************
*** 268,274 ****
    "rgm", "r grad mag",
    "rn", "r normal",
!   "pgv", "p grad vec",
!   "pgm", "p grad mag",
!   "pn", "p normal",
    "an", "aniso", "anisotropies",
    ""
--- 268,274 ----
    "rgm", "r grad mag",
    "rn", "r normal",
!   "thgv", "th grad vec",
!   "thgm", "th grad mag",
!   "thn", "th normal",
    "an", "aniso", "anisotropies",
    ""
***************
*** 286,290 ****
    tenGageFA,
    tenGageR,
!   tenGageP,
    tenGageEval,
    tenGageEval0,
--- 286,290 ----
    tenGageFA,
    tenGageR,
!   tenGageTheta, tenGageTheta,
    tenGageEval,
    tenGageEval0,
***************
*** 317,323 ****
    tenGageRGradMag, tenGageRGradMag,
    tenGageRNormal, tenGageRNormal,
!   tenGagePGradVec, tenGagePGradVec,
!   tenGagePGradMag, tenGagePGradMag,
!   tenGagePNormal, tenGagePNormal,
    tenGageAniso, tenGageAniso, tenGageAniso
  };
--- 317,323 ----
    tenGageRGradMag, tenGageRGradMag,
    tenGageRNormal, tenGageRNormal,
!   tenGageThetaGradVec, tenGageThetaGradVec,
!   tenGageThetaGradMag, tenGageThetaGradMag,
!   tenGageThetaNormal, tenGageThetaNormal,
    tenGageAniso, tenGageAniso, tenGageAniso
  };

Index: tenGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tenGage.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** tenGage.c	15 Apr 2004 14:55:07 -0000	1.16
--- tenGage.c	22 Apr 2004 07:14:54 -0000	1.17
***************
*** 35,39 ****
    {tenGageFA,                  1,  0,  {tenGageQ, tenGageS, -1, -1, -1},                                                      -1,  -1},
    {tenGageR,                   1,  0,  {tenGageTrace, tenGageB, tenGageDet, tenGageS, -1},                                    -1,  -1},
!   {tenGageP,                   1,  0,  {tenGageR, tenGageQ, -1, -1, -1},                                                      -1,  -1},
  
    {tenGageEval,                3,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
--- 35,39 ----
    {tenGageFA,                  1,  0,  {tenGageQ, tenGageS, -1, -1, -1},                                                      -1,  -1},
    {tenGageR,                   1,  0,  {tenGageTrace, tenGageB, tenGageDet, tenGageS, -1},                                    -1,  -1},
!   {tenGageTheta,               1,  0,  {tenGageR, tenGageQ, -1, -1, -1},                                                      -1,  -1},
  
    {tenGageEval,                3,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
***************
*** 76,82 ****
    {tenGageRNormal,             3,  1,  {tenGageRGradVec, tenGageRGradMag, -1, -1, -1},                                        -1,  -1},
  
!   {tenGagePGradVec,            3,  1,  {tenGageRGradVec, tenGageQGradVec, tenGageP, -1, -1},                                  -1,  -1},
!   {tenGagePGradMag,            1,  1,  {tenGagePGradVec, -1, -1, -1, -1},                                                     -1,  -1},
!   {tenGagePNormal,             3,  1,  {tenGagePGradVec, tenGagePGradMag, -1, -1, -1},                                        -1,  -1},
  
    {tenGageAniso, TEN_ANISO_MAX+1,  0,  {tenGageEval0, tenGageEval1, tenGageEval2, -1, -1},                                    -1,  -1}
--- 76,82 ----
    {tenGageRNormal,             3,  1,  {tenGageRGradVec, tenGageRGradMag, -1, -1, -1},                                        -1,  -1},
  
!   {tenGageThetaGradVec,        3,  1,  {tenGageRGradVec, tenGageQGradVec, tenGageTheta, -1, -1},                              -1,  -1},
!   {tenGageThetaGradMag,        1,  1,  {tenGageThetaGradVec, -1, -1, -1, -1},                                                 -1,  -1},
!   {tenGageThetaNormal,         3,  1,  {tenGageThetaGradVec, tenGageThetaGradMag, -1, -1, -1},                                -1,  -1},
  
    {tenGageAniso, TEN_ANISO_MAX+1,  0,  {tenGageEval0, tenGageEval1, tenGageEval2, -1, -1},                                    -1,  -1}
***************
*** 175,181 ****
      }
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageConfidence)) {
-     pvl->directAnswer[tenGageConfidence][0] = tenAns[0];
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTrace)) {
      cbA = -(pvl->directAnswer[tenGageTrace][0] = dtA + dtD + dtF);
--- 175,182 ----
      }
    }
+   /* done if doV 
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageConfidence)) {
    }
+   */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTrace)) {
      cbA = -(pvl->directAnswer[tenGageTrace][0] = dtA + dtD + dtF);
***************
*** 203,211 ****
      cbR = pvl->directAnswer[tenGageR][0] = (5*cbA*cbB - 27*cbC - 2*cbA*cbS)/54;
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageP)) {
      cbQQQ = cbQ*cbQ*cbQ;
      tmp0 = cbR/(epsilon + sqrt(cbQQQ));
!     tmp0 = AIR_CLAMP(0.0, tmp0, 1.0);
!     pvl->directAnswer[tenGageP][0] = acos(tmp0);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvec)) {
--- 204,212 ----
      cbR = pvl->directAnswer[tenGageR][0] = (5*cbA*cbB - 27*cbC - 2*cbA*cbS)/54;
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTheta)) {
      cbQQQ = cbQ*cbQ*cbQ;
      tmp0 = cbR/(epsilon + sqrt(cbQQQ));
!     tmp0 = AIR_CLAMP(-1.0, tmp0, 1.0);
!     pvl->directAnswer[tenGageTheta][0] = acos(tmp0)/3;
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvec)) {
***************
*** 356,362 ****
  		 1.0/(epsilon + magTmp), vecTmp);
    }
!   /* --- P --- */
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGagePGradVec)) {
!     vecTmp = pvl->directAnswer[tenGagePGradVec];
      tmp1 = cbQ*cbQ*cbQ;
      tmp1 = sqrt(tmp1)*sqrt(1.0 - cbR*cbR/(epsilon + tmp1));
--- 357,363 ----
  		 1.0/(epsilon + magTmp), vecTmp);
    }
!   /* --- Theta --- */
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageThetaGradVec)) {
!     vecTmp = pvl->directAnswer[tenGageThetaGradVec];
      tmp1 = cbQ*cbQ*cbQ;
      tmp1 = sqrt(tmp1)*sqrt(1.0 - cbR*cbR/(epsilon + tmp1));
***************
*** 367,375 ****
  		      -tmp1, gradCbR);
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGagePGradMag)) {
!     magTmp = pvl->directAnswer[tenGagePGradMag][0] = ELL_3V_LEN(vecTmp);
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGagePNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGagePNormal],
  		 1.0/(epsilon + magTmp), vecTmp);
    }
--- 368,376 ----
  		      -tmp1, gradCbR);
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageThetaGradMag)) {
!     magTmp = pvl->directAnswer[tenGageThetaGradMag][0] = ELL_3V_LEN(vecTmp);
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageThetaNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageThetaNormal],
  		 1.0/(epsilon + magTmp), vecTmp);
    }

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.83
retrieving revision 1.84
diff -C2 -d -r1.83 -r1.84
*** ten.h	22 Apr 2004 04:54:33 -0000	1.83
--- ten.h	22 Apr 2004 07:14:54 -0000	1.84
***************
*** 153,157 ****
  ** R = (9*A*B - 2*A^3 - 27*C)/54 
       = (5*A*B - 2*A*S - 27*C)/54 = thirdmoment({v1,v2,v3})/2
! ** P = arccos(R/sqrt(Q)^3) = phase angle of cubic solution
  **
  ** !!! Changes to this list need to be propogated to tenGage.c's
--- 153,157 ----
  ** R = (9*A*B - 2*A^3 - 27*C)/54 
       = (5*A*B - 2*A*S - 27*C)/54 = thirdmoment({v1,v2,v3})/2
! ** P = arccos(R/sqrt(Q)^3)/3 = phase angle of cubic solution
  **
  ** !!! Changes to this list need to be propogated to tenGage.c's
***************
*** 171,175 ****
    tenGageFA,            /*  7: "fa", fractional anisotropy: GT[1] */
    tenGageR,             /*  8: "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
!   tenGageP,             /*  9: "p", arccos(R/sqrt(Q^3)): GT[1] */
  
    tenGageEval,          /* 10: "eval", all eigenvalues of tensor : GT[3] */
--- 171,175 ----
    tenGageFA,            /*  7: "fa", fractional anisotropy: GT[1] */
    tenGageR,             /*  8: "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
!   tenGageTheta,         /*  9: "th", arccos(R/sqrt(Q^3))/3: GT[1] */
  
    tenGageEval,          /* 10: "eval", all eigenvalues of tensor : GT[3] */
***************
*** 213,219 ****
    tenGageRNormal,       /* 39: "rn", normalized gradient of Q: GT[3] */
  
!   tenGagePGradVec,      /* 40: "pgv", gradient vector of P: GT[3] */
!   tenGagePGradMag,      /* 41: "pgm", gradient magnitude of P: GT[1] */
!   tenGagePNormal,       /* 42: "pn", normalized gradient of P: GT[3] */
  
    tenGageAniso,         /* 43: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
--- 213,219 ----
    tenGageRNormal,       /* 39: "rn", normalized gradient of Q: GT[3] */
  
!   tenGageThetaGradVec,  /* 40: "thgv", gradient vector of Th: GT[3] */
!   tenGageThetaGradMag,  /* 41: "thgm", gradient magnitude of Th: GT[1] */
!   tenGageThetaNormal,   /* 42: "thn", normalized gradient of Th: GT[3] */
  
    tenGageAniso,         /* 43: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */

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

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

Update of /cvsroot/teem/teem/src/ten/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22601

Modified Files:
	tt.c 
Log Message:
allows tt to make glyphs for whole trace plane instead of usual barycentric space

Index: tt.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/test/tt.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** tt.c	7 Jan 2004 15:34:31 -0000	1.12
--- tt.c	22 Apr 2004 04:58:34 -0000	1.13
***************
*** 21,32 ****
  #include "../ten.h"
  
! char *info = ("Sample space of tensor orientation.");
  
  void
! _cap2xyz(double xyz[3], double ca, double cp, int version) {
!   double cl, cs;
    
    cs = 1 - ca;
    cl = 1 - cs - cp;
    /*
    xyz[0] = cs*0.333 + cl*1.0 + cp*0.5;
--- 21,33 ----
  #include "../ten.h"
  
! char *info = ("Sample space of tensor shape.");
  
  void
! _cap2xyz(double xyz[3], double ca, double cp, int version, int whole) {
!   double cl, cs, mean;
    
    cs = 1 - ca;
    cl = 1 - cs - cp;
+   mean = (cs + cp + cl)/3;
    /*
    xyz[0] = cs*0.333 + cl*1.0 + cp*0.5;
***************
*** 37,48 ****
    xyz[2] = AIR_AFFINE(0, ca, 1, 1.1*xyz[2], 0.86*xyz[2]);
    */
!   if (1 == version) {
!     xyz[0] = (3 + 3*cl - cs)/6;
!     xyz[1] = (2 - 2*cl + cp)/6;
!     xyz[2] = 2*cs/6;
    } else {
!     xyz[0] = 1;
!     xyz[1] = 1 - cl;
!     xyz[2] = cs;
    }
  }
--- 38,55 ----
    xyz[2] = AIR_AFFINE(0, ca, 1, 1.1*xyz[2], 0.86*xyz[2]);
    */
!   if (whole) {
!     ELL_3V_SET(xyz,
! 	       AIR_AFFINE(0.0, 0.9, 1.0, mean, cl),
! 	       AIR_AFFINE(0.0, 0.9, 1.0, mean, cp),
! 	       AIR_AFFINE(0.0, 0.9, 1.0, mean, cs));
    } else {
!     if (1 == version) {
!       ELL_3V_SET(xyz,
! 		 (3 + 3*cl - cs)/6,
! 		 (2 - 2*cl + cp)/6,
! 		 2*cs/6);
!     } else {
!       ELL_3V_SET(xyz, 1, 1 - cl, cs);
!     }
    }
  }
***************
*** 81,87 ****
    airArray *mop;
    
!   int xi, yi, samp, version;
    float *tdata;
!   double p[3], xyz[3], q[4], len, hackcp, maxca;
    double ca, cp, mD[9], mRF[9], mRI[9], mT[9], hack;
    Nrrd *nten;
--- 88,94 ----
    airArray *mop;
    
!   int xi, yi, samp, version, whole;
    float *tdata;
!   double p[3], xyz[3], q[4], len, hackcp=0, maxca;
    double ca, cp, mD[9], mRF[9], mRI[9], mT[9], hack;
    Nrrd *nten;
***************
*** 95,98 ****
--- 102,110 ----
    hestOptAdd(&hopt, "ca", "max ca", airTypeDouble, 1, 1, &maxca, "0.8",
  	     "maximum ca to use at bottom edge of triangle");
+   hestOptAdd(&hopt, "w", NULL, airTypeInt, 0, 0, &whole, NULL,
+ 	     "sample the whole triangle of constant trace, "
+ 	     "instead of just the "
+ 	     "sixth of it in which the eigenvalues have the "
+ 	     "traditional sorted order. ");
    hestOptAdd(&hopt, "hack", "hack", airTypeDouble, 1, 1, &hack, "0.04",
  	     "this is a hack");
***************
*** 131,139 ****
    ELL_3M_TRANSPOSE(mRI, mRF);
    for (yi=0; yi<samp; yi++) {
!     ca = AIR_AFFINE(0, yi, samp-1, hack, maxca);
!     hackcp = AIR_AFFINE(0, yi, samp-1, hack, 0);
      for (xi=0; xi<=yi; xi++) {
!       cp = AIR_AFFINE(0, xi, samp-1, hackcp, maxca-hack/2.0);
!       _cap2xyz(xyz, ca, cp, version);
        /*
        fprintf(stderr, "%s: (%d,%d) -> (%g,%g) -> %g %g %g\n", me,
--- 143,159 ----
    ELL_3M_TRANSPOSE(mRI, mRF);
    for (yi=0; yi<samp; yi++) {
!     if (whole) {
!       ca = AIR_AFFINE(0, yi, samp-1, 0.0, 1.0);
!     } else {
!       ca = AIR_AFFINE(0, yi, samp-1, hack, maxca);
!       hackcp = AIR_AFFINE(0, yi, samp-1, hack, 0);
!     }
      for (xi=0; xi<=yi; xi++) {
!       if (whole) {
! 	cp = AIR_AFFINE(0, xi, samp-1, 0.0, 1.0);
!       } else {
! 	cp = AIR_AFFINE(0, xi, samp-1, hackcp, maxca-hack/2.0);
!       }
!       _cap2xyz(xyz, ca, cp, version, whole);
        /*
        fprintf(stderr, "%s: (%d,%d) -> (%g,%g) -> %g %g %g\n", me,

[Teem-commit] teem/src/ten ten.h,1.82,1.83

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22041

Modified Files:
	ten.h 
Log Message:
fixed description of FA and RA in comments

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.82
retrieving revision 1.83
diff -C2 -d -r1.82 -r1.83
*** ten.h	15 Apr 2004 14:55:07 -0000	1.82
--- ten.h	22 Apr 2004 04:54:33 -0000	1.83
***************
*** 67,71 ****
    tenAnisoLast
  };
! #define TEN_ANISO_MAX    22
  
  /*
--- 67,71 ----
    tenAnisoLast
  };
! #define TEN_ANISO_MAX    25
  
  /*
***************
*** 134,139 ****
    "\b\bo \"cs1\", \"cs2\": Westin's spherical (1-ca)\n " \
    "\b\bo \"ct1\", \"ct2\": GK's anisotropy type (cp/ca)\n " \
!   "\b\bo \"ra\": Basser/Pierpaoli relative anisotropy\n " \
!   "\b\bo \"fa\": Basser/Pierpaoli fractional anisotropy/sqrt(2)\n " \
    "\b\bo \"vf\": volume fraction = 1-(Basser/Pierpaoli volume ratio)\n " \
    "\b\bo \"tr\": trace"
--- 134,139 ----
    "\b\bo \"cs1\", \"cs2\": Westin's spherical (1-ca)\n " \
    "\b\bo \"ct1\", \"ct2\": GK's anisotropy type (cp/ca)\n " \
!   "\b\bo \"ra\": Basser/Pierpaoli relative anisotropy/sqrt(2)\n " \
!   "\b\bo \"fa\": Basser/Pierpaoli fractional anisotropy\n " \
    "\b\bo \"vf\": volume fraction = 1-(Basser/Pierpaoli volume ratio)\n " \
    "\b\bo \"tr\": trace"

[Teem-commit] teem/src/ten aniso.c,1.28,1.29 enumsTen.c,1.20,1.21

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv21467

Modified Files:
	aniso.c enumsTen.c 
Log Message:
added hacks to learn eigenvalues from aniso

Index: aniso.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/aniso.c,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** aniso.c	30 Mar 2004 19:25:14 -0000	1.28
--- aniso.c	22 Apr 2004 04:49:26 -0000	1.29
***************
*** 108,111 ****
--- 108,114 ----
    c[tenAniso_Det] = e0*e1*e2;
    c[tenAniso_Tr] = e0 + e1 + e2;
+   c[TEN_ANISO_MAX-2] = e0;
+   c[TEN_ANISO_MAX-1] = e1;
+   c[TEN_ANISO_MAX-0] = e2;
    return;
  }

Index: enumsTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/enumsTen.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** enumsTen.c	15 Apr 2004 14:55:07 -0000	1.20
--- enumsTen.c	22 Apr 2004 04:49:27 -0000	1.21
***************
*** 47,51 ****
    "Cz",
    "Det",
!   "Tr"
  };
  
--- 47,54 ----
    "Cz",
    "Det",
!   "Tr",
!   "hack0",
!   "hack1",
!   "hack2"
  };
  

[Teem-commit] teem/src/limn/test off2eps.c,1.7,1.8

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

Update of /cvsroot/teem/teem/src/limn/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20434

Modified Files:
	off2eps.c 
Log Message:
added -bg flag

Index: off2eps.c
===================================================================
RCS file: /cvsroot/teem/teem/src/limn/test/off2eps.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** off2eps.c	3 Mar 2004 13:14:08 -0000	1.7
--- off2eps.c	22 Apr 2004 04:40:39 -0000	1.8
***************
*** 27,31 ****
    char *me, *err, *inS, *outS;
    limnCamera *cam;
!   float winscale, edgeWidth[5], creaseAngle;
    hestOpt *hopt=NULL;
    airArray *mop;
--- 27,31 ----
    char *me, *err, *inS, *outS;
    limnCamera *cam;
!   float bg[3], winscale, edgeWidth[5], creaseAngle;
    hestOpt *hopt=NULL;
    airArray *mop;
***************
*** 73,76 ****
--- 73,78 ----
    hestOptAdd(&hopt, "describe", NULL, airTypeInt, 0, 0, &describe, NULL,
  	     "for debugging: list object definition of OFF read");
+   hestOptAdd(&hopt, "bg", "background", airTypeFloat, 3, 3, bg, "1 1 1",
+ 	     "background RGB color; each component in range [0.0,1.0]");
    hestOptAdd(&hopt, "nobg", NULL, airTypeInt, 0, 0, &nobg, NULL,
  	     "don't initially fill with background color");
***************
*** 139,142 ****
--- 141,145 ----
    win->ps.creaseAngle = creaseAngle;
    win->ps.noBackground = nobg;
+   ELL_3V_COPY(win->ps.bg, bg);
  
    win->file = airFopen(outS, stdout, "w");

[Teem-commit] teem/src/ten enumsTen.c,1.19,1.20 ten.h,1.81,1.82 tenGage.c,1.15,1.16

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1888

Modified Files:
	enumsTen.c ten.h tenGage.c 
Log Message:
shockingly, tensor confidence was not a gage-accessible value until now

Index: enumsTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/enumsTen.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** enumsTen.c	30 Mar 2004 19:25:14 -0000	1.19
--- enumsTen.c	15 Apr 2004 14:55:07 -0000	1.20
***************
*** 68,71 ****
--- 68,73 ----
  
    "tensor",
+   "confidence",
+   
    "trace",
    "B",
***************
*** 127,130 ****
--- 129,133 ----
    "(unknown tenGage item)",
    "tensor",
+   "confidence",
    "trace",
    "B",
***************
*** 175,178 ****
--- 178,182 ----
    tenGageUnknown,
    tenGageTensor,        /* "t", the reconstructed tensor: GT[7] */
+   tenGageConfidence,    /* "c", first of seven tensor values: GT[1] */
    tenGageTrace,         /* "tr", trace of tensor: GT[1] */
    tenGageB,             /* "b": GT[1] */
***************
*** 222,225 ****
--- 226,230 ----
  _tenGageStrEqv[][AIR_STRLEN_SMALL] = {
    "t", "tensor",
+   "c", "conf",
    "tr", "trace",
    "b",
***************
*** 270,273 ****
--- 275,279 ----
  _tenGageValEqv[] = {
    tenGageTensor, tenGageTensor,
+   tenGageConfidence, tenGageConfidence,
    tenGageTrace, tenGageTrace,
    tenGageB,
***************
*** 392,396 ****
    "length", "len",
    "steps",
!   "confidence", "conf",
    "bounds",
    ""
--- 398,402 ----
    "length", "len",
    "steps",
!   "confidence", "conf", "c",
    "bounds",
    ""
***************
*** 402,406 ****
    tenFiberStopLength, tenFiberStopLength,
    tenFiberStopNumSteps,
!   tenFiberStopConfidence, tenFiberStopConfidence,
    tenFiberStopBounds
  };
--- 408,412 ----
    tenFiberStopLength, tenFiberStopLength,
    tenFiberStopNumSteps,
!   tenFiberStopConfidence, tenFiberStopConfidence, tenFiberStopConfidence,
    tenFiberStopBounds
  };

Index: tenGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tenGage.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** tenGage.c	23 Feb 2004 06:03:13 -0000	1.15
--- tenGage.c	15 Apr 2004 14:55:07 -0000	1.16
***************
*** 26,29 ****
--- 26,30 ----
    /* enum value              len,deriv,  prereqs,                                                                     parent item, index*/
    {tenGageTensor,              7,  0,  {-1, -1, -1, -1, -1},                                                                  -1,  -1},
+   {tenGageConfidence,          1,  0,  {tenGageTensor, -1, -1, -1, -1},                                            tenGageTensor,   0},
  
    {tenGageTrace,               1,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
***************
*** 174,177 ****
--- 175,181 ----
      }
    }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageConfidence)) {
+     pvl->directAnswer[tenGageConfidence][0] = tenAns[0];
+   }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTrace)) {
      cbA = -(pvl->directAnswer[tenGageTrace][0] = dtA + dtD + dtF);

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.81
retrieving revision 1.82
diff -C2 -d -r1.81 -r1.82
*** ten.h	30 Mar 2004 19:25:14 -0000	1.81
--- ten.h	15 Apr 2004 14:55:07 -0000	1.82
***************
*** 154,157 ****
--- 154,161 ----
       = (5*A*B - 2*A*S - 27*C)/54 = thirdmoment({v1,v2,v3})/2
  ** P = arccos(R/sqrt(Q)^3) = phase angle of cubic solution
+ **
+ ** !!! Changes to this list need to be propogated to tenGage.c's
+ ** !!! _tenGageTable[] and _tenGageAnswer(), 
+ ** !!! and to enumsTen.c's tenGage airEnum.
  */
  enum {
***************
*** 159,219 ****
  
    tenGageTensor,        /*  0: "t", the reconstructed tensor: GT[7] */
!   tenGageTrace,         /*  1: "tr", trace of tensor: GT[1] */
!   tenGageB,             /*  2: "b": GT[1] */
!   tenGageDet,           /*  3: "det", determinant of tensor: GT[1] */
!   tenGageS,             /*  4: "s", square of frobenius norm: GT[1] */
!   tenGageQ,             /*  5: "q", (S - B)/9: GT[1] */
!   tenGageFA,            /*  6: "fa", fractional anisotropy: GT[1] */
!   tenGageR,             /*  7: "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
!   tenGageP,             /*  8: "p", arccos(R/sqrt(Q^3)): GT[1] */
  
!   tenGageEval,          /*  9: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /* 10: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /* 11: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* 12: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* 13: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* 14: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* 15: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 16: "evec2", minor eigenvectors of tensor: GT[3] */
  
!   tenGageTensorGrad,    /* 17: "tg, all tensor component gradients, starting
  			       with the confidence gradient: GT[21] */
  
!   tenGageTraceGradVec,  /* 18: "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* 19: "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* 20: "trn": normal of trace: GT[3] */
    
!   tenGageBGradVec,      /* 21: "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* 22: "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* 23: "bn", normal of B: GT[3] */
  
!   tenGageDetGradVec,    /* 24: "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* 25: "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* 26: "detn", normal of Det: GT[3] */
  
!   tenGageSGradVec,      /* 27: "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* 28: "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* 29: "sn", normal of S: GT[3] */
  
!   tenGageQGradVec,      /* 30: "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 31: "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 32: "qn", normalized gradient of Q: GT[3] */
  
!   tenGageFAGradVec,     /* 33: "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* 34: "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* 35: "fan", normalized gradient of FA: GT[3] */
  
!   tenGageRGradVec,      /* 36: "rgv", gradient vector of Q: GT[3] */
!   tenGageRGradMag,      /* 37: "rgm", gradient magnitude of Q: GT[1] */
!   tenGageRNormal,       /* 38: "rn", normalized gradient of Q: GT[3] */
  
!   tenGagePGradVec,      /* 39: "pgv", gradient vector of P: GT[3] */
!   tenGagePGradMag,      /* 40: "pgm", gradient magnitude of P: GT[1] */
!   tenGagePNormal,       /* 41: "pn", normalized gradient of P: GT[3] */
  
!   tenGageAniso,         /* 42: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  42
  
  /*
--- 163,224 ----
  
    tenGageTensor,        /*  0: "t", the reconstructed tensor: GT[7] */
!   tenGageConfidence,    /*  1: "c", first of seven tensor values: GT[1] */
!   tenGageTrace,         /*  2: "tr", trace of tensor: GT[1] */
!   tenGageB,             /*  3: "b": GT[1] */
!   tenGageDet,           /*  4: "det", determinant of tensor: GT[1] */
!   tenGageS,             /*  5: "s", square of frobenius norm: GT[1] */
!   tenGageQ,             /*  6: "q", (S - B)/9: GT[1] */
!   tenGageFA,            /*  7: "fa", fractional anisotropy: GT[1] */
!   tenGageR,             /*  8: "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
!   tenGageP,             /*  9: "p", arccos(R/sqrt(Q^3)): GT[1] */
  
!   tenGageEval,          /* 10: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /* 11: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /* 12: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* 13: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* 14: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* 15: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* 16: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 17: "evec2", minor eigenvectors of tensor: GT[3] */
  
!   tenGageTensorGrad,    /* 18: "tg, all tensor component gradients, starting
  			       with the confidence gradient: GT[21] */
  
!   tenGageTraceGradVec,  /* 19: "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* 20: "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* 21: "trn": normal of trace: GT[3] */
    
!   tenGageBGradVec,      /* 22: "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* 23: "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* 24: "bn", normal of B: GT[3] */
  
!   tenGageDetGradVec,    /* 25: "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* 26: "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* 27: "detn", normal of Det: GT[3] */
  
!   tenGageSGradVec,      /* 28: "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* 29: "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* 30: "sn", normal of S: GT[3] */
  
!   tenGageQGradVec,      /* 31: "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 32: "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 33: "qn", normalized gradient of Q: GT[3] */
  
!   tenGageFAGradVec,     /* 34: "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* 35: "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* 36: "fan", normalized gradient of FA: GT[3] */
  
!   tenGageRGradVec,      /* 37: "rgv", gradient vector of Q: GT[3] */
!   tenGageRGradMag,      /* 38: "rgm", gradient magnitude of Q: GT[1] */
!   tenGageRNormal,       /* 39: "rn", normalized gradient of Q: GT[3] */
  
!   tenGagePGradVec,      /* 40: "pgv", gradient vector of P: GT[3] */
!   tenGagePGradMag,      /* 41: "pgm", gradient magnitude of P: GT[1] */
!   tenGagePNormal,       /* 42: "pn", normalized gradient of P: GT[3] */
  
!   tenGageAniso,         /* 43: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  43
  
  /*

[Teem-commit] teem/src/mite txf.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-serv1762

Modified Files:
	txf.c 
Log Message:
comment change

Index: txf.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/txf.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** txf.c	4 Mar 2004 14:04:08 -0000	1.20
--- txf.c	15 Apr 2004 14:54:38 -0000	1.21
***************
*** 499,503 ****
    if (!isp->kind) {
      /* we got a NULL kind (as happens with output of
!        gageItemSpecNew()); only NULL return is sensible */
      return NULL;
    }
--- 499,504 ----
    if (!isp->kind) {
      /* we got a NULL kind (as happens with output of
!        gageItemSpecNew(), or miteVariableParse of an
!        empty string); only NULL return is sensible */
      return NULL;
    }

[Teem-commit] teem/src/mite ray.c,1.22,1.23

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

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1678/mite

Modified Files:
	ray.c 
Log Message:
pretty serious bug: crashed if a normal spec had not been given, even if it wasn't needed, BUT, I'm not sure this is the right fix

Index: ray.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/ray.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** ray.c	11 Apr 2004 15:07:27 -0000	1.22
--- ray.c	15 Apr 2004 14:54:04 -0000	1.23
***************
*** 175,182 ****
      ELL_3V_COPY(mtt->directAnsMiteVal[miteValView], mtt->V);
      NN = mtt->directAnsMiteVal[miteValNormal];
!     if (1 == muu->normalSide) {
!       ELL_3V_SCALE(NN, -1, mtt->_normal);
!     } else {
!       ELL_3V_COPY(NN, mtt->_normal);
      }
  
--- 175,184 ----
      ELL_3V_COPY(mtt->directAnsMiteVal[miteValView], mtt->V);
      NN = mtt->directAnsMiteVal[miteValNormal];
!     if (mtt->_normal) {
!       if (1 == muu->normalSide) {
! 	ELL_3V_SCALE(NN, -1, mtt->_normal);
!       } else {
! 	ELL_3V_COPY(NN, mtt->_normal);
!       }
      }
  

[Teem-commit] teem/src/mite kindnot.c,1.3,1.4 mite.h,1.29,1.30 ray.c,1.21,1.22 user.c,1.18,1.19

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

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29580

Modified Files:
	kindnot.c mite.h ray.c user.c 
Log Message:
added fakeFrom for faking out view-dependent txfs, and started to added miteValWdotD

Index: ray.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/ray.c,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** ray.c	25 Mar 2004 03:13:33 -0000	1.21
--- ray.c	11 Apr 2004 15:07:27 -0000	1.22
***************
*** 145,148 ****
--- 145,154 ----
    }
  
+   /* set (fake) view based on fake from */
+   if (AIR_EXISTS(muu->fakeFrom[0])) {
+     ELL_3V_SUB(mtt->V, samplePosWorld, muu->fakeFrom);
+     ELL_3V_NORM(mtt->V, mtt->V, len);
+   }
+ 
    /* do probing at this location to determine values of everything
       that might appear in the txf domain */

Index: kindnot.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/kindnot.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** kindnot.c	4 Mar 2004 14:04:07 -0000	1.3
--- kindnot.c	11 Apr 2004 15:07:27 -0000	1.4
***************
*** 39,43 ****
    "GTdotV",
    "VdefT",
!   "VdefTdotV"
  };
  
--- 39,44 ----
    "GTdotV",
    "VdefT",
!   "VdefTdotV",
!   "WdotD"
  };
  
***************
*** 60,64 ****
    miteValGTdotV,
    miteValVdefT,
!   miteValVdefTdotV
  };
  
--- 61,66 ----
    miteValGTdotV,
    miteValVdefT,
!   miteValVdefTdotV,
!   miteValWdotD,
  };
  
***************
*** 80,84 ****
    "gtdotv",
    "vdeft",
!   "vdeftdotv"
    ""
  };
--- 82,87 ----
    "gtdotv",
    "vdeft",
!   "vdeftdotv",
!   "wdotd",
    ""
  };
***************
*** 101,105 ****
    miteValGTdotV,
    miteValVdefT,
!   miteValVdefTdotV
  };
  
--- 104,109 ----
    miteValGTdotV,
    miteValVdefT,
!   miteValVdefTdotV,
!   miteValWdotD
  };
  
***************
*** 140,144 ****
    {miteValGTdotV,        1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVdefT,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {miteValVdefTdotV,     1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1}
  };
  
--- 144,149 ----
    {miteValGTdotV,        1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {miteValVdefT,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {miteValVdefTdotV,     1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {miteValWdotD,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1}
  };
  

Index: user.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/user.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** user.c	13 Mar 2004 20:03:10 -0000	1.18
--- user.c	11 Apr 2004 15:07:27 -0000	1.19
***************
*** 48,51 ****
--- 48,53 ----
    muu->opacNear1 = miteDefOpacNear1;
    muu->hctx = hooverContextNew();
+   ELL_3V_SET(muu->fakeFrom, AIR_NAN, AIR_NAN, AIR_NAN);
+   ELL_3V_SET(muu->vectorD, 0, 0, 0);
    airMopAdd(muu->umop, muu->hctx, (airMopper)hooverContextNix, airMopAlways);
    for (i=0; i<GAGE_KERNEL_NUM; i++) {

Index: mite.h
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/mite.h,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** mite.h	4 Mar 2004 14:04:08 -0000	1.29
--- mite.h	11 Apr 2004 15:07:27 -0000	1.30
***************
*** 150,153 ****
--- 150,157 ----
    hooverContext *hctx;   /* context and input for all hoover-related things,
  			    including camera and image parameters */
+   double fakeFrom[3],    /* if non-NaN, then the "V"-dependent miteVal's will
+ 			    use this as the nominal eye point, instead of what
+ 			    is actually being used in the hooverContext */
+     vectorD[3];          /* some vector to use for something */
    /* local initial copies of kernels, later passed to gageKernelSet */
    NrrdKernelSpec *ksp[GAGE_KERNEL_NUM];
***************
*** 187,191 ****
    miteShadeMethodNone,        /* 1: no direction shading based on anything
  				 in the miteShadeSpec: just ambient, though
! 				 things are still compositited with the over
  				 operator, and transfer functions are free
  				 to implement whatever shading they can */
--- 191,195 ----
    miteShadeMethodNone,        /* 1: no direction shading based on anything
  				 in the miteShadeSpec: just ambient, though
! 				 things are still composited with the over
  				 operator, and transfer functions are free
  				 to implement whatever shading they can */
***************
*** 333,337 ****
    miteValGTdotV,        /* 13: "GTdotV", normal curvature in view direction,
  			       the contraction of the geometry tensor along
! 				he view vector (gage_t[1]) */
    miteValVdefT,         /* 14: "defT", view direction, deflected by tensor,
  			       then normalized (gage_t[3]) */
--- 337,341 ----
    miteValGTdotV,        /* 13: "GTdotV", normal curvature in view direction,
  			       the contraction of the geometry tensor along
! 			       the view vector (gage_t[1]) */
    miteValVdefT,         /* 14: "defT", view direction, deflected by tensor,
  			       then normalized (gage_t[3]) */
***************
*** 339,345 ****
  			       same as the tensor contraction along V,
  			       (gage_t[1]) */
    miteValLast
  };
! #define MITE_VAL_ITEM_MAX  15
  
  /*
--- 343,351 ----
  			       same as the tensor contraction along V,
  			       (gage_t[1]) */
+   miteValWdotD,         /* 16: "WdotD", world space position dotted with
+ 			       muu->vectorD */
    miteValLast
  };
! #define MITE_VAL_ITEM_MAX  16
  
  /*

[Teem-commit] teem/src/ell/test wheel.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/ell/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29410

Modified Files:
	wheel.c 
Log Message:
something

Index: wheel.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/test/wheel.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** wheel.c	29 Mar 2004 21:15:17 -0000	1.1
--- wheel.c	11 Apr 2004 15:06:35 -0000	1.2
***************
*** 217,224 ****
    
    double tval[6], ABC[3], geom[3], xroot[3], yroot[3], bbox[4], psc;
-   me = argv[0];
    wheelPS wps;
    int correct, labels;
  
    mop = airMopNew();
    hparm = hestParmNew();
--- 217,224 ----
    
    double tval[6], ABC[3], geom[3], xroot[3], yroot[3], bbox[4], psc;
    wheelPS wps;
    int correct, labels;
  
+   me = argv[0];
    mop = airMopNew();
    hparm = hestParmNew();
***************
*** 363,367 ****
    }
  
- 
    wheelEpilog(&wps);
  
--- 363,366 ----

[Teem-commit] teem/src/bin miter.c,1.26,1.27

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29321

Modified Files:
	miter.c 
Log Message:
added -ffr fake from option

Index: miter.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/miter.c,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** miter.c	4 Mar 2004 14:04:52 -0000	1.26
--- miter.c	11 Apr 2004 15:06:05 -0000	1.27
***************
*** 49,52 ****
--- 49,53 ----
    
    hparm->respFileEnable = AIR_TRUE;
+   hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
    hestOptAdd(&hopt, "i", "nsin", airTypeOther, 1, 1, &(muu->nsin), "",
  	     "input scalar volume to render", NULL, NULL, nrrdHestNrrd);
***************
*** 62,65 ****
--- 63,71 ----
  		       NULL, NULL, NULL,
  		       "-1 1", "-1 1");
+   hestOptAdd(&hopt, "ffr", "fake from", airTypeDouble, 3, 3,
+ 	     &(muu->fakeFrom), "nan nan nan",
+ 	     "eye point to use for view-dependent transfer functions. "
+ 	     "By default (not using this option), the point used is the "
+ 	     "normally specified camera eye point.");
    hestOptAdd(&hopt, "am", "ambient", airTypeFloat, 3, 3, muu->lit->amb,
  	     "1 1 1", "ambient light color");

[Teem-commit] teem/src/bin GNUmakefile,1.31,1.32

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29219

Modified Files:
	GNUmakefile 
Log Message:
added gkms back to list of binaries, even though its probably broken

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/GNUmakefile,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** GNUmakefile	26 Feb 2004 06:26:49 -0000	1.31
--- GNUmakefile	11 Apr 2004 15:05:42 -0000	1.32
***************
*** 50,54 ****
  #  pos2idx unu pprobe vprobe qbert mrender miter gkms ungantry ilk tend spots
  BINS = airSanity affine cubic nrrdSanity overrgb idx2pos emap undos talkweb \
!   pos2idx unu pprobe vprobe qbert mrender miter ungantry ilk tend spots
  
  ## _binD(bins): list of development locations for given bins
--- 50,54 ----
  #  pos2idx unu pprobe vprobe qbert mrender miter gkms ungantry ilk tend spots
  BINS = airSanity affine cubic nrrdSanity overrgb idx2pos emap undos talkweb \
!   pos2idx unu pprobe vprobe qbert mrender miter gkms ungantry ilk tend spots
  
  ## _binD(bins): list of development locations for given bins

[Teem-commit] teem/src/bane gkmsTxf.c,1.7,1.8

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

Update of /cvsroot/teem/teem/src/bane
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29105

Modified Files:
	gkmsTxf.c 
Log Message:
brought txf axis labels up to par with recent mite; added minimum value width at bottom of Levoy triangle

Index: gkmsTxf.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bane/gkmsTxf.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** gkmsTxf.c	7 Jan 2004 15:34:27 -0000	1.7
--- gkmsTxf.c	11 Apr 2004 15:04:56 -0000	1.8
***************
*** 35,39 ****
    airArray *mop;
    int pret, E, res[2], vi, gi, step;
!   float min[2], max[2], top[2], v0, g0, *data, v, g, gwidth, width,
      tvl, tvr, vl, vr, tmp, maxa;
  
--- 35,40 ----
    airArray *mop;
    int pret, E, res[2], vi, gi, step;
!   float min[2], max[2], top[2], v0, g0, *data, v, g,
!     gwidth, width, mwidth, 
      tvl, tvr, vl, vr, tmp, maxa;
  
***************
*** 56,59 ****
--- 57,62 ----
    hestOptAdd(&opt, "w", "value width", airTypeFloat, 1, 1, &width, NULL,
  	     "range of values to be spanned at top of triangle");
+   hestOptAdd(&opt, "mw", "value width", airTypeFloat, 1, 1, &mwidth, "0",
+ 	     "range of values to be spanned at BOTTOM of triangle");
    hestOptAdd(&opt, "step", NULL, airTypeInt, 0, 0, &step, NULL,
  	     "instead of assigning opacity inside a triangular region, "
***************
*** 76,85 ****
    if (!E) E |= nrrdMaybeAlloc(nout, nrrdTypeFloat, 3, 1, res[0], res[1]);
    if (!E) E |= !(nout->axis[0].label = airStrdup("A"));
!   if (!E) E |= !(nout->axis[1].label = airStrdup("gage(v)"));
    if (!E) nrrdAxisInfoSet(nout, nrrdAxisInfoMin,
  			  AIR_NAN, (double)min[0], (double)min[1]);
    if (!E) nrrdAxisInfoSet(nout, nrrdAxisInfoMax,
  			  AIR_NAN, (double)max[0], (double)max[1]);
!   if (!E) E |= !(nout->axis[2].label = airStrdup("gage(gm)"));
    if (E) {
      sprintf(err, "%s: trouble creating opacity function nrrd", me);
--- 79,88 ----
    if (!E) E |= nrrdMaybeAlloc(nout, nrrdTypeFloat, 3, 1, res[0], res[1]);
    if (!E) E |= !(nout->axis[0].label = airStrdup("A"));
!   if (!E) E |= !(nout->axis[1].label = airStrdup("gage(scalar:v)"));
    if (!E) nrrdAxisInfoSet(nout, nrrdAxisInfoMin,
  			  AIR_NAN, (double)min[0], (double)min[1]);
    if (!E) nrrdAxisInfoSet(nout, nrrdAxisInfoMax,
  			  AIR_NAN, (double)max[0], (double)max[1]);
!   if (!E) E |= !(nout->axis[2].label = airStrdup("gage(scalar:gm)"));
    if (E) {
      sprintf(err, "%s: trouble creating opacity function nrrd", me);
***************
*** 89,98 ****
    tvl = top[0] - width/2; 
    tvr = top[0] + width/2;
    for (gi=0; gi<res[1]; gi++) {
      g = NRRD_CELL_POS(min[1], max[1], res[1], gi);
      for (vi=0; vi<res[0]; vi++) {
        v = NRRD_CELL_POS(min[0], max[0], res[0], vi);
!       vl = AIR_AFFINE(0, g, top[1], v0, tvl);
!       vr = AIR_AFFINE(0, g, top[1], v0, tvr);
        if (g > top[1]) {
  	data[vi + res[0]*gi] = 0;
--- 92,102 ----
    tvl = top[0] - width/2; 
    tvr = top[0] + width/2;
+   mwidth /= 2;
    for (gi=0; gi<res[1]; gi++) {
      g = NRRD_CELL_POS(min[1], max[1], res[1], gi);
      for (vi=0; vi<res[0]; vi++) {
        v = NRRD_CELL_POS(min[0], max[0], res[0], vi);
!       vl = AIR_AFFINE(0, g, top[1], v0-mwidth, tvl);
!       vr = AIR_AFFINE(0, g, top[1], v0+mwidth, tvr);
        if (g > top[1]) {
  	data[vi + res[0]*gi] = 0;

[Teem-commit] teem/src/gage gage.h,1.64,1.65 vecGage.c,1.19,1.20

[xav <xa...@us...>]

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7404

Modified Files:
	gage.h vecGage.c 
Log Message:
added new functions in vecGage.c, especially useful in the context of 
vortical flows. 


Index: gage.h
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/gage.h,v
retrieving revision 1.64
retrieving revision 1.65
diff -C2 -d -r1.64 -r1.65
*** gage.h	1 Apr 2004 22:37:26 -0000	1.64
--- gage.h	11 Apr 2004 02:31:41 -0000	1.65
***************
*** 287,294 ****
    gageVecDivergence, /*  4: "d", divergence (based on Jacobian): GT[1] */
    gageVecCurl,       /*  5: "c", curl (based on Jacobian): GT[3] */
!   gageVecHelicity,   /*  6: "h", helicity: vec . curl: GT[1] */
!   gageVecNormHelicity,/* 7: "nh", normalized helicity: GT[1] */
!   gageVecLambda2,    /*  8: "lmabda2", lambda2 criterion: GT[1] */
!   gageVecHessian,    /*  9: "vh", second-order derivative: GT[27] 
  			    0:d2v_x/dxdx   1:d2v_x/dxdy   2:d2v_x/dxdz
  	                    3:d2v_x/dydx   4:d2v_x/dydy   5:d2v_x/dydz
--- 287,296 ----
    gageVecDivergence, /*  4: "d", divergence (based on Jacobian): GT[1] */
    gageVecCurl,       /*  5: "c", curl (based on Jacobian): GT[3] */
!   gageVecCurlNorm,   /*  6: "cm", curl magnitude: GT[1] */
!   gageVecHelicity,   /*  7: "h", helicity: vec . curl: GT[1] */
!   gageVecNormHelicity,/* 8: "nh", normalized helicity: GT[1] */
!   gageVecLambda2,    /*  9: "lmbda2", lambda2 criterion: GT[1] */
!   gageVecImaginaryPart,/* 10: "imag", imag. part of jacobian's eigenv: GT[1] */
!   gageVecHessian,    /* 11: "vh", second-order derivative: GT[27] 
  			    0:d2v_x/dxdx   1:d2v_x/dxdy   2:d2v_x/dxdz
  	                    3:d2v_x/dydx   4:d2v_x/dydy   5:d2v_x/dydz
***************
*** 297,316 ****
  			        [...]
  			   24:dv2_z/dzdx  25:d2v_z/dzdy  26:d2v_z/dzdz */
!   gageVecCurlGradient,/*10: "cg", curl gradient: GT[9] */
!   gageVecCurlNormGrad,/*11: "cng", curl norm gradient: GT[3] */
!   gageVecNCurlNormGrad, /* 12: "ncng", normalized curl norm gradient: GT[3] */
!   gageVecHelGradient,/* 13: "hg", helicity gradient: GT[3] */
!   gageVecDirHelDeriv,/* 14: "dhd", directional derivative of helicity: GT[1] */ 
!   gageVecProjHelGradient, /* 15: "phg", projected helicity gradient: GT[3] */
!   gageVecGradient0,  /* 16: "g0", gradient of 1st component of vector: GT[3] */
!   gageVecGradient1,  /* 17: "g1", gradient of 2nd component of vector: GT[3] */
!   gageVecGradient2,  /* 18: "g2", gradient of 3rd component of vector: GT[3] */
!   gageVecMultiGrad,  /* 19: "mg", sum of outer products of gradients: GT[9] */
!   gageVecMGFrob,     /* 20: "mgfrob", frob norm of multi-gradient: GT[1] */
!   gageVecMGEval,     /* 21: "mgeval", eigenvalues of multi-gradient: GT[3] */
!   gageVecMGEvec,     /* 22: "mgevec", eigenvectors of multi-gradient: GT[9] */
    gageVecLast
  };
! #define GAGE_VEC_ITEM_MAX     22
  
  struct gageKind_t;       /* dumb forward declaraction, ignore */
--- 299,319 ----
  			        [...]
  			   24:dv2_z/dzdx  25:d2v_z/dzdy  26:d2v_z/dzdz */
!   gageVecDivGradient,/* 12: "dg", divergence gradient: GT[3] */
!   gageVecCurlGradient,/*13: "cg", curl gradient: GT[9] */
!   gageVecCurlNormGrad,/*14: "cng", curl norm gradient: GT[3] */
!   gageVecNCurlNormGrad, /* 15: "ncng", normalized curl norm gradient: GT[3] */
!   gageVecHelGradient,/* 16: "hg", helicity gradient: GT[3] */
!   gageVecDirHelDeriv,/* 17: "dhd", directional derivative of helicity: GT[1] */ 
!   gageVecProjHelGradient, /* 18: "phg", projected helicity gradient: GT[3] */
!   gageVecGradient0,  /* 19: "g0", gradient of 1st component of vector: GT[3] */
!   gageVecGradient1,  /* 20: "g1", gradient of 2nd component of vector: GT[3] */
!   gageVecGradient2,  /* 21: "g2", gradient of 3rd component of vector: GT[3] */
!   gageVecMultiGrad,  /* 22: "mg", sum of outer products of gradients: GT[9] */
!   gageVecMGFrob,     /* 23: "mgfrob", frob norm of multi-gradient: GT[1] */
!   gageVecMGEval,     /* 24: "mgeval", eigenvalues of multi-gradient: GT[3] */
!   gageVecMGEvec,     /* 25: "mgevec", eigenvectors of multi-gradient: GT[9] */
    gageVecLast
  };
! #define GAGE_VEC_ITEM_MAX     25
  
  struct gageKind_t;       /* dumb forward declaraction, ignore */

Index: vecGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/vecGage.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** vecGage.c	1 Apr 2004 22:37:27 -0000	1.19
--- vecGage.c	11 Apr 2004 02:31:41 -0000	1.20
***************
*** 21,24 ****
--- 21,61 ----
  #include "privateGage.h"
  
+ /*
+  * highly inefficient computation of the imaginary part of complex 
+  * conjugate eigenvalues of a 3x3 non-symmetric matrix
+  */ 
+ double
+ gage_imaginary_part_eigenvalues( gage_t *M )
+ {
+     double A, B, C, scale, frob, m[9], _eval[3];
+     double beta, gamma;
+     int roots;
+ 
+     frob = ELL_3M_FROB(M);
+     scale = frob > 10 ? 10.0/frob : 1.0;
+     ELL_3M_SCALE(m, scale, M);
+     /* 
+     ** from gordon with mathematica; these are the coefficients of the
+     ** cubic polynomial in x: det(x*I - M).  The full cubic is
+     ** x^3 + A*x^2 + B*x + C.
+     */
+     A = -m[0] - m[4] - m[8];
+     B = m[0]*m[4] - m[3]*m[1] 
+ 	+ m[0]*m[8] - m[6]*m[2] 
+ 	+ m[4]*m[8] - m[7]*m[5];
+     C = (m[6]*m[4] - m[3]*m[7])*m[2]
+ 	+ (m[0]*m[7] - m[6]*m[1])*m[5]
+ 	+ (m[3]*m[1] - m[0]*m[4])*m[8];
+     roots = ell_cubic(_eval, A, B, C, AIR_TRUE);
+     if ( roots != ell_cubic_root_single )
+ 	return 0.;
+ 
+     /* 2 complex conjuguate eigenvalues */
+     beta = A + _eval[0];
+     gamma = -C/_eval[0];
+     return sqrt( 4.*gamma - beta*beta );
+ }
+ 
+ 
  gageItemEntry
  _gageVecTable[GAGE_VEC_ITEM_MAX+1] = {
***************
*** 30,37 ****
--- 67,77 ----
    {gageVecDivergence,    1,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
    {gageVecCurl,          3,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
+   {gageVecCurlNorm,      1,  1,  {gageVecCurl, -1, -1, -1, -1},                                  -1,  -1},
    {gageVecHelicity,      1,  1,  {gageVecVector, gageVecCurl, -1, -1, -1},                       -1,  -1},
    {gageVecNormHelicity,  1,  1,  {gageVecNormalized, gageVecCurl, -1, -1, -1},                   -1,  -1},
    {gageVecLambda2,       1,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1},
+   {gageVecImaginaryPart, 1,  1,  {gageVecJacobian, -1, -1, -1, -1},                              -1,  -1}, 
    {gageVecHessian,      27,  2,  {-1, -1, -1, -1, -1},                                           -1,  -1},
+   {gageVecDivGradient,   3,  1,  {gageVecHessian, -1, -1, -1, -1},                              -1,  -1},
    {gageVecCurlGradient,  9,  2,  {gageVecHessian, -1, -1, -1, -1},                               -1,  -1},
    {gageVecCurlNormGrad,  3,  2,  {gageVecHessian, gageVecCurl, -1, -1, -1},                      -1,  -1},
***************
*** 59,65 ****
  
    fd = GAGE_FD(ctx);
!   vec = pvl->directAnswer[gageVecVector];
!   jac = pvl->directAnswer[gageVecJacobian];
!   hes = pvl->directAnswer[gageVecHessian];
    if (!ctx->parm.k3pack) {
      fprintf(stderr, "!%s: sorry, 6pack filtering not implemented\n", me);
--- 99,105 ----
  
    fd = GAGE_FD(ctx);
!   vec  = pvl->directAnswer[gageVecVector];
!   jac  = pvl->directAnswer[gageVecJacobian];
!   hes  = pvl->directAnswer[gageVecHessian];
    if (!ctx->parm.k3pack) {
      fprintf(stderr, "!%s: sorry, 6pack filtering not implemented\n", me);
***************
*** 165,168 ****
--- 205,212 ----
  	       jacAns[3] - jacAns[1]);
    }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurlNorm)) {
+     pvl->directAnswer[gageVecCurlNorm][0] =
+ 	ELL_3V_LEN( curlAns );	
+   }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecHelicity)) {
      pvl->directAnswer[gageVecHelicity][0] = 
***************
*** 191,194 ****
--- 235,242 ----
        pvl->directAnswer[gageVecLambda2][0] = eval[1];
    }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecImaginaryPart)) {
+       pvl->directAnswer[gageVecImaginaryPart][0] =
+ 	  gage_imaginary_part_eigenvalues( jacAns ); 
+   }
    /* 2nd order vector derivative continued */ 
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecHessian)) {
***************
*** 207,210 ****
--- 255,263 ----
      }
    }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecDivGradient)) {
+       pvl->directAnswer[gageVecDivGradient][0] = hesAns[0] + hesAns[12] + hesAns[24];
+       pvl->directAnswer[gageVecDivGradient][1] = hesAns[1] + hesAns[13] + hesAns[25];
+       pvl->directAnswer[gageVecDivGradient][2] = hesAns[2] + hesAns[14] + hesAns[26];
+   }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurlGradient)) {
        pvl->directAnswer[gageVecCurlGradient][0] = hesAns[21]-hesAns[15];
***************
*** 335,342 ****
--- 388,397 ----
    "divergence",
    "curl",
+   "curl norm",
    "helicity",
    "normalized helicity",
    "lambda2",
    "vector hessian",
+   "div gradient",
    "curl gradient",
    "curl norm gradient",
***************
*** 363,370 ****
--- 418,427 ----
    "divergence",
    "curl",
+   "curl magnitude",
    "helicity: dot(vector,curl)",
    "normalized helicity",
    "lambda2 value for vortex characterization",
    "3x3x3 second-order vector derivative",
+   "gradient of divergence",
    "3x3 derivative of curl",
    "gradient of curl norm",
***************
*** 391,398 ****
--- 448,458 ----
    gageVecDivergence,
    gageVecCurl,
+   gageVecCurlNorm,
    gageVecHelicity,
    gageVecNormHelicity,
    gageVecLambda2,
+   gageVecImaginaryPart,
    gageVecHessian,
+   gageVecDivGradient,
    gageVecCurlGradient,
    gageVecCurlNormGrad,
***************
*** 416,423 ****
--- 476,486 ----
  #define GV_D   gageVecDivergence
  #define GV_C   gageVecCurl
+ #define GV_CM  gageVecCurlNorm
  #define GV_H   gageVecHelicity
  #define GV_NH  gageVecNormHelicity
  #define GV_LB  gageVecLambda2
+ #define GV_IM  gageVecImaginaryPart
  #define GV_VH  gageVecHessian
+ #define GV_DG  gageVecDivGradient
  #define GV_CG  gageVecCurlGradient
  #define GV_CNG gageVecCurlNormGrad
***************
*** 442,449 ****
--- 505,515 ----
    "divergence", "div", "d",
    "curl", "c",
+   "curlnorm", "curl magnitude", "cm",
    "h", "hel", "hell",
    "nh", "nhel", "normhel", "normhell",
    "lbda2", "lambda2",
+   "imag", "imagpart",
    "vh", "vhes", "vhessian", "vector hessian",
+   "dg", "divgrad",
    "cg", "curlgrad", "curlg", "curljac", "curl gradient",
    "cng", "curl norm gradient",
***************
*** 470,477 ****
--- 536,546 ----
    GV_D, GV_D, GV_D,
    GV_C, GV_C,
+   GV_CM, GV_CM, GV_CM,
    GV_H, GV_H, GV_H,
    GV_NH, GV_NH, GV_NH, GV_NH,
    GV_LB, GV_LB,
+   GV_IM, GV_IM,
    GV_VH, GV_VH, GV_VH, GV_VH,
+   GV_DG, GV_DG,
    GV_CG, GV_CG, GV_CG, GV_CG, GV_CG,
    GV_CNG, GV_CNG,

[Teem-commit] teem/src/bin vprobe.c,1.20,1.21

[xav <xa...@us...>]

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6564

Modified Files:
	vprobe.c 
Log Message:
removed the annoying explicit '-o' requirement


Index: vprobe.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/vprobe.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** vprobe.c	13 Feb 2004 23:01:12 -0000	1.20
--- vprobe.c	11 Apr 2004 02:28:15 -0000	1.21
***************
*** 125,129 ****
    hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &otype, "float",
  	     "type of output volume", NULL, nrrdType);
!   hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL,
  	     "output volume");
    hestParseOrDie(hopt, argc-1, argv+1, hparm,
--- 125,129 ----
    hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &otype, "float",
  	     "type of output volume", NULL, nrrdType);
!   hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
  	     "output volume");
    hestParseOrDie(hopt, argc-1, argv+1, hparm,

[Teem-commit] teem/src/nrrd enumsNrrd.c,1.34,1.35 arith.c,1.34,1.35 nrrdEnums.h,1.45,1.46

[xav <xa...@us...>]

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv905

Modified Files:
	enumsNrrd.c arith.c nrrdEnums.h 
Log Message:
added log2 as new unary op

Index: arith.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/arith.c,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** arith.c	14 Feb 2004 20:01:07 -0000	1.34
--- arith.c	9 Apr 2004 19:47:26 -0000	1.35
***************
*** 124,127 ****
--- 124,128 ----
  double _nrrdUnaryOpExp(double a)        {return exp(a);}
  double _nrrdUnaryOpLog(double a)        {return log(a);}
+ double _nrrdUnaryOpLog2(double a)       {return log(a)/0.69314718;}
  double _nrrdUnaryOpLog10(double a)      {return log10(a);}
  double _nrrdUnaryOpLog1p(double a)      {
***************
*** 160,163 ****
--- 161,165 ----
    _nrrdUnaryOpExp,
    _nrrdUnaryOpLog,
+   _nrrdUnaryOpLog2,
    _nrrdUnaryOpLog10,
    _nrrdUnaryOpLog1p,

Index: nrrdEnums.h
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/nrrdEnums.h,v
retrieving revision 1.45
retrieving revision 1.46
diff -C2 -d -r1.45 -r1.46
*** nrrdEnums.h	1 Apr 2004 19:29:35 -0000	1.45
--- nrrdEnums.h	9 Apr 2004 19:47:26 -0000	1.46
***************
*** 398,417 ****
    nrrdUnaryOpExp,        /*  9 */
    nrrdUnaryOpLog,        /* 10 */
!   nrrdUnaryOpLog10,      /* 11 */
!   nrrdUnaryOpLog1p,      /* 12 */
!   nrrdUnaryOpSqrt,       /* 13 */
!   nrrdUnaryOpCbrt,       /* 14 */
!   nrrdUnaryOpErf,        /* 15 */
!   nrrdUnaryOpCeil,       /* 16 */
!   nrrdUnaryOpFloor,      /* 17 */
!   nrrdUnaryOpRoundUp,    /* 18 */
!   nrrdUnaryOpRoundDown,  /* 19 */
!   nrrdUnaryOpAbs,        /* 20 */
!   nrrdUnaryOpSgn,        /* 21 */
!   nrrdUnaryOpExists,     /* 22 */
!   nrrdUnaryOpRand,       /* 23 */
    nrrdUnaryOpLast
  };
! #define NRRD_UNARY_OP_MAX   23
  
  /*
--- 398,418 ----
    nrrdUnaryOpExp,        /*  9 */
    nrrdUnaryOpLog,        /* 10 */
!   nrrdUnaryOpLog2,       /* 11 */
!   nrrdUnaryOpLog10,      /* 12 */
!   nrrdUnaryOpLog1p,      /* 13 */
!   nrrdUnaryOpSqrt,       /* 14 */
!   nrrdUnaryOpCbrt,       /* 15 */
!   nrrdUnaryOpErf,        /* 16 */
!   nrrdUnaryOpCeil,       /* 17 */
!   nrrdUnaryOpFloor,      /* 18 */
!   nrrdUnaryOpRoundUp,    /* 19 */
!   nrrdUnaryOpRoundDown,  /* 20 */
!   nrrdUnaryOpAbs,        /* 21 */
!   nrrdUnaryOpSgn,        /* 22 */
!   nrrdUnaryOpExists,     /* 23 */
!   nrrdUnaryOpRand,       /* 24 */
    nrrdUnaryOpLast
  };
! #define NRRD_UNARY_OP_MAX   24
  
  /*

Index: enumsNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/enumsNrrd.c,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** enumsNrrd.c	9 Apr 2004 17:27:59 -0000	1.34
--- enumsNrrd.c	9 Apr 2004 19:47:25 -0000	1.35
***************
*** 699,702 ****
--- 699,703 ----
  #define nuExp nrrdUnaryOpExp
  #define nuLge nrrdUnaryOpLog
+ #define nuLg2 nrrdUnaryOpLog2
  #define nuLgt nrrdUnaryOpLog10
  #define nuL1p nrrdUnaryOpLog1p
***************
*** 726,729 ****
--- 727,731 ----
    "exp",
    "log",
+   "log2",
    "log10",
    "log1p",
***************
*** 754,757 ****
--- 756,760 ----
    "e raised to something",
    "natural (base e) logarithm",
+   "base 2 logarithm",
    "base 10 logarithm",
    "ln(1+x), accurate for small x",
***************
*** 781,784 ****
--- 784,788 ----
    "exp",
    "ln", "log",
+   "log2",
    "log10",
    "ln1p", "log1p",
***************
*** 809,812 ****
--- 813,817 ----
    nuExp,
    nuLge, nuLge,
+   nuLg2,
    nuLgt,
    nuL1p, nuL1p,

[Teem-commit] teem/src/nrrd enumsNrrd.c,1.33,1.34

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5181

Modified Files:
	enumsNrrd.c 
Log Message:
added some aliases for different tensor kinds

Index: enumsNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/enumsNrrd.c,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** enumsNrrd.c	1 Apr 2004 19:29:34 -0000	1.33
--- enumsNrrd.c	9 Apr 2004 17:27:59 -0000	1.34
***************
*** 359,365 ****
    "2D-tensor", "2Dtensor",
    "2D-mask-tensor", "2Dmasktensor",
!   "3D-sym-tensor", "3Dsymtensor",
!   "3D-mask-sym-tensor", "3Dmasksymtensor",
!   "3D-tensor", "3Dtensor",
    "3D-mask-tensor", "3Dmasktensor",
    ""
--- 359,365 ----
    "2D-tensor", "2Dtensor",
    "2D-mask-tensor", "2Dmasktensor",
!   "3D-sym-tensor", "3Dsymtensor", "6-tensor",
!   "3D-mask-sym-tensor", "3Dmasksymtensor", "7-tensor",
!   "3D-tensor", "3Dtensor", "9-tensor",
    "3D-mask-tensor", "3Dmasktensor",
    ""
***************
*** 383,389 ****
    nrrdKind2DTensor, nrrdKind2DTensor,
    nrrdKind2DMaskedTensor, nrrdKind2DMaskedTensor,
!   nrrdKind3DSymTensor, nrrdKind3DSymTensor,
    nrrdKind3DMaskedSymTensor, nrrdKind3DMaskedSymTensor,
!   nrrdKind3DTensor, nrrdKind3DTensor,
    nrrdKind3DMaskedTensor, nrrdKind3DMaskedTensor
  };
--- 383,390 ----
    nrrdKind2DTensor, nrrdKind2DTensor,
    nrrdKind2DMaskedTensor, nrrdKind2DMaskedTensor,
!   nrrdKind3DSymTensor, nrrdKind3DSymTensor, nrrdKind3DSymTensor,
    nrrdKind3DMaskedSymTensor, nrrdKind3DMaskedSymTensor,
!              nrrdKind3DMaskedSymTensor,
!   nrrdKind3DTensor, nrrdKind3DTensor, nrrdKind3DTensor,
    nrrdKind3DMaskedTensor, nrrdKind3DMaskedTensor
  };

[Teem-commit] teem/src/nrrd apply1D.c,1.24,1.25 nrrd.h,1.137,1.138

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20500/nrrd

Modified Files:
	apply1D.c nrrd.h 
Log Message:
unused variable, better usage info

Index: nrrd.h
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/nrrd.h,v
retrieving revision 1.137
retrieving revision 1.138
diff -C2 -d -r1.137 -r1.138
*** nrrd.h	30 Mar 2004 19:25:09 -0000	1.137
--- nrrd.h	4 Apr 2004 21:26:11 -0000	1.138
***************
*** 711,717 ****
--- 711,723 ----
  			    const Nrrd *nin, const NrrdRange *range,
  			    const Nrrd *nlut, int typeOut, int rescale);
+ TEEM_API int nrrdApplyMulti1DLut(Nrrd *nout, const Nrrd *nin,
+ 				 const NrrdRange *_range, const Nrrd *nmlut,
+ 				 int typeOut, int rescale);
  TEEM_API int nrrdApply1DRegMap(Nrrd *nout,
  			       const Nrrd *nin, const NrrdRange *range,
  			       const Nrrd *nmap, int typeOut, int rescale);
+ TEEM_API int nrrdApplyMulti1DRegMap(Nrrd *nout, const Nrrd *nin,
+ 				    const NrrdRange *_range, const Nrrd *nmmap,
+ 				    int typeOut, int rescale);
  TEEM_API int nrrd1DIrregMapCheck(const Nrrd *nmap);
  TEEM_API int nrrd1DIrregAclGenerate(Nrrd *nacl, const Nrrd *nmap, int aclLen);

Index: apply1D.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/apply1D.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** apply1D.c	27 Feb 2004 19:10:31 -0000	1.24
--- apply1D.c	4 Apr 2004 21:26:11 -0000	1.25
***************
*** 49,57 ****
  
  double
! _nrrdApply1DDomainMin(const Nrrd *nmap, int ramps) {
    double ret;
-   int mapAxis;
  
-   mapAxis = nmap->dim-1;
    ret = nmap->axis[mapAxis].min;
    ret = AIR_EXISTS(ret) ? ret : 0;
--- 49,55 ----
  
  double
! _nrrdApply1DDomainMin(const Nrrd *nmap, int ramps, int mapAxis) {
    double ret;
  
    ret = nmap->axis[mapAxis].min;
    ret = AIR_EXISTS(ret) ? ret : 0;
***************
*** 60,68 ****
  
  double
! _nrrdApply1DDomainMax(const Nrrd *nmap, int ramps) {
    double ret;
-   int mapAxis;
    
-   mapAxis = nmap->dim-1;
    ret = nmap->axis[mapAxis].max;
    if (!AIR_EXISTS(ret)) {
--- 58,64 ----
  
  double
! _nrrdApply1DDomainMax(const Nrrd *nmap, int ramps, int mapAxis) {
    double ret;
    
    ret = nmap->axis[mapAxis].max;
    if (!AIR_EXISTS(ret)) {
***************
*** 88,100 ****
  int
  _nrrdApply1DSetUp(Nrrd *nout, const Nrrd *nin, const NrrdRange *range, 
! 		  const Nrrd *nmap, int kind, int typeOut, int rescale) {
    char me[]="_nrrdApply1DSetUp", err[AIR_STRLEN_MED], *mapcnt;
    char nounStr[][AIR_STRLEN_SMALL]={"lut",
  				    "regular map",
  				    "irregular map"};
    char verbStr[][AIR_STRLEN_SMALL]={"lut",
  				    "rmap",
  				    "imap"};
!   int mapAxis, size[NRRD_DIM_MAX], axisMap[NRRD_DIM_MAX], d, colLen;
    double domMin, domMax;
  
--- 84,104 ----
  int
  _nrrdApply1DSetUp(Nrrd *nout, const Nrrd *nin, const NrrdRange *range, 
! 		  const Nrrd *nmap, int kind, int typeOut,
! 		  int rescale, int multi) {
    char me[]="_nrrdApply1DSetUp", err[AIR_STRLEN_MED], *mapcnt;
    char nounStr[][AIR_STRLEN_SMALL]={"lut",
  				    "regular map",
  				    "irregular map"};
+   char mnounStr[][AIR_STRLEN_SMALL]={"multi lut",
+ 				     "multi regular map",
+ 				     "multi irregular map"}; 
+                                       /* wishful thinking */
    char verbStr[][AIR_STRLEN_SMALL]={"lut",
  				    "rmap",
  				    "imap"};
!   char mverbStr[][AIR_STRLEN_SMALL]={"mlut",
! 				     "mrmap",
! 				     "mimap"}; /* wishful thinking */
!   int mapAxis, ax, size[NRRD_DIM_MAX], axisMap[NRRD_DIM_MAX], d, colLen;
    double domMin, domMax;
  
***************
*** 120,131 ****
    }
    if (kindLut == kind || kindRmap == kind) {
!     mapAxis = nmap->dim - 1;
!     if (!(0 == mapAxis || 1 == mapAxis)) {
!       sprintf(err, "%s: dimension of %s should be 1 or 2, not %d", 
! 	      me, nounStr[kind], nmap->dim);
!       biffAdd(NRRD, err); return 1;
      }
!     domMin = _nrrdApply1DDomainMin(nmap, AIR_FALSE);
!     domMax = _nrrdApply1DDomainMax(nmap, AIR_FALSE);
      if (!( domMin < domMax )) {
        sprintf(err, "%s: (axis %d) domain min (%g) not less than max (%g)", me,
--- 124,155 ----
    }
    if (kindLut == kind || kindRmap == kind) {
!     if (!multi) {
!       mapAxis = nmap->dim - 1;
!       if (!(0 == mapAxis || 1 == mapAxis)) {
! 	sprintf(err, "%s: dimension of %s should be 1 or 2, not %d", 
! 		me, nounStr[kind], nmap->dim);
! 	biffAdd(NRRD, err); return 1;
!       }
!     } else {
!       mapAxis = nmap->dim - nin->dim - 1;
!       if (!(0 == mapAxis || 1 == mapAxis)) {
! 	sprintf(err, "%s: dimension of %s should be %d or %d, not %d", 
! 		me, mnounStr[kind],
! 		nin->dim + 1, nin->dim + 2, nmap->dim);
! 	biffAdd(NRRD, err); return 1;
!       }
!       /* need to make sure the relevant sizes match */
!       for (ax=0; ax<nin->dim; ax++) {
! 	if (nin->axis[ax].size != nmap->axis[mapAxis + 1 + ax].size) {
! 	  sprintf(err, "%s: input and mmap don't have compatible sizes: "
! 		  "nin->axis[%d].size (%d) != nmap->axis[%d].size (%d): ",
! 		  me, ax, nin->axis[ax].size, 
! 		  mapAxis + 1 + ax, nmap->axis[mapAxis + 1 + ax].size);
! 	  biffAdd(NRRD, err); return 1;
! 	}
!       }
      }
!     domMin = _nrrdApply1DDomainMin(nmap, AIR_FALSE, mapAxis);
!     domMax = _nrrdApply1DDomainMax(nmap, AIR_FALSE, mapAxis);
      if (!( domMin < domMax )) {
        sprintf(err, "%s: (axis %d) domain min (%g) not less than max (%g)", me,
***************
*** 135,143 ****
      if (nrrdHasNonExist(nmap)) {
        sprintf(err, "%s: %s nrrd has non-existent values",
! 	      me, nounStr[kind]);
        biffAdd(NRRD, err); return 1;
      }
      colLen = mapAxis ? nmap->axis[0].size : 1;
    } else {
      /* its an irregular map */
      if (nrrd1DIrregMapCheck(nmap)) {
--- 159,171 ----
      if (nrrdHasNonExist(nmap)) {
        sprintf(err, "%s: %s nrrd has non-existent values",
! 	      me, multi ? mnounStr[kind] : nounStr[kind]);
        biffAdd(NRRD, err); return 1;
      }
      colLen = mapAxis ? nmap->axis[0].size : 1;
    } else {
+     if (multi) {
+       sprintf(err, "%s: sorry, multi irregular maps not implemented", me);
+       biffAdd(NRRD, err); return 1;
+     }
      /* its an irregular map */
      if (nrrd1DIrregMapCheck(nmap)) {
***************
*** 152,156 ****
      sprintf(err, "%s: input nrrd dim %d through non-scalar %s exceeds "
  	    "NRRD_DIM_MAX %d",
! 	    me, nin->dim, nounStr[kind], NRRD_DIM_MAX);
      biffAdd(NRRD, err); return 1;
    }
--- 180,185 ----
      sprintf(err, "%s: input nrrd dim %d through non-scalar %s exceeds "
  	    "NRRD_DIM_MAX %d",
! 	    me, nin->dim,
! 	    multi ? mnounStr[kind] : nounStr[kind], NRRD_DIM_MAX);
      biffAdd(NRRD, err); return 1;
    }
***************
*** 193,197 ****
    }
    mapcnt = _nrrdContentGet(nmap);
!   if (nrrdContentSet(nout, verbStr[kind], nin, "%s", mapcnt)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); free(mapcnt); return 1;
--- 222,227 ----
    }
    mapcnt = _nrrdContentGet(nmap);
!   if (nrrdContentSet(nout, multi ? mverbStr[kind] : verbStr[kind],
! 		     nin, "%s", mapcnt)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); free(mapcnt); return 1;
***************
*** 224,228 ****
  int
  _nrrdApply1DLutOrRegMap(Nrrd *nout, const Nrrd *nin, const NrrdRange *range, 
! 			const Nrrd *nmap, int ramps, int rescale) {
    /* char me[]="_nrrdApply1DLutOrRegMap"; */
    char *inData, *outData, *mapData, *entData0, *entData1;
--- 254,258 ----
  int
  _nrrdApply1DLutOrRegMap(Nrrd *nout, const Nrrd *nin, const NrrdRange *range, 
! 			const Nrrd *nmap, int ramps, int rescale, int multi) {
    /* char me[]="_nrrdApply1DLutOrRegMap"; */
    char *inData, *outData, *mapData, *entData0, *entData1;
***************
*** 233,242 ****
    int i, mapAxis, mapLen, mapIdx, entSize, entLen, inSize, outSize;
  
!   mapAxis = nmap->dim - 1;             /* axis of nmap containing entries */
    mapData = nmap->data;                /* map data, as char* */
                                         /* low end of map domain */
!   domMin = _nrrdApply1DDomainMin(nmap, ramps);
                                         /* high end of map domain */
!   domMax = _nrrdApply1DDomainMax(nmap, ramps);
    mapLen = nmap->axis[mapAxis].size;   /* number of entries in map */
    mapLup = nrrdDLookup[nmap->type];    /* how to get doubles out of map */
--- 263,276 ----
    int i, mapAxis, mapLen, mapIdx, entSize, entLen, inSize, outSize;
  
!   if (!multi) {
!     mapAxis = nmap->dim - 1;           /* axis of nmap containing entries */
!   } else {
!     mapAxis = nmap->dim - nin->dim - 1;
!   }
    mapData = nmap->data;                /* map data, as char* */
                                         /* low end of map domain */
!   domMin = _nrrdApply1DDomainMin(nmap, ramps, mapAxis);
                                         /* high end of map domain */
!   domMax = _nrrdApply1DDomainMax(nmap, ramps, mapAxis);
    mapLen = nmap->axis[mapAxis].size;   /* number of entries in map */
    mapLup = nrrdDLookup[nmap->type];    /* how to get doubles out of map */
***************
*** 291,294 ****
--- 325,331 ----
        inData += inSize;
        outData += outSize;
+       if (multi) {
+ 	mapData += mapLen*entSize;
+       }
      }    
    } else {
***************
*** 313,316 ****
--- 350,356 ----
        inData += inSize;
        outData += outSize;
+       if (multi) {
+ 	mapData += mapLen*entSize;
+       }
      }
    }
***************
*** 356,361 ****
    }
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
!   if (_nrrdApply1DSetUp(nout, nin, range, nlut, kindLut, typeOut, rescale)
!       || _nrrdApply1DLutOrRegMap(nout, nin, range, nlut, AIR_FALSE, rescale)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); airMopError(mop); return 1;
--- 396,434 ----
    }
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
!   if (_nrrdApply1DSetUp(nout, nin, range, nlut, kindLut, typeOut,
! 			rescale, AIR_FALSE)
!       || _nrrdApply1DLutOrRegMap(nout, nin, range, nlut, AIR_FALSE,
! 				 rescale, AIR_FALSE)) {
!     sprintf(err, "%s:", me);
!     biffAdd(NRRD, err); airMopError(mop); return 1;
!   }
!   airMopOkay(mop);
!   return 0;
! }
! 
! int
! nrrdApplyMulti1DLut(Nrrd *nout, const Nrrd *nin,
! 		    const NrrdRange *_range, const Nrrd *nmlut,
! 		    int typeOut, int rescale) {
!   char me[]="nrrdApplyMulti1DLut", err[AIR_STRLEN_MED];
!   NrrdRange *range;
!   airArray *mop;
!   
!   if (!(nout && nmlut && nin)) {
!     sprintf(err, "%s: got NULL pointer", me);
!     biffAdd(NRRD, err); return 1;
!   }
!   mop = airMopNew();
!   if (_range) {
!     range = nrrdRangeCopy(_range);
!     nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
!   } else {
!     range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
!   }
!   airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
!   if (_nrrdApply1DSetUp(nout, nin, range, nmlut, kindLut, typeOut,
! 			rescale, AIR_TRUE)
!       || _nrrdApply1DLutOrRegMap(nout, nin, range, nmlut, AIR_FALSE,
! 				 rescale, AIR_TRUE)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); airMopError(mop); return 1;
***************
*** 412,417 ****
    }
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
!   if (_nrrdApply1DSetUp(nout, nin, range, nmap, kindRmap, typeOut, rescale)
!       || _nrrdApply1DLutOrRegMap(nout, nin, range, nmap, AIR_TRUE, rescale)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); airMopError(mop); return 1;
--- 485,523 ----
    }
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
!   if (_nrrdApply1DSetUp(nout, nin, range, nmap, kindRmap, typeOut,
! 			rescale, AIR_FALSE)
!       || _nrrdApply1DLutOrRegMap(nout, nin, range, nmap, AIR_TRUE,
! 				 rescale, AIR_FALSE)) {
!     sprintf(err, "%s:", me);
!     biffAdd(NRRD, err); airMopError(mop); return 1;
!   }
!   airMopOkay(mop);
!   return 0;
! }
! 
! int
! nrrdApplyMulti1DRegMap(Nrrd *nout, const Nrrd *nin,
! 		       const NrrdRange *_range, const Nrrd *nmmap,
! 		       int typeOut, int rescale) {
!   char me[]="nrrdApplyMulti1DRegMap", err[AIR_STRLEN_MED];
!   NrrdRange *range;
!   airArray *mop;
! 
!   if (!(nout && nmmap && nin)) {
!     sprintf(err, "%s: got NULL pointer", me);
!     biffAdd(NRRD, err); return 1;
!   }
!   mop = airMopNew();
!   if (_range) {
!     range = nrrdRangeCopy(_range);
!     nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
!   } else {
!     range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
!   }
!   airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
!   if (_nrrdApply1DSetUp(nout, nin, range, nmmap, kindRmap, typeOut,
! 			rescale, AIR_TRUE)
!       || _nrrdApply1DLutOrRegMap(nout, nin, range, nmmap, AIR_TRUE,
! 				 rescale, AIR_TRUE)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); airMopError(mop); return 1;
***************
*** 734,738 ****
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
    if (_nrrdApply1DSetUp(nout, nin, range, nmap,
! 			kindImap, typeOut, rescale)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); airMopError(mop); return 1;
--- 840,844 ----
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
    if (_nrrdApply1DSetUp(nout, nin, range, nmap,
! 			kindImap, typeOut, rescale, AIR_FALSE)) {
      sprintf(err, "%s:", me);
      biffAdd(NRRD, err); airMopError(mop); return 1;

[Teem-commit] teem/src/unrrdu mrmap.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20500/unrrdu

Modified Files:
	mrmap.c 
Log Message:
unused variable, better usage info

Index: mrmap.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/mrmap.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** mrmap.c	4 Apr 2004 21:21:06 -0000	1.1
--- mrmap.c	4 Apr 2004 21:26:11 -0000	1.2
***************
*** 25,29 ****
  (INFO
   ", one map per sample in input. The \"mmap\" nrrd has the same dimensional "
!  "constraints as the \"mlut\" nrrd for \"unu mlut\".  ");
  
  int
--- 25,31 ----
  (INFO
   ", one map per sample in input. The \"mmap\" nrrd has the same dimensional "
!  "constraints as the \"mlut\" nrrd for \"unu mlut\".  This functionality "
!  "is a generalization of \"unu 3op lerp\": it allows you to lerp through "
!  "multiple nrrds, instead of just two.");
  
  int

[Teem-commit] teem/src/ell eigen.c,1.20,1.21

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

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20500/ell

Modified Files:
	eigen.c 
Log Message:
unused variable, better usage info

Index: eigen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/eigen.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** eigen.c	1 Apr 2004 15:02:47 -0000	1.20
--- eigen.c	4 Apr 2004 21:26:11 -0000	1.21
***************
*** 175,179 ****
  int
  ell_3m_eigenvalues_d(double _eval[3], double _m[9], int newton) {
!   double A, B, C, scale, frob, m[9], eval[3], tmp;
    int roots;
  
--- 175,179 ----
  int
  ell_3m_eigenvalues_d(double _eval[3], double _m[9], int newton) {
!   double A, B, C, scale, frob, m[9], eval[3];
    int roots;
  

[Teem-commit] teem/src/unrrdu mlut.c,NONE,1.1 mrmap.c,NONE,1.1 GNUmakefile,1.21,1.22 lut.c,1.19,1.20 rmap.c,1.19,1.20 subst.c,1.2,1.3 unrrdu.h,1.26,1.27

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19622

Modified Files:
	GNUmakefile lut.c rmap.c subst.c unrrdu.h 
Added Files:
	mlut.c mrmap.c 
Log Message:
added nrrdApplyMulti1DLut (unu mlut) and nrrdApplyMulti1DRegMap (unu mrmap), which seem to work, but no promises

--- NEW FILE: mlut.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 "unrrdu.h"
#include "privateUnrrdu.h"

#define INFO "Map nrrd through whole nrrd of univariate lookup tables"
char *_unrrdu_mlutInfoL =
(INFO
 ", with one lookup table per element of input nrrd.  The multiple "
 "tables are stored in a nrrd with a dimension which is either 1 or 2 "
 "more than the dimension of the input nrrd, resulting in an output "
 "which has either the same or one more dimension than the input, "
 "resptectively. ");

int
unrrdu_mlutMain(int argc, char **argv, char *me, hestParm *hparm) {
  hestOpt *opt = NULL;
  char *out, *err;
  Nrrd *nin, **_nmlut, *nmlut, *nout;
  airArray *mop;
  int typeOut, rescale, pret, mapAxis, _nmlutLen;
  double min, max;
  NrrdRange *range=NULL;

  hestOptAdd(&opt, "m", "mlut", airTypeOther, 1, -1, &_nmlut, NULL,
	     "one nrrd of lookup tables to map input nrrd through, or, "
	     "list of nrrds which contain the individual entries of "
	     "the lookup table at each voxel, which will be joined together.",
	     &_nmlutLen, NULL, nrrdHestNrrd);
  hestOptAdd(&opt, "r", NULL, airTypeInt, 0, 0, &rescale, NULL,
	     "rescale the input values from the input range to the "
	     "lut domain.  The lut domain is either explicitly "
	     "defined by the axis min,max along axis 0 or 1, or, it "
	     "is implicitly defined as zero to the length of that axis "
	     "minus one.");
  hestOptAdd(&opt, "min", "value", airTypeDouble, 1, 1, &min, "nan",
	     "Low end of input range. Defaults to lowest value "
	     "found in input nrrd.  Explicitly setting this is useful "
	     "only with rescaling (\"-r\")");
  hestOptAdd(&opt, "max", "value", airTypeDouble, 1, 1, &max, "nan",
	     "High end of input range. Defaults to highest value "
	     "found in input nrrd.  Explicitly setting this is useful "
	     "only with rescaling (\"-r\")");
  hestOptAdd(&opt, "t", "type", airTypeOther, 1, 1, &typeOut, "default",
	     "specify the type (\"int\", \"float\", etc.) of the "
	     "output nrrd. "
	     "By default (not using this option), the output type "
	     "is the lut's type.",
             NULL, NULL, &unrrduHestMaybeTypeCB);
  OPT_ADD_NIN(nin, "input nrrd");
  OPT_ADD_NOUT(out, "output nrrd");

  mop = airMopNew();
  airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);

  USAGE(_unrrdu_mlutInfoL);
  PARSE();
  airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);

  nout = nrrdNew();
  airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);

  /* by the end of this block we need to have nmlut and mapAxis */
  if (1 == _nmlutLen) {
    /* we got the mlut as a single nrrd */
    nmlut = _nmlut[0];
    mapAxis = nmlut->dim - nin->dim - 1;
    /* its not our job to do real error checking ... */
    mapAxis = AIR_CLAMP(0, mapAxis, nmlut->dim - 1);
  } else {
    /* we have to join together multiple nrrds to get the mlut */
    nmlut = nrrdNew();
    airMopAdd(mop, nmlut, (airMopper)nrrdNuke, airMopAlways);
    /* assume that mlut component nrrds are all compatible sizes,
       nrrdJoin will fail if they aren't */
    mapAxis = _nmlut[0]->dim - nin->dim;
    if (nrrdJoin(nmlut, (const Nrrd**)_nmlut, _nmlutLen, mapAxis, AIR_TRUE)) {
      airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
      fprintf(stderr, "%s: trouble joining mlut:\n%s", me, err);
      airMopError(mop);
      return 1;
    }
    /* set these if they were given, they'll be NaN otherwise */
    nmlut->axis[mapAxis].min = min;
    nmlut->axis[mapAxis].max = max;
  }

  if (!( AIR_EXISTS(nmlut->axis[mapAxis].min) && 
	 AIR_EXISTS(nmlut->axis[mapAxis].max) )) {
    rescale = AIR_TRUE;
  }
  if (rescale) {
    range = nrrdRangeNew(min, max);
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
    nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
  }

  if (nrrdTypeDefault == typeOut) {
    typeOut = nmlut->type;
  }
  if (nrrdApplyMulti1DLut(nout, nin, range, nmlut, typeOut, rescale)) {
    airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
    fprintf(stderr, "%s: trouble applying multi-LUT:\n%s", me, err);
    airMopError(mop);
    return 1;
  }

  SAVE(out, nout, NULL);

  airMopOkay(mop);
  return 0;
}

UNRRDU_CMD(mlut, INFO);

Index: subst.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/subst.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** subst.c	27 Feb 2004 06:05:18 -0000	1.2
--- subst.c	4 Apr 2004 21:21:06 -0000	1.3
***************
*** 21,25 ****
  #include "privateUnrrdu.h"
  
! #define INFO "Map nrrd through univariate substitution table"
  char *_unrrdu_substInfoL =
  (INFO
--- 21,25 ----
  #include "privateUnrrdu.h"
  
! #define INFO "Map nrrd through a univariate substitution table"
  char *_unrrdu_substInfoL =
  (INFO

Index: lut.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/lut.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** lut.c	7 Jan 2004 15:34:31 -0000	1.19
--- lut.c	4 Apr 2004 21:21:06 -0000	1.20
***************
*** 21,25 ****
  #include "privateUnrrdu.h"
  
! #define INFO "Map nrrd through univariate lookup table"
  char *_unrrdu_lutInfoL =
  (INFO
--- 21,25 ----
  #include "privateUnrrdu.h"
  
! #define INFO "Map nrrd through one univariate lookup table"
  char *_unrrdu_lutInfoL =
  (INFO
***************
*** 48,52 ****
  	     "lut domain.  The lut domain is either explicitly "
  	     "defined by the axis min,max along axis 0 or 1, or, it "
! 	     "is implicitly defined as zero to the length of that axis.");
    hestOptAdd(&opt, "min", "value", airTypeDouble, 1, 1, &min, "nan",
  	     "Low end of input range. Defaults to lowest value "
--- 48,53 ----
  	     "lut domain.  The lut domain is either explicitly "
  	     "defined by the axis min,max along axis 0 or 1, or, it "
! 	     "is implicitly defined as zero to the length of that axis "
! 	     "minus one.");
    hestOptAdd(&opt, "min", "value", airTypeDouble, 1, 1, &min, "nan",
  	     "Low end of input range. Defaults to lowest value "

Index: unrrdu.h
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/unrrdu.h,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** unrrdu.h	26 Feb 2004 20:59:45 -0000	1.26
--- unrrdu.h	4 Apr 2004 21:21:06 -0000	1.27
***************
*** 129,134 ****
--- 129,136 ----
  F(3op) \
  F(lut) \
+ F(mlut) \
  F(subst) \
  F(rmap) \
+ F(mrmap) \
  F(imap) \
  F(ccfind) \

--- NEW FILE: mrmap.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 "unrrdu.h"
#include "privateUnrrdu.h"

#define INFO "Map nrrd through a whole nrrd of regular univariate maps"
char *_unrrdu_mrmapInfoL =
(INFO
 ", one map per sample in input. The \"mmap\" nrrd has the same dimensional "
 "constraints as the \"mlut\" nrrd for \"unu mlut\".  ");

int
unrrdu_mrmapMain(int argc, char **argv, char *me, hestParm *hparm) {
  hestOpt *opt = NULL;
  char *out, *err;
  Nrrd *nin, **_nmmap, *nmmap, *nout;
  airArray *mop;
  NrrdRange *range=NULL;
  int typeOut, rescale, pret, mapAxis, _nmmapLen;
  double min, max;

  hestOptAdd(&opt, "m", "mmap", airTypeOther, 1, -1, &_nmmap, NULL,
	     "one nrrd of regular maps to map input nrrd through, or, "
	     "list of nrrds which contain the individual entries of the map "
	     "at each voxel, which will be joined together.",
	     &_nmmapLen, NULL, nrrdHestNrrd);
  hestOptAdd(&opt, "r", NULL, airTypeInt, 0, 0, &rescale, NULL,
	     "rescale the input values from the input range to the "
	     "map domain.  The map domain is either explicitly "
	     "defined by the axis min,max along axis 0 or 1, or, it "
	     "is implicitly defined as zero to one minus the length of "
	     "that axis.");
  hestOptAdd(&opt, "min", "value", airTypeDouble, 1, 1, &min, "nan",
	     "Low end of input range. Defaults to lowest value "
	     "found in input nrrd.  Explicitly setting this is useful "
	     "only with rescaling (\"-r\") or if the map domain is only "
	     "implicitly defined");
  hestOptAdd(&opt, "max", "value", airTypeDouble, 1, 1, &max, "nan",
	     "High end of input range. Defaults to highest value "
	     "found in input nrrd.  Explicitly setting this is useful "
	     "only with rescaling (\"-r\") or if the map domain is only "
	     "implicitly defined");
  hestOptAdd(&opt, "t", "type", airTypeOther, 1, 1, &typeOut, "default",
	     "specify the type (\"int\", \"float\", etc.) of the "
	     "output nrrd. "
	     "By default (not using this option), the output type "
	     "is the map's type.",
             NULL, NULL, &unrrduHestMaybeTypeCB);
  OPT_ADD_NIN(nin, "input nrrd");
  OPT_ADD_NOUT(out, "output nrrd");

  mop = airMopNew();
  airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);

  USAGE(_unrrdu_mrmapInfoL);
  PARSE();
  airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);

  nout = nrrdNew();
  airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);

  /* see comment rmap.c */

  /* by the end of this block we need to have nmmap and mapAxis */
  if (1 == _nmmapLen) {
    /* we got the mmap as a single nrrd */
    nmmap = _nmmap[0];
    mapAxis = nmmap->dim - nin->dim - 1;
    /* its not our job to do real error checking ... */
    mapAxis = AIR_CLAMP(0, mapAxis, nmmap->dim - 1);
  } else {
    /* we have to join together multiple nrrds to get the mmap */
    nmmap = nrrdNew();
    airMopAdd(mop, nmmap, (airMopper)nrrdNuke, airMopAlways);
    /* assume that mmap component nrrds are all compatible sizes,
       nrrdJoin will fail if they aren't */
    mapAxis = _nmmap[0]->dim - nin->dim;
    if (nrrdJoin(nmmap, (const Nrrd**)_nmmap, _nmmapLen, mapAxis, AIR_TRUE)) {
      airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
      fprintf(stderr, "%s: trouble joining mmap:\n%s", me, err);
      airMopError(mop);
      return 1;
    }
    /* set these if they were given, they'll be NaN otherwise */
    nmmap->axis[mapAxis].min = min;
    nmmap->axis[mapAxis].max = max;
  }

  if (!( AIR_EXISTS(nmmap->axis[mapAxis].min) && 
	 AIR_EXISTS(nmmap->axis[mapAxis].max) )) {
    rescale = AIR_TRUE;
  }
  if (rescale) {
    range = nrrdRangeNew(min, max);
    airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
    nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
  }

  if (nrrdTypeDefault == typeOut) {
    typeOut = nmmap->type;
  }
  if (nrrdApplyMulti1DRegMap(nout, nin, range, nmmap, typeOut, rescale)) {
    airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
    fprintf(stderr, "%s: trouble applying map:\n%s", me, err);
    airMopError(mop);
    return 1;
  }

  SAVE(out, nout, NULL);

  airMopOkay(mop);
  return 0;
}

UNRRDU_CMD(mrmap, INFO);

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/GNUmakefile,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** GNUmakefile	26 Feb 2004 20:59:45 -0000	1.21
--- GNUmakefile	4 Apr 2004 21:21:06 -0000	1.22
***************
*** 58,62 ****
  	lut.o subst.o rmap.o imap.o save.o head.o data.o splice.o inset.o \
  	axinsert.o axdelete.o axinfo.o ccfind.o ccadj.o ccmerge.o \
! 	ccsettle.o about.o axsplit.o axmerge.o
  ####
  ####
--- 58,62 ----
  	lut.o subst.o rmap.o imap.o save.o head.o data.o splice.o inset.o \
  	axinsert.o axdelete.o axinfo.o ccfind.o ccadj.o ccmerge.o \
! 	ccsettle.o about.o axsplit.o axmerge.o mlut.o mrmap.o
  ####
  ####

Index: rmap.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/rmap.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** rmap.c	7 Jan 2004 15:34:31 -0000	1.19
--- rmap.c	4 Apr 2004 21:21:06 -0000	1.20
***************
*** 21,25 ****
  #include "privateUnrrdu.h"
  
! #define INFO "Map nrrd through *regular* univariate map (\"colormap\")"
  char *_unrrdu_rmapInfoL =
  (INFO
--- 21,25 ----
  #include "privateUnrrdu.h"
  
! #define INFO "Map nrrd through one *regular* univariate map (\"colormap\")"
  char *_unrrdu_rmapInfoL =
  (INFO
***************
*** 55,60 ****
  	     "map domain.  The map domain is either explicitly "
  	     "defined by the axis min,max along axis 0 or 1, or, it "
! 	     "is implicitly defined as zero to one minus the length of "
! 	     "that axis.");
    hestOptAdd(&opt, "min", "value", airTypeDouble, 1, 1, &min, "nan",
  	     "Low end of input range. Defaults to lowest value "
--- 55,60 ----
  	     "map domain.  The map domain is either explicitly "
  	     "defined by the axis min,max along axis 0 or 1, or, it "
! 	     "is implicitly defined as zero to the length of "
! 	     "that axis minus one.");
    hestOptAdd(&opt, "min", "value", airTypeDouble, 1, 1, &min, "nan",
  	     "Low end of input range. Defaults to lowest value "

[Teem-commit] teem/src/gage gage.h,1.63,1.64 vecGage.c,1.18,1.19

[xav <xa...@us...>]

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29029

Modified Files:
	gage.h vecGage.c 
Log Message:
added 2 new vector-derived quantities:

- gageVecCurlNormGrad: gradient of curl norm ("cng")
- gageVecNCurlNormGrad: normalized version of this gradient ("ncng")


Index: gage.h
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/gage.h,v
retrieving revision 1.63
retrieving revision 1.64
diff -C2 -d -r1.63 -r1.64
*** gage.h	1 Apr 2004 07:07:35 -0000	1.63
--- gage.h	1 Apr 2004 22:37:26 -0000	1.64
***************
*** 290,308 ****
    gageVecNormHelicity,/* 7: "nh", normalized helicity: GT[1] */
    gageVecLambda2,    /*  8: "lmabda2", lambda2 criterion: GT[1] */
!   gageVecHessian,    /*  9: "vh", second-order derivative: GT[27] */
    gageVecCurlGradient,/*10: "cg", curl gradient: GT[9] */
!   gageVecHelGradient,/* 11: "hg", helicity gradient: GT[3] */
!   gageVecDirHelDeriv,/* 12: "dhd", directional derivative of helicity: GT[1] */ 
!   gageVecProjHelGradient,/* 13: "phg", projected helicity gradient: GT[3] */
!   gageVecGradient0,  /* 14: "g0", gradient of 1st component of vector: GT[3] */
!   gageVecGradient1,  /* 15: "g1", gradient of 2nd component of vector: GT[3] */
!   gageVecGradient2,  /* 16: "g2", gradient of 3rd component of vector: GT[3] */
!   gageVecMultiGrad,  /* 17: "mg", sum of outer products of gradients: GT[9] */
!   gageVecMGFrob,     /* 18: "mgfrob", frob norm of multi-gradient: GT[1] */
!   gageVecMGEval,     /* 19: "mgeval", eigenvalues of multi-gradient: GT[3] */
!   gageVecMGEvec,     /* 20: "mgevec", eigenvectors of multi-gradient: GT[9] */
    gageVecLast
  };
! #define GAGE_VEC_ITEM_MAX     20
  
  struct gageKind_t;       /* dumb forward declaraction, ignore */
--- 290,316 ----
    gageVecNormHelicity,/* 7: "nh", normalized helicity: GT[1] */
    gageVecLambda2,    /*  8: "lmabda2", lambda2 criterion: GT[1] */
!   gageVecHessian,    /*  9: "vh", second-order derivative: GT[27] 
! 			    0:d2v_x/dxdx   1:d2v_x/dxdy   2:d2v_x/dxdz
! 	                    3:d2v_x/dydx   4:d2v_x/dydy   5:d2v_x/dydz
! 			    6:d2v_x/dzdx   7:d2v_x/dzdy   8:d2v_x/dzdz
! 			    9:d2v_y/dxdx       [...]
! 			        [...]
! 			   24:dv2_z/dzdx  25:d2v_z/dzdy  26:d2v_z/dzdz */
    gageVecCurlGradient,/*10: "cg", curl gradient: GT[9] */
!   gageVecCurlNormGrad,/*11: "cng", curl norm gradient: GT[3] */
!   gageVecNCurlNormGrad, /* 12: "ncng", normalized curl norm gradient: GT[3] */
!   gageVecHelGradient,/* 13: "hg", helicity gradient: GT[3] */
!   gageVecDirHelDeriv,/* 14: "dhd", directional derivative of helicity: GT[1] */ 
!   gageVecProjHelGradient, /* 15: "phg", projected helicity gradient: GT[3] */
!   gageVecGradient0,  /* 16: "g0", gradient of 1st component of vector: GT[3] */
!   gageVecGradient1,  /* 17: "g1", gradient of 2nd component of vector: GT[3] */
!   gageVecGradient2,  /* 18: "g2", gradient of 3rd component of vector: GT[3] */
!   gageVecMultiGrad,  /* 19: "mg", sum of outer products of gradients: GT[9] */
!   gageVecMGFrob,     /* 20: "mgfrob", frob norm of multi-gradient: GT[1] */
!   gageVecMGEval,     /* 21: "mgeval", eigenvalues of multi-gradient: GT[3] */
!   gageVecMGEvec,     /* 22: "mgevec", eigenvectors of multi-gradient: GT[9] */
    gageVecLast
  };
! #define GAGE_VEC_ITEM_MAX     22
  
  struct gageKind_t;       /* dumb forward declaraction, ignore */

Index: vecGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/vecGage.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** vecGage.c	1 Apr 2004 07:07:35 -0000	1.18
--- vecGage.c	1 Apr 2004 22:37:27 -0000	1.19
***************
*** 35,38 ****
--- 35,40 ----
    {gageVecHessian,      27,  2,  {-1, -1, -1, -1, -1},                                           -1,  -1},
    {gageVecCurlGradient,  9,  2,  {gageVecHessian, -1, -1, -1, -1},                               -1,  -1},
+   {gageVecCurlNormGrad,  3,  2,  {gageVecHessian, gageVecCurl, -1, -1, -1},                      -1,  -1},
+   {gageVecNCurlNormGrad, 3,  2,  {gageVecCurlNormGrad, -1, -1, -1, -1},                          -1,  -1},
    {gageVecHelGradient,   3,  2,  {gageVecVector, gageVecJacobian, gageVecCurl, 
  				  gageVecCurlGradient, -1},                                      -1,  -1},
***************
*** 105,121 ****
    char me[]="_gageVecAnswer";
    double cmag, tmpMat[9], mgevec[9], mgeval[3];
!   double symm[9], asym[9], tran[9], eval[3];
    gage_t *vecAns, *normAns, *jacAns, *curlAns, *hesAns, *curlGradAns, 
!          *helGradAns, *dirHelDirAns;
    int asw;
  
!   vecAns       = pvl->directAnswer[gageVecVector];
!   normAns      = pvl->directAnswer[gageVecNormalized];
!   jacAns       = pvl->directAnswer[gageVecJacobian];
!   curlAns      = pvl->directAnswer[gageVecCurl];
!   hesAns       = pvl->directAnswer[gageVecHessian];
!   curlGradAns  = pvl->directAnswer[gageVecCurlGradient];
!   helGradAns   = pvl->directAnswer[gageVecHelGradient];
!   dirHelDirAns = pvl->directAnswer[gageVecDirHelDeriv];
  
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecVector)) {
--- 107,124 ----
    char me[]="_gageVecAnswer";
    double cmag, tmpMat[9], mgevec[9], mgeval[3];
!   double symm[9], asym[9], tran[9], eval[3], tmpVec[3], norm;
    gage_t *vecAns, *normAns, *jacAns, *curlAns, *hesAns, *curlGradAns, 
!          *helGradAns, *dirHelDirAns, *curlnormgradAns;
    int asw;
  
!   vecAns          = pvl->directAnswer[gageVecVector];
!   normAns         = pvl->directAnswer[gageVecNormalized];
!   jacAns          = pvl->directAnswer[gageVecJacobian];
!   curlAns         = pvl->directAnswer[gageVecCurl];
!   hesAns          = pvl->directAnswer[gageVecHessian];
!   curlGradAns     = pvl->directAnswer[gageVecCurlGradient];
!   curlnormgradAns = pvl->directAnswer[gageVecCurlNormGrad];
!   helGradAns      = pvl->directAnswer[gageVecHelGradient];
!   dirHelDirAns    = pvl->directAnswer[gageVecDirHelDeriv];
  
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecVector)) {
***************
*** 173,211 ****
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecLambda2)) {
        ELL_3M_TRANSPOSE(tran, jacAns);
!       // symmetric part
        ELL_3M_SCALE_ADD2(symm, 0.5, jacAns,  0.5, tran);
!       // antisymmetric part
        ELL_3M_SCALE_ADD2(asym, 0.5, jacAns, -0.5, tran);
!       // square symmetric part
        ELL_3M_MUL(tmpMat, symm, symm);
        ELL_3M_COPY(symm, tmpMat);
!       // square antisymmetric part
        ELL_3M_MUL(tmpMat, asym, asym);
!       // sum of both
        ELL_3M_ADD2(symm, symm, tmpMat);
        asw = ell_3m_eigenvalues_d(eval, symm, AIR_TRUE);
!       if (asw == ell_cubic_root_triple)
! 	  pvl->directAnswer[gageVecLambda2][0] = eval[0];
!       else if (asw == ell_cubic_root_single_double)
! 	  pvl->directAnswer[gageVecLambda2][0] = eval[1];
!       else if (asw == ell_cubic_root_three)
!       {
! 	  if (eval[0]<=eval[1])
! 	      if (eval[1]<=eval[2])
! 		  pvl->directAnswer[gageVecLambda2][0] = eval[1];
! 	      else 
! 		  if (eval[0]<=eval[2])
! 		      pvl->directAnswer[gageVecLambda2][0] = eval[2];
! 		  else
! 		      pvl->directAnswer[gageVecLambda2][0] = eval[0];
! 	  else
! 	      if (eval[2]<=eval[1])
! 		  pvl->directAnswer[gageVecLambda2][0] = eval[1];
! 	      else
! 		  if (eval[0]<=eval[2])
! 		      pvl->directAnswer[gageVecLambda2][0] = eval[0];
! 		  else
! 		      pvl->directAnswer[gageVecLambda2][0] = eval[2];
!       }
    }
    /* 2nd order vector derivative continued */ 
--- 176,193 ----
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecLambda2)) {
        ELL_3M_TRANSPOSE(tran, jacAns);
!       /* symmetric part */
        ELL_3M_SCALE_ADD2(symm, 0.5, jacAns,  0.5, tran);
!       /* antisymmetric part */
        ELL_3M_SCALE_ADD2(asym, 0.5, jacAns, -0.5, tran);
!       /* square symmetric part */
        ELL_3M_MUL(tmpMat, symm, symm);
        ELL_3M_COPY(symm, tmpMat);
!       /* square antisymmetric part */
        ELL_3M_MUL(tmpMat, asym, asym);
!       /* sum of both */
        ELL_3M_ADD2(symm, symm, tmpMat);
+       /* get eigenvalues in sorted order */
        asw = ell_3m_eigenvalues_d(eval, symm, AIR_TRUE);
!       pvl->directAnswer[gageVecLambda2][0] = eval[1];
    }
    /* 2nd order vector derivative continued */ 
***************
*** 236,239 ****
--- 218,247 ----
        pvl->directAnswer[gageVecCurlGradient][8] = hesAns[11]-hesAns[ 3];
    }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurlNormGrad)) {
+       norm = 1./ELL_3V_LEN(curlAns);
+ 
+       tmpVec[0] = hesAns[21] - hesAns[15];
+       tmpVec[1] = hesAns[ 6] - hesAns[18];
+       tmpVec[2] = hesAns[ 9] - hesAns[ 3];      
+       pvl->directAnswer[gageVecCurlNormGrad][0]=
+ 	  norm*ELL_3V_DOT(tmpVec, curlAns);
+ 
+       tmpVec[0] = hesAns[22] - hesAns[16];
+       tmpVec[1] = hesAns[ 7] - hesAns[19];
+       tmpVec[2] = hesAns[10] - hesAns[ 4];      
+       pvl->directAnswer[gageVecCurlNormGrad][1]=
+ 	  norm*ELL_3V_DOT(tmpVec, curlAns);
+ 
+       tmpVec[0] = hesAns[23] - hesAns[17];
+       tmpVec[1] = hesAns[ 8] - hesAns[20];
+       tmpVec[2] = hesAns[11] - hesAns[ 5];      
+       pvl->directAnswer[gageVecCurlNormGrad][2]=
+ 	  norm*ELL_3V_DOT(tmpVec, curlAns);      
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecNCurlNormGrad)) {
+       norm = 1./ELL_3V_LEN(curlnormgradAns);
+       ELL_3V_SCALE(pvl->directAnswer[gageVecNCurlNormGrad],
+ 		   norm, pvl->directAnswer[gageVecCurlNormGrad]);
+   }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecHelGradient)) {
        pvl->directAnswer[gageVecHelGradient][0] = 
***************
*** 332,335 ****
--- 340,345 ----
    "vector hessian",
    "curl gradient",
+   "curl norm gradient",
+   "normalized curl norm gradient",
    "helicity gradient",
    "directional helicity derivative",
***************
*** 358,361 ****
--- 368,373 ----
    "3x3x3 second-order vector derivative",
    "3x3 derivative of curl",
+   "gradient of curl norm",
+   "normalized gradient of curl norm",
    "gradient of helicity",
    "directional derivative of helicity along flow",
***************
*** 384,387 ****
--- 396,401 ----
    gageVecHessian,
    gageVecCurlGradient,
+   gageVecCurlNormGrad,
+   gageVecNCurlNormGrad,
    gageVecHelGradient,
    gageVecDirHelDeriv,
***************
*** 396,420 ****
  };
  
! #define GV_V gageVecVector
! #define GV_L gageVecLength
! #define GV_N gageVecNormalized
! #define GV_J gageVecJacobian
! #define GV_D gageVecDivergence
! #define GV_C gageVecCurl
! #define GV_H  gageVecHelicity
! #define GV_NH gageVecNormHelicity
! #define GV_LB gageVecLambda2
! #define GV_VH gageVecHessian
! #define GV_CG gageVecCurlGradient
! #define GV_HG gageVecHelGradient
! #define GV_DH gageVecDirHelDeriv
! #define GV_PH gageVecProjHelGradient
! #define GV_G0 gageVecGradient0
! #define GV_G1 gageVecGradient1
! #define GV_G2 gageVecGradient2
! #define GV_MG gageVecMultiGrad
! #define GV_MF gageVecMGFrob
! #define GV_ML gageVecMGEval
! #define GV_MC gageVecMGEvec
  
  char
--- 410,436 ----
  };
  
! #define GV_V   gageVecVector
! #define GV_L   gageVecLength
! #define GV_N   gageVecNormalized
! #define GV_J   gageVecJacobian
! #define GV_D   gageVecDivergence
! #define GV_C   gageVecCurl
! #define GV_H   gageVecHelicity
! #define GV_NH  gageVecNormHelicity
! #define GV_LB  gageVecLambda2
! #define GV_VH  gageVecHessian
! #define GV_CG  gageVecCurlGradient
! #define GV_CNG gageVecCurlNormGrad
! #define GV_NCG gageVecNCurlNormGrad
! #define GV_HG  gageVecHelGradient
! #define GV_DH  gageVecDirHelDeriv
! #define GV_PH  gageVecProjHelGradient
! #define GV_G0  gageVecGradient0
! #define GV_G1  gageVecGradient1
! #define GV_G2  gageVecGradient2
! #define GV_MG  gageVecMultiGrad
! #define GV_MF  gageVecMGFrob
! #define GV_ML  gageVecMGEval
! #define GV_MC  gageVecMGEvec
  
  char
***************
*** 431,434 ****
--- 447,452 ----
    "vh", "vhes", "vhessian", "vector hessian",
    "cg", "curlgrad", "curlg", "curljac", "curl gradient",
+   "cng", "curl norm gradient",
+   "ncng", "norm curl norm gradient",
    "hg", "helg", "helgrad", "helicity gradient",
    "dirhelderiv", "dhd", "ddh", "directional helicity derivative",
***************
*** 457,460 ****
--- 475,480 ----
    GV_VH, GV_VH, GV_VH, GV_VH,
    GV_CG, GV_CG, GV_CG, GV_CG, GV_CG,
+   GV_CNG, GV_CNG,
+   GV_NCG, GV_NCG,
    GV_HG, GV_HG, GV_HG, GV_HG,
    GV_DH, GV_DH, GV_DH, GV_DH,