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[Teem-commit] teem/src/ten tendGrads.c,1.2,1.3

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17013

Modified Files:
	tendGrads.c 
Log Message:
improved usage info

Index: tendGrads.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendGrads.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** tendGrads.c	27 Feb 2004 10:23:56 -0000	1.2
--- tendGrads.c	27 Feb 2004 10:41:03 -0000	1.3
***************
*** 26,30 ****
     ", based on a simulation of anti-podal point pairs repelling each other "
     "on the unit sphere surface. This can either distribute more uniformly a given "
!    "set of gradients, or it can make a new distribution from scratch. ");
  
  int
--- 26,33 ----
     ", based on a simulation of anti-podal point pairs repelling each other "
     "on the unit sphere surface. This can either distribute more uniformly a given "
!    "set of gradients, or it can make a new distribution from scratch.  A more "
!    "clever implementation could decrease drag with time, as the solution converges, "
!    "to get closer to the minimum energy configuration faster.  In the mean time, you "
!    "can run a second pass on the output of the first pass, using lower drag. ");
  
  int

[Teem-commit] teem/src/ten grads.c,NONE,1.1

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14744

Added Files:
	grads.c 
Log Message:
added tenGradientGenerate and tenGradientDistributed, which are accessed via "tend grads"

--- NEW FILE: grads.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 "ten.h"
#include "privateTen.h"

tenGradientParm *
tenGradientParmNew(void) {
  tenGradientParm *ret;

  ret = (tenGradientParm *)calloc(1, sizeof(tenGradientParm));
  if (ret) {
    ret->mass = 1;
    ret->charge = 0.2;
    ret->drag = 0.01;
    ret->dt = 0.05;
    ret->minVelocity = 0.00001;
    ret->jitter = 0.05;
    ret->srand = AIR_TRUE;
    ret->snap = 0;
    ret->single = AIR_FALSE;
    ret->minIteration = 20;
    ret->maxIteration = 1000000;
  }
  return ret;
}

tenGradientParm *
tenGradientParmNix(tenGradientParm *tgparm) {

  return airFree(tgparm);
}


int
tenGradientCheck(Nrrd *ngrad, int type, int minnum) {
  char me[]="tenGradientCheck", err[AIR_STRLEN_MED];
  
  if (nrrdCheck(ngrad)) {
    sprintf(err, "%s: basic validity check failed", me);
    biffMove(TEN, err, NRRD); return 1;
  }
  if (!( 3 == ngrad->axis[0].size && 2 == ngrad->dim )) {
    sprintf(err, "%s: need a 3xN 2-D array (not a %dx? %d-D array)",
	    me, ngrad->axis[0].size, ngrad->dim);
    biffAdd(TEN, err); return 1;
  }
  if (nrrdTypeUnknown != type && type != ngrad->type) {
    sprintf(err, "%s: requested type %s but got type %s", me,
	    airEnumStr(nrrdType, type), airEnumStr(nrrdType, ngrad->type));
    biffAdd(TEN, err); return 1;
  }
  if (!( minnum <= ngrad->axis[1].size )) {
    sprintf(err, "%s: have only %d gradients, need at least %d",
	    me, ngrad->axis[1].size, minnum);
    biffAdd(TEN, err); return 1;
  }

  return 0;
}

/*
******** tenGradientRandom
**
** generates num random unit vectors of type double
*/
int
tenGradientRandom(Nrrd *ngrad, int num, int srand) {
  char me[]="tenGradientRandom", err[AIR_STRLEN_MED];
  double *grad, len;
  int gi;
  
  if (nrrdMaybeAlloc(ngrad, nrrdTypeDouble, 2, 3, num)) {
    sprintf(err, "%s: couldn't allocate output", me);
    biffMove(TEN, err, NRRD); return 1;
  }
  if (srand) {
    airSrand();
  }
  grad = (double*)(ngrad->data);
  for (gi=0; gi<num; gi++) {
    do {
      grad[0] = AIR_AFFINE(0, airRand(), 1, -1, 1);
      grad[1] = AIR_AFFINE(0, airRand(), 1, -1, 1);
      grad[2] = AIR_AFFINE(0, airRand(), 1, -1, 1);
      len = ELL_3V_LEN(grad);
    } while (len > 1 || !len);
    ELL_3V_SCALE(grad, 1.0/len, grad);
    grad += 3;
  }
  return 0;
}

/*
******** tenGradientJitter
**
** moves all gradients by amount dist on tangent plane, in a random
** direction, and then renormalizes
*/
int
tenGradientJitter(Nrrd *nout, Nrrd *nin, double dist) {
  char me[]="tenGradientJitter", err[AIR_STRLEN_MED];
  double *grad, perp0[3], perp1[3], len, theta, cc, ss;
  int gi;

  if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
    sprintf(err, "%s: trouble converting input to double", me);
    biffMove(TEN, err, NRRD); return 1;
  }
  if (tenGradientCheck(nout, nrrdTypeDouble, 3)) {
    sprintf(err, "%s: didn't get valid gradients", me);
    biffAdd(TEN, err); return 1;
  }
  grad = (double*)(nout->data);
  for (gi=0; gi<nout->axis[1].size; gi++) {
    ELL_3V_NORM(grad, grad, len);
    ell_3v_perp_d(perp0, grad);
    ELL_3V_CROSS(perp1, perp0, grad);
    theta = AIR_AFFINE(0, airRand(), 1, 0, 2*AIR_PI);
    cc = dist*cos(theta);
    ss = dist*sin(theta);
    ELL_3V_SCALE_ADD3(grad, 1.0, grad, cc, perp0, ss, perp1);
    ELL_3V_NORM(grad, grad, len);
    grad += 3;
  }
  
  return 0;
}

void
_tenGradientChangeFind(Nrrd *ndvdt, Nrrd *ndpdt,
		       Nrrd *nvel, Nrrd *npos,
		       tenGradientParm *tgparm) {
  double *dvdt, *dpdt, *vel, *pos, qq, force[3], ff[3],
    pdir[3], mdir[3], plen, mlen, prep, mrep;
  int num, ii, jj;
  
  dvdt = (double *)(ndvdt->data);
  dpdt = (double *)(ndpdt->data);
  vel = (double *)(nvel->data);
  pos = (double *)(npos->data);
  num = ndvdt->axis[1].size;
  qq = (tgparm->charge)*(tgparm->charge);

  for (ii=0; ii<num; ii++) {
    /* find forces acting on ii from position of all other pairs jj */
    ELL_3V_SET(force, 0, 0, 0);
    for (jj=0; jj<num; jj++) {
      if (ii == jj) {
	continue;
      }
      ELL_3V_SUB(pdir, pos + 3*ii, pos + 3*jj);
      ELL_3V_NORM(pdir, pdir, plen);
      prep = qq/(plen*plen);
      if (tgparm->single) {
	mrep = 0;
	ELL_3V_SET(mdir, 0, 0, 0);
      } else {
	ELL_3V_ADD2(mdir, pos + 3*ii, pos + 3*jj);
	ELL_3V_NORM(mdir, mdir, mlen);
	mrep = qq/(mlen*mlen);
      }
      ELL_3V_SCALE_ADD3(ff,
			prep, pdir,
			mrep, mdir,
			-tgparm->drag, vel + 3*ii);
      ELL_3V_ADD2(force, force, ff);
    }
    ELL_3V_SCALE(dvdt + 3*ii, 1.0/tgparm->mass, force);
    ELL_3V_COPY(dpdt + 3*ii, vel + 3*ii);
  }
  return;
}

void
_tenGradientChangeApply(Nrrd *nvel1, Nrrd *npos1,
			Nrrd *ndvdt, Nrrd *ndpdt, 
			Nrrd *nvel0, Nrrd *npos0,
			tenGradientParm *tgparm, double amount) {
  double *dvdt, *dpdt, *vel0, *pos0, *vel1, *pos1, len, dot;
  int ii, num;

  dvdt = (double *)(ndvdt->data);
  dpdt = (double *)(ndpdt->data);
  vel0 = (double *)(nvel0->data);
  pos0 = (double *)(npos0->data);
  vel1 = (double *)(nvel1->data);
  pos1 = (double *)(npos1->data);
  num = ndvdt->axis[1].size;

  for (ii=0; ii<num; ii++) {
    ELL_3V_SCALE_ADD2(vel1,
		      1.0, vel0,
		      amount*tgparm->dt, dvdt);
    ELL_3V_SCALE_ADD2(pos1,
		      1.0, pos0,
		      amount*tgparm->dt, dpdt);
    ELL_3V_NORM(pos1, pos1, len);
    dot = ELL_3V_DOT(vel1, pos1);
    ELL_3V_SCALE_ADD2(vel1, 1.0, vel1, -dot, pos1);
    vel1 += 3;
    pos1 += 3;
    vel0 += 3;
    pos0 += 3;
    dvdt += 3;
    dpdt += 3;
  }
  
  return;
}

double
_tenGradientMeanVelocity(Nrrd *nvel) {
  double *vel, mv;
  int ii, num;

  vel = (double*)(nvel->data);
  num = nvel->axis[1].size;
  mv = 0;
  for (ii=0; ii<num; ii++) {
    mv += ELL_3V_LEN(vel + 3*ii);
  }
  mv /= num;
  return mv;
}

/*
******** tenGradientDistribute
**
** takes the given list of gradients, normalizes their lengths, optionally jitters
** their positions, does point repulsion, and then selects a combination of
** directions with minimum vector sum.
*/
int
tenGradientDistribute(Nrrd *nout, Nrrd *nin, tenGradientParm *tgparm) {
  char me[]="tenGradientDistribute", err[AIR_STRLEN_MED], *serr,
    filename[AIR_STRLEN_SMALL];
  int gi, iter;
  airArray *mop;
  Nrrd *nvel, *npos, *nveltmp, *npostmp, *ndvdt, *ndpdt;
  double *grad, len, meanVelocity;

  if (!nout || tenGradientCheck(nin, nrrdTypeUnknown, 2) || !tgparm) {
    sprintf(err, "%s: got NULL pointer or invalid input", me);
    biffAdd(TEN, err); return 1;
  }

  if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
    sprintf(err, "%s: can't initialize output with input", me);
    biffMove(TEN, err, NRRD); return 1;
  }
  grad = (double*)(nout->data);
  for (gi=0; gi<nout->axis[1].size; gi++) {
    ELL_3V_NORM(grad, grad, len);
    grad += 3;
  }
  if (tgparm->jitter) {
    if (tenGradientJitter(nout, nout, tgparm->jitter)) {
      sprintf(err, "%s: problem jittering input", me);
      biffAdd(TEN, err); return 1;
    }
  }

  mop = airMopNew();
  ndvdt = nrrdNew();
  ndpdt = nrrdNew();
  nvel = nrrdNew();
  npos = nrrdNew();
  nveltmp = nrrdNew();
  npostmp = nrrdNew();
  airMopAdd(mop, ndvdt, (airMopper)nrrdNuke, airMopAlways);
  airMopAdd(mop, ndpdt, (airMopper)nrrdNuke, airMopAlways);
  airMopAdd(mop, nvel, (airMopper)nrrdNuke, airMopAlways);
  airMopAdd(mop, npos, (airMopper)nrrdNuke, airMopAlways);
  airMopAdd(mop, nveltmp, (airMopper)nrrdNuke, airMopAlways);
  airMopAdd(mop, npostmp, (airMopper)nrrdNuke, airMopAlways);
  if (nrrdCopy(ndvdt, nout)
      || nrrdCopy(ndpdt, nout)
      || nrrdCopy(nvel, nout)
      || nrrdCopy(npos, nout)
      || nrrdCopy(nveltmp, nout)
      || nrrdCopy(npostmp, nout)) {
    sprintf(err, "%s: trouble allocating temp buffers", me);
    biffMove(TEN, err, NRRD); airMopError(mop); return 1;
  }

  /*
    while mean velocity is small:
    - compute forces based on positions and velocities
    - compute change in velocity (by f=ma  -->  a=f/m)
    - compute change in position (by definition)
    - apply HALF those changes to create temp world
    - compute forces based on positions and velocities
    - compute change in velocity (by f=ma)
    - compute change in position (by definition)
    - apply those changes to the real world
  */
  /* npos is already initialized (via nrrdCopy) */
  memset(nvel->data, 0, nrrdElementSize(nvel)*nrrdElementNumber(nvel));
  meanVelocity = _tenGradientMeanVelocity(nvel);
  for (iter=0;
       (iter < tgparm->minIteration 
	|| (iter < tgparm->maxIteration
	    && meanVelocity > tgparm->minVelocity)); 
       iter++) {
    _tenGradientChangeFind(ndvdt, ndpdt,
			   nvel, npos, tgparm);
    _tenGradientChangeApply(nveltmp, npostmp,
			    ndvdt, ndpdt, 
			    nvel, npos, tgparm, 0.5);
    _tenGradientChangeFind(ndvdt, ndpdt,
			   nveltmp, npostmp, tgparm);
    _tenGradientChangeApply(nvel, npos,
			    ndvdt, ndpdt, 
			    nvel, npos, tgparm, 1.0);
    meanVelocity = _tenGradientMeanVelocity(nvel);
    if (tgparm->snap) {
      if (!(iter % tgparm->snap)) {
	sprintf(filename, "%05d.nrrd", iter/tgparm->snap);
	fprintf(stderr, "%s: %d: meanVelocity = %g; saving %s\n",
		me, iter, meanVelocity, filename);
	if (nrrdSave(filename, npos, NULL)) {
	  serr = biffGetDone(NRRD);
	  fprintf(stderr, "%s: iter=%d, couldn't save snapshot:\n%s"
		  "continuing ...\n", me, iter, serr);
	  free(serr);
	}
      }
    } else {
      if (!(iter % 25)) {
	fprintf(stderr, "%s: %d: meanVelocity = %g\n", me, iter, meanVelocity);
      }
    }
  }

  /* select output gradients
     - either do the trivial thing
     - or run through 2^(#grads) to find one with maximum covariance
     print covariance matrix eigenvalues
  */
  nrrdCopy(nout, npos);

  airMopOkay(mop); 
  return 0;
}

int
tenGradientGenerate(Nrrd *nout, int num, tenGradientParm *tgparm) {
  char me[]="tenGradientGenerate", err[AIR_STRLEN_MED];
  Nrrd *nin;
  airArray *mop;

  if (!(nout && tgparm)) {
    sprintf(err, "%s: got NULL pointer", me);
    biffAdd(TEN, err); return 1;
  }
  if (!( num >= 3 )) {
    sprintf(err, "%s: can generate at minimum 3 gradient directions (not %d)", me, num);
    biffAdd(TEN, err); return 1;
  }
  mop = airMopNew();
  nin = nrrdNew();
  airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);

  if (tenGradientRandom(nin, num, tgparm->srand)
      || tenGradientDistribute(nout, nin, tgparm)) {
    sprintf(err, "%s: trouble", me);
    biffAdd(TEN, err); airMopError(mop); return 1;
  }

  airMopOkay(mop);
  return 0;
}

[Teem-commit] teem/src/ten GNUmakefile,1.37,1.38 chan.c,1.29,1.30 epireg.c,1.24,1.25 miscTen.c,1.21,1.22 ten.h,1.76,1.77 tendGrads.c,1.1,1.2

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13768

Modified Files:
	GNUmakefile chan.c epireg.c miscTen.c ten.h tendGrads.c 
Log Message:
added tenGradientGenerate and tenGradientDistributed, which are accessed via "tend grads"

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/GNUmakefile,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** GNUmakefile	26 Feb 2004 18:42:23 -0000	1.37
--- GNUmakefile	27 Feb 2004 10:23:55 -0000	1.38
***************
*** 47,51 ****
  $(L).PUBLIC_HEADERS = ten.h tenMacros.h
  $(L).PRIVATE_HEADERS = privateTen.h
! $(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o miscTen.o mod.o \
  	tenGage.o fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o \
  	tendFlotsam.o tendGrads.o tendAnplot.o tendAnvol.o tendEval.o \
--- 47,51 ----
  $(L).PUBLIC_HEADERS = ten.h tenMacros.h
  $(L).PRIVATE_HEADERS = privateTen.h
! $(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o grads.o miscTen.o mod.o \
  	tenGage.o fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o \
  	tendFlotsam.o tendGrads.o tendAnplot.o tendAnvol.o tendEval.o \

Index: chan.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/chan.c,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** chan.c	7 Jan 2004 15:34:31 -0000	1.29
--- chan.c	27 Feb 2004 10:23:56 -0000	1.30
***************
*** 44,48 ****
    airArray *mop;
  
!   if (!(nbmat && _ngrad && !tenGradCheck(_ngrad))) {
      sprintf(err, "%s: got NULL pointer or invalid arg", me);
      biffAdd(TEN, err); return 1;
--- 44,48 ----
    airArray *mop;
  
!   if (!(nbmat && _ngrad && !tenGradientCheck(_ngrad, nrrdTypeUnknown, 1))) {
      sprintf(err, "%s: got NULL pointer or invalid arg", me);
      biffAdd(TEN, err); return 1;

Index: epireg.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/epireg.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** epireg.c	16 Jan 2004 17:35:12 -0000	1.24
--- epireg.c	27 Feb 2004 10:23:56 -0000	1.25
***************
*** 60,64 ****
      biffAdd(TEN, err); return 1;
    }
!   if (tenGradCheck(ngrad)) {
      sprintf(err, "%s: problem with given gradient list", me);
      biffAdd(TEN, err); return 1;
--- 60,64 ----
      biffAdd(TEN, err); return 1;
    }
!   if (tenGradientCheck(ngrad, nrrdTypeUnknown, 6 /* <-- HEY: not sure */)) {
      sprintf(err, "%s: problem with given gradient list", me);
      biffAdd(TEN, err); return 1;

Index: miscTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/miscTen.c,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** miscTen.c	7 Jan 2004 15:34:31 -0000	1.21
--- miscTen.c	27 Feb 2004 10:23:56 -0000	1.22
***************
*** 183,208 ****
  
  int
- tenGradCheck(Nrrd *ngrad) {
-   char me[]="tenGradCheck", err[AIR_STRLEN_MED];
- 
-   if (nrrdCheck(ngrad)) {
-     sprintf(err, "%s: basic validity check failed", me);
-     biffMove(TEN, err, NRRD); return 1;
-   }
-   if (!( 3 == ngrad->axis[0].size && 2 == ngrad->dim )) {
-     sprintf(err, "%s: need a 3xN 2-D array (not a %dxN %d-D array)",
- 	    me, ngrad->axis[0].size, ngrad->dim);
-     biffAdd(TEN, err); return 1;
-   }
-   if (!( 6 <= ngrad->axis[1].size )) {
-     sprintf(err, "%s: have only %d gradients, need at least 6",
- 	    me, ngrad->axis[1].size);
-     biffAdd(TEN, err); return 1;
-   }
- 
-   return 0;
- }
- 
- int
  tenBMatrixCheck(Nrrd *nbmat) {
    char me[]="tenBMatrixCheck", err[AIR_STRLEN_MED];
--- 183,186 ----

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.76
retrieving revision 1.77
diff -C2 -d -r1.76 -r1.77
*** ten.h	26 Feb 2004 18:42:23 -0000	1.76
--- ten.h	27 Feb 2004 10:23:56 -0000	1.77
***************
*** 380,384 ****
      minVelocity,
      jitter; 
!   int snap, single, minIteration, maxIteration;
  } tenGradientParm;
  
--- 380,384 ----
      minVelocity,
      jitter; 
!   int srand, snap, single, minIteration, maxIteration;
  } tenGradientParm;
  
***************
*** 395,398 ****
--- 395,405 ----
  
  /* grads.c */
+ TEEM_API tenGradientParm *tenGradientParmNew(void);
+ TEEM_API tenGradientParm *tenGradientParmNix(tenGradientParm *tgparm);
+ TEEM_API int tenGradientCheck(Nrrd *ngrad, int type, int minnum);
+ TEEM_API int tenGradientRandom(Nrrd *ngrad, int num, int srand);
+ TEEM_API int tenGradientJitter(Nrrd *nout, Nrrd *nin, double dist);
+ TEEM_API int tenGradientDistribute(Nrrd *nout, Nrrd *nin, tenGradientParm *tgparm);
+ TEEM_API int tenGradientGenerate(Nrrd *nout, int num, tenGradientParm *tgparm);
  
  /* enumsTen.c */
***************
*** 457,461 ****
  TEEM_API int tenEvqVolume(Nrrd *nout, Nrrd *nin, int which,
  			  int aniso, int scaleByAniso);
- TEEM_API int tenGradCheck(Nrrd *ngrad);
  TEEM_API int tenBMatrixCheck(Nrrd *nbmat);
  TEEM_API int _tenFindValley(float *valP, Nrrd *nhist, float tweak);
--- 464,467 ----

Index: tendGrads.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendGrads.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** tendGrads.c	26 Feb 2004 18:44:50 -0000	1.1
--- tendGrads.c	27 Feb 2004 10:23:56 -0000	1.2
***************
*** 25,29 ****
    (INFO
     ", based on a simulation of anti-podal point pairs repelling each other "
!    "on the unit sphere surface. ");
  
  int
--- 25,30 ----
    (INFO
     ", based on a simulation of anti-podal point pairs repelling each other "
!    "on the unit sphere surface. This can either distribute more uniformly a given "
!    "set of gradients, or it can make a new distribution from scratch. ");
  
  int
***************
*** 34,46 ****
    airArray *mop;
  
!   Nrrd *ngrad, *nout;
    char *outS;
! 
!   hestOptAdd(&hopt, "i", "grads", airTypeOther, 1, 1, &ngrad, NULL,
! 	     "array of gradient directions", NULL, NULL, nrrdHestNrrd);
!   hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
! 	     "output B matrix");
  
    mop = airMopNew();
    airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
    USAGE(_tend_gradsInfoL);
--- 35,76 ----
    airArray *mop;
  
!   int num, E, nosrand;
!   Nrrd *nin, *nout;
    char *outS;
!   tenGradientParm *tgparm;
  
    mop = airMopNew();
+   tgparm = tenGradientParmNew();
+   airMopAdd(mop, tgparm, (airMopper)tenGradientParmNix, airMopAlways);
+ 
+   hestOptAdd(&hopt, "n", "# dir", airTypeInt, 1, 1, &num, "6",
+ 	     "desired number of diffusion gradient directions");
+   hestOptAdd(&hopt, "i", "grads", airTypeOther, 1, 1, &nin, "",
+ 	     "initial gradient directions to start with, instead "
+ 	     "of default random initial directions (overrides \"-n\")",
+              NULL, NULL, nrrdHestNrrd);
+   hestOptAdd(&hopt, "nosrand", NULL, airTypeInt, 0, 0, &nosrand, NULL,
+ 	     "do NOT call srand() to initialize random number generator");
+   hestOptAdd(&hopt, "dt", "dt", airTypeDouble, 1, 1, &(tgparm->dt), "0.05",
+ 	     "time increment in solver");
+   hestOptAdd(&hopt, "drag", "drag", airTypeDouble, 1, 1, &(tgparm->drag), "0.01",
+ 	     "viscous drag, to keep things stable");
+   hestOptAdd(&hopt, "charge", "charge", airTypeDouble, 1, 1, &(tgparm->charge), "0.2",
+ 	     "amount of charge on each particle");
+   hestOptAdd(&hopt, "single", NULL, airTypeInt, 0, 0, &(tgparm->single), NULL,
+ 	     "instead of the default behavior of tracking a pair of "
+ 	     "antipodal points (appropriate for determining DWI gradients), "
+ 	     "use only single points (appropriate for who knows what).");
+   hestOptAdd(&hopt, "snap", "interval", airTypeInt, 1, 1, &(tgparm->snap), "0",
+ 	     "specifies an interval between which snapshots of the point "
+ 	     "positions should be saved out.  By default (not using this "
+ 	     "option), there is no such snapshot behavior");
+   hestOptAdd(&hopt, "jitter", "jitter", airTypeDouble, 1, 1, &(tgparm->jitter), "0.05",
+ 	     "amount by which to perturb points when given an input nrrd");
+   hestOptAdd(&hopt, "maxiter", "# iters", airTypeInt, 1, 1,
+ 	     &(tgparm->maxIteration), "1000000",
+ 	     "max number of iterations for which to run the simulation");
+   hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
+ 	     "file to write output nrrd to");
    airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
    USAGE(_tend_gradsInfoL);
***************
*** 50,53 ****
--- 80,92 ----
    airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
  
+   tgparm->srand = !nosrand;
+   E = (nin
+        ? tenGradientDistribute(nout, nin, tgparm)
+        : tenGradientGenerate(nout, num, tgparm));
+   if (E) {
+     airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+     fprintf(stderr, "%s: trouble making distribution:\n%s\n", me, err);
+     airMopError(mop); return 1;
+   }
    
    if (nrrdSave(outS, nout, NULL)) {

[Teem-commit] teem/src/ten glyph.c,1.34,1.35

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5823/ten

Modified Files:
	glyph.c 
Log Message:
fixed handling of glyphParm->sliceBias in combination with negative sliceGamma

Index: glyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/glyph.c,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** glyph.c	26 Feb 2004 18:42:23 -0000	1.34
--- glyph.c	27 Feb 2004 06:08:35 -0000	1.35
***************
*** 285,293 ****
  	  continue;
  	sliceGray = aniso[parm->sliceAnisoType];
- 	sliceGray = AIR_AFFINE(0, sliceGray, 1, parm->sliceBias, 1);
        }
        if (parm->sliceGamma > 0) {
  	sliceGray = pow(sliceGray, 1.0/parm->sliceGamma);
        } else {
  	sliceGray = 1.0 - pow(sliceGray, -1.0/parm->sliceGamma);
        }
--- 285,294 ----
  	  continue;
  	sliceGray = aniso[parm->sliceAnisoType];
        }
        if (parm->sliceGamma > 0) {
+ 	sliceGray = AIR_AFFINE(0, sliceGray, 1, parm->sliceBias, 1);
  	sliceGray = pow(sliceGray, 1.0/parm->sliceGamma);
        } else {
+ 	sliceGray = AIR_AFFINE(0, sliceGray, 1, 0, 1-parm->sliceBias);
  	sliceGray = 1.0 - pow(sliceGray, -1.0/parm->sliceGamma);
        }

[Teem-commit] teem/src/nrrd apply1D.c,1.21,1.22

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5350/nrrd

Modified Files:
	apply1D.c 
Log Message:
more comments and minor edits.  TEAT approved.

Index: apply1D.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/apply1D.c,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** apply1D.c	26 Feb 2004 20:59:45 -0000	1.21
--- apply1D.c	27 Feb 2004 06:05:16 -0000	1.22
***************
*** 859,869 ****
  ******** nrrdApply1DSubstitution
  **
! ** A "subst" is a substitution table, i.e. a list of pairs that describes
! ** what values should be substituted with what (substitution rules).
! ** The output is a copy of the input with values substituted using this table.
  */
  int
! nrrdApply1DSubstitution(Nrrd *nout, const Nrrd *nin, const Nrrd *nsubst)
! {
    char me[]="nrrdApply1DSubstitution", err[AIR_STRLEN_MED];
    double (*lup)(const void *, size_t);
--- 859,877 ----
  ******** nrrdApply1DSubstitution
  **
! ** A "subst" is a substitution table, i.e. a list of pairs that
! ** describes what values should be substituted with what (substitution
! ** rules).  So, nsubst must be a scalar 2xN array.  The output is a
! ** copy of the input with values substituted using this table.
! **
! ** Unlike with lookup tables and maps (irregular and regular), we
! ** aren't at liberty to change the dimensionality of the data (can't
! ** substitute a grayscale with a color).  The ability to apply
! ** substitutions to non-scalar data will be in a different function.
! ** Also unlike lookup tables and maps, the output type is the SAME as
! ** the input type; the output does NOT inherit the type of the
! ** substitution
  */
  int
! nrrdApply1DSubstitution(Nrrd *nout, const Nrrd *nin, const Nrrd *nsubst) {
    char me[]="nrrdApply1DSubstitution", err[AIR_STRLEN_MED];
    double (*lup)(const void *, size_t);
***************
*** 885,889 ****
    }
    if (2 != nsubst->dim) {
!     sprintf(err, "%s: substitution table hasize to be 2 dimensional, not %d",
  	    me, nsubst->dim);
      biffAdd(NRRD, err); return 1;
--- 893,897 ----
    }
    if (2 != nsubst->dim) {
!     sprintf(err, "%s: substitution table has to be 2-D, not %d-D",
  	    me, nsubst->dim);
      biffAdd(NRRD, err); return 1;
***************
*** 891,895 ****
    nrrdAxisInfoGet(nsubst, nrrdAxisInfoSize, &asize0, &asize1);
    if (2 != asize0) {
!     sprintf(err, "%s: substitution table hasize to be 2xN, not %dxN",
  	    me, asize0);
      biffAdd(NRRD, err); return 1;
--- 899,903 ----
    nrrdAxisInfoGet(nsubst, nrrdAxisInfoSize, &asize0, &asize1);
    if (2 != asize0) {
!     sprintf(err, "%s: substitution table has to be 2xN, not %dxN",
  	    me, asize0);
      biffAdd(NRRD, err); return 1;
***************
*** 909,913 ****
      changed = AIR_FALSE;
      for (jj=0; jj<asize1; jj++) {
!       sval = slup(nsubst->data, jj*2);
        if (val == sval) {
  	val = slup(nsubst->data, jj*2+1);
--- 917,921 ----
      changed = AIR_FALSE;
      for (jj=0; jj<asize1; jj++) {
!       sval = slup(nsubst->data, jj*2+0);
        if (val == sval) {
  	val = slup(nsubst->data, jj*2+1);

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

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5350/unrrdu

Modified Files:
	subst.c 
Log Message:
more comments and minor edits.  TEAT approved.

Index: subst.c
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/subst.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** subst.c	26 Feb 2004 20:59:45 -0000	1.1
--- subst.c	27 Feb 2004 06:05:18 -0000	1.2
***************
*** 25,30 ****
  (INFO
   " (itself represented as a nrrd). The substitution table "
!  "has to be a 2 by N table containing a list of pairs aka. "
!  "substitution rules.");
  
  int
--- 25,33 ----
  (INFO
   " (itself represented as a nrrd). The substitution table "
!  "is a 2-by-N table: a list of pairs giving the old value (to replace) "
!  "and the the new value (to change to), in that order.  A plain text file "
!  "makes this easy.  Unlike with \"unu lut\", \"unu rmap\", and \"unu imap\", "
!  "the output type is the same as the input type, rather than the type of "
!  "the lut or map. ");
  
  int

[Teem-commit] teem/src/unrrdu subst.c,NONE,1.1 GNUmakefile,1.20,1.21 unrrdu.h,1.25,1.26

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

Update of /cvsroot/teem/teem/src/unrrdu
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26791/unrrdu

Modified Files:
	GNUmakefile unrrdu.h 
Added Files:
	subst.c 
Log Message:
added nrrdApply1DSubstitution and unu subst ... waiting for TEAT approval

--- NEW FILE: subst.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 univariate substitution table"
char *_unrrdu_substInfoL =
(INFO
 " (itself represented as a nrrd). The substitution table "
 "has to be a 2 by N table containing a list of pairs aka. "
 "substitution rules.");

int
unrrdu_substMain(int argc, char **argv, char *me, hestParm *hparm) {
  hestOpt *opt = NULL;
  char *out, *err;
  int pret;
  Nrrd *nin, *nsubst, *nout;
  airArray *mop;

  hestOptAdd(&opt, "s", "subst", airTypeOther, 1, 1, &nsubst, NULL,
	     "substition table to map input nrrd through",
	     NULL, NULL, nrrdHestNrrd);
  OPT_ADD_NIN(nin, "input nrrd");
  OPT_ADD_NOUT(out, "output nrrd");

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

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

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

  if (nrrdApply1DSubstitution(nout, nin, nsubst)) {
    airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
    fprintf(stderr, "%s: trouble applying SUBST:\n%s", me, err);
    airMopError(mop);
    return 1;
  }

  SAVE(out, nout, NULL);

  airMopOkay(mop);
  return 0;
}

UNRRDU_CMD(subst, INFO);

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/GNUmakefile,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** GNUmakefile	7 Jan 2004 15:34:31 -0000	1.20
--- GNUmakefile	26 Feb 2004 20:59:45 -0000	1.21
***************
*** 56,60 ****
  	unquantize.o block.o unblock.o project.o swap.o join.o dhisto.o \
  	jhisto.o dice.o heq.o histax.o gamma.o make.o 1op.o 2op.o 3op.o \
! 	lut.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
--- 56,60 ----
  	unquantize.o block.o unblock.o project.o swap.o join.o dhisto.o \
  	jhisto.o dice.o heq.o histax.o gamma.o make.o 1op.o 2op.o 3op.o \
! 	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

Index: unrrdu.h
===================================================================
RCS file: /cvsroot/teem/teem/src/unrrdu/unrrdu.h,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** unrrdu.h	19 Feb 2004 03:44:06 -0000	1.25
--- unrrdu.h	26 Feb 2004 20:59:45 -0000	1.26
***************
*** 129,132 ****
--- 129,133 ----
  F(3op) \
  F(lut) \
+ F(subst) \
  F(rmap) \
  F(imap) \

[Teem-commit] teem/src/nrrd apply1D.c,1.20,1.21 nrrd.h,1.133,1.134

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26791/nrrd

Modified Files:
	apply1D.c nrrd.h 
Log Message:
added nrrdApply1DSubstitution and unu subst ... waiting for TEAT approval

Index: apply1D.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/apply1D.c,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** apply1D.c	7 Jan 2004 15:34:30 -0000	1.20
--- apply1D.c	26 Feb 2004 20:59:45 -0000	1.21
***************
*** 855,856 ****
--- 855,922 ----
    return 0;
  }
+ 
+ /*
+ ******** nrrdApply1DSubstitution
+ **
+ ** A "subst" is a substitution table, i.e. a list of pairs that describes
+ ** what values should be substituted with what (substitution rules).
+ ** The output is a copy of the input with values substituted using this table.
+ */
+ int
+ nrrdApply1DSubstitution(Nrrd *nout, const Nrrd *nin, const Nrrd *nsubst)
+ {
+   char me[]="nrrdApply1DSubstitution", err[AIR_STRLEN_MED];
+   double (*lup)(const void *, size_t);
+   double (*slup)(const void *, size_t);
+   double (*ins)(void *, size_t, double);
+   double val, sval;
+   size_t ii, num;
+   int jj, asize0, asize1;
+   int changed;
+ 
+   if (!(nout && nsubst && nin)) {
+     sprintf(err, "%s: got NULL pointer", me);
+     biffAdd(NRRD, err); return 1;
+   }
+   if (nrrdTypeBlock == nin->type || nrrdTypeBlock == nsubst->type) {
+     sprintf(err, "%s: input or substitution type is %s, need scalar",
+ 	    me, airEnumStr(nrrdType, nrrdTypeBlock));
+     biffAdd(NRRD, err); return 1;
+   }
+   if (2 != nsubst->dim) {
+     sprintf(err, "%s: substitution table hasize to be 2 dimensional, not %d",
+ 	    me, nsubst->dim);
+     biffAdd(NRRD, err); return 1;
+   }
+   nrrdAxisInfoGet(nsubst, nrrdAxisInfoSize, &asize0, &asize1);
+   if (2 != asize0) {
+     sprintf(err, "%s: substitution table hasize to be 2xN, not %dxN",
+ 	    me, asize0);
+     biffAdd(NRRD, err); return 1;
+   }
+   if (nout != nin) {
+     if (nrrdCopy(nout, nin)) {
+       sprintf(err, "%s: couldn't initialize by copy to output", me);
+       biffAdd(NRRD, err); return 1;
+     }
+   }
+   lup = nrrdDLookup[nout->type];
+   slup = nrrdDLookup[nsubst->type];
+   ins = nrrdDInsert[nout->type];
+   num = nrrdElementNumber(nout);
+   for (ii=0; ii<num; ii++) {
+     val = lup(nout->data, ii);
+     changed = AIR_FALSE;
+     for (jj=0; jj<asize1; jj++) {
+       sval = slup(nsubst->data, jj*2);
+       if (val == sval) {
+ 	val = slup(nsubst->data, jj*2+1);
+ 	changed = AIR_TRUE;
+       }
+     }
+     if (changed) {
+       ins(nout->data, ii, val);
+     }
+   }
+   return 0;
+ }

Index: nrrd.h
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/nrrd.h,v
retrieving revision 1.133
retrieving revision 1.134
diff -C2 -d -r1.133 -r1.134
*** nrrd.h	14 Feb 2004 19:14:31 -0000	1.133
--- nrrd.h	26 Feb 2004 20:59:45 -0000	1.134
***************
*** 716,719 ****
--- 716,721 ----
  				 const Nrrd *nmap, const Nrrd *nacl,
  				 int typeOut, int rescale);
+ TEEM_API int nrrdApply1DSubstitution(Nrrd *nout,
+ 				     const Nrrd *nin, const Nrrd *nsubst);
  
  /******** sampling, slicing, cropping */

[Teem-commit] teem/src/ten tendGrads.c,NONE,1.1

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29162

Added Files:
	tendGrads.c 
Log Message:
started added tend grads stuff

--- NEW FILE: tendGrads.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 "ten.h"
#include "privateTen.h"

#define INFO "Calculate gradient directions for DWI acquisition"
char *_tend_gradsInfoL =
  (INFO
   ", based on a simulation of anti-podal point pairs repelling each other "
   "on the unit sphere surface. ");

int
tend_gradsMain(int argc, char **argv, char *me, hestParm *hparm) {
  int pret;
  hestOpt *hopt = NULL;
  char *perr, *err;
  airArray *mop;

  Nrrd *ngrad, *nout;
  char *outS;

  hestOptAdd(&hopt, "i", "grads", airTypeOther, 1, 1, &ngrad, NULL,
	     "array of gradient directions", NULL, NULL, nrrdHestNrrd);
  hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
	     "output B matrix");

  mop = airMopNew();
  airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
  USAGE(_tend_gradsInfoL);
  PARSE();
  airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
  nout = nrrdNew();
  airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);

  
  if (nrrdSave(outS, nout, NULL)) {
    airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
    fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
    airMopError(mop); return 1;
  }

  airMopOkay(mop);
  return 0;
}
unrrduCmd tend_gradsCmd = { "grads", INFO, tend_gradsMain };

[Teem-commit] teem/src/ten GNUmakefile,1.36,1.37 glyph.c,1.33,1.34 ten.h,1.75,1.76 tendGlyph.c,1.24,1.25

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28557

Modified Files:
	GNUmakefile glyph.c ten.h tendGlyph.c 
Log Message:
added sliceBias to handling of slice gray levels, started added tend grads stuff

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/GNUmakefile,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** GNUmakefile	7 Jan 2004 15:34:31 -0000	1.36
--- GNUmakefile	26 Feb 2004 18:42:23 -0000	1.37
***************
*** 49,53 ****
  $(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o miscTen.o mod.o \
  	tenGage.o fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o \
! 	tendFlotsam.o tendAnplot.o tendAnvol.o tendEval.o \
  	tendEvec.o tendSten.o tendExpand.o tendEvq.o tendPoint.o \
  	tendAnhist.o tendMake.o tendSatin.o tendShrink.o tendGlyph.o \
--- 49,53 ----
  $(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o miscTen.o mod.o \
  	tenGage.o fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o \
! 	tendFlotsam.o tendGrads.o tendAnplot.o tendAnvol.o tendEval.o \
  	tendEvec.o tendSten.o tendExpand.o tendEvq.o tendPoint.o \
  	tendAnhist.o tendMake.o tendSatin.o tendShrink.o tendGlyph.o \

Index: glyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/glyph.c,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** glyph.c	19 Feb 2004 06:45:13 -0000	1.33
--- glyph.c	26 Feb 2004 18:42:23 -0000	1.34
***************
*** 52,55 ****
--- 52,56 ----
      parm->sliceAnisoType = tenAnisoUnknown;
      parm->sliceOffset = 0.0;
+     parm->sliceBias = 0.05;
      parm->sliceGamma = 1.0;
    }
***************
*** 284,290 ****
  	  continue;
  	sliceGray = aniso[parm->sliceAnisoType];
! 	/* HEY: look, a visualization parameter (0.03) that is not
! 	   exposed anywhere in an API, just super ... */
! 	sliceGray = AIR_AFFINE(0, sliceGray, 1, 0.03, 1);
        }
        if (parm->sliceGamma > 0) {
--- 285,289 ----
  	  continue;
  	sliceGray = aniso[parm->sliceAnisoType];
! 	sliceGray = AIR_AFFINE(0, sliceGray, 1, parm->sliceBias, 1);
        }
        if (parm->sliceGamma > 0) {

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.75
retrieving revision 1.76
diff -C2 -d -r1.75 -r1.76
*** ten.h	23 Feb 2004 06:03:13 -0000	1.75
--- ten.h	26 Feb 2004 18:42:23 -0000	1.76
***************
*** 119,126 ****
       with glyphs, these are thresholded by confThresh and maskThresh
       (but not anisoThresh).  Things can be lightened up with a
!      sliceGamma > 1.  The squares will be at their corresponding
       sample locations, but offset by sliceOffset */
    int doSlice, sliceAxis, slicePos, sliceAnisoType;
!   float sliceOffset, sliceGamma;
  } tenGlyphParm;
  
--- 119,127 ----
       with glyphs, these are thresholded by confThresh and maskThresh
       (but not anisoThresh).  Things can be lightened up with a
!      sliceGamma > 1, after the slice's gray values have been mapped from
!      [0,1] to [sliceBias,1]. The squares will be at their corresponding
       sample locations, but offset by sliceOffset */
    int doSlice, sliceAxis, slicePos, sliceAnisoType;
!   float sliceOffset, sliceBias, sliceGamma;
  } tenGlyphParm;
  
***************
*** 367,370 ****
--- 368,386 ----
  } tenEMBimodalParm;
  
+ /*
+ ******** struct tenGradientParm
+ **
+ ** all parameters for repulsion-based generation of gradient directions
+ */
+ typedef struct {
+   double mass, 
+     charge,
+     drag, 
+     dt,
+     minVelocity,
+     jitter; 
+   int snap, single, minIteration, maxIteration;
+ } tenGradientParm;
+ 
  /* defaultsTen.c */
  TEEM_API const char *tenBiffKey;
***************
*** 378,381 ****
--- 394,399 ----
  TEEM_API double tenDefFiberWPunct;
  
+ /* grads.c */
+ 
  /* enumsTen.c */
  TEEM_API airEnum *tenAniso;
***************
*** 401,405 ****
  TEEM_API int tenShrink(Nrrd *tseven, Nrrd *nconf, Nrrd *tnine);
  TEEM_API int tenEigensolve(float eval[3], float evec[9], float ten[7]);
! TEEM_API void tenMakeOne(float ten[7], float conf, float eval[3], float evec[9]);
  TEEM_API int tenMake(Nrrd *nout, Nrrd *nconf, Nrrd *neval, Nrrd *nevec);
  TEEM_API int tenSlice(Nrrd *nout, Nrrd *nten, int axis, int pos, int dim);
--- 419,424 ----
  TEEM_API int tenShrink(Nrrd *tseven, Nrrd *nconf, Nrrd *tnine);
  TEEM_API int tenEigensolve(float eval[3], float evec[9], float ten[7]);
! TEEM_API void tenMakeOne(float ten[7],
! 			 float conf, float eval[3], float evec[9]);
  TEEM_API int tenMake(Nrrd *nout, Nrrd *nconf, Nrrd *neval, Nrrd *nevec);
  TEEM_API int tenSlice(Nrrd *nout, Nrrd *nten, int axis, int pos, int dim);
***************
*** 460,464 ****
  
  /* epireg.c */
! TEEM_API int tenEpiRegister3D(Nrrd **nout, Nrrd **ndwi, int dwiLen, Nrrd *ngrad,
  			      int reference,
  			      float bwX, float bwY, float fitFrac, float DWthr,
--- 479,484 ----
  
  /* epireg.c */
! TEEM_API int tenEpiRegister3D(Nrrd **nout, Nrrd **ndwi,
! 			      int dwiLen, Nrrd *ngrad,
  			      int reference,
  			      float bwX, float bwY, float fitFrac, float DWthr,
***************
*** 496,499 ****
--- 516,520 ----
  /* removed from below (superseded by estim): F(calc) \ */
  #define TEND_MAP(F) \
+ F(grads) \
  F(epireg) \
  F(bmat) \

Index: tendGlyph.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tendGlyph.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** tendGlyph.c	19 Feb 2004 03:51:31 -0000	1.24
--- tendGlyph.c	26 Feb 2004 18:42:23 -0000	1.25
***************
*** 163,166 ****
--- 163,169 ----
  	     &(gparm->sliceGamma), "1.7",
  	     "Gamma to apply to values on slice.");
+   hestOptAdd(&hopt, "sb", "slice bias", airTypeFloat, 1, 1, 
+ 	     &(gparm->sliceBias), "0.05",
+ 	     "amount by which to bump up slice gray values prior to gamma.");
  
    /* camera */

[Teem-commit] teem/src/bin miter.c,1.24,1.25

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28440

Modified Files:
	miter.c 
Log Message:
fixed bug in handling of volume sizes

Index: miter.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/miter.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** miter.c	26 Feb 2004 06:45:23 -0000	1.24
--- miter.c	26 Feb 2004 18:41:51 -0000	1.25
***************
*** 35,42 ****
    miteUser *muu;
    char *me, *errS, *outS, *shadeStr;
!   int renorm;
    int E, Ecode;
    float ads[3];
    double gmc;
  
    me = argv[0];
--- 35,43 ----
    miteUser *muu;
    char *me, *errS, *outS, *shadeStr;
!   int renorm, baseDim;
    int E, Ecode;
    float ads[3];
    double gmc;
+   Nrrd *nin;
  
    me = argv[0];
***************
*** 119,122 ****
--- 120,138 ----
    airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
  
+   if (muu->nsin) {
+     nin = muu->nsin;
+     baseDim = 0;
+   } else if (muu->nvin) {
+     nin = muu->nvin;
+     baseDim = 1;
+   } else if (muu->ntin) {
+     nin = muu->ntin;
+     baseDim = 1;
+   } else {
+     fprintf(stderr, "%s: didn't get any volumes to render!\n", me);
+     airMopError(mop);
+     return 1;
+   }
+ 
    /* finish processing command-line args */
    muu->rangeInit[miteRangeKa] = ads[0];
***************
*** 140,145 ****
    strncpy(muu->shadeStr, shadeStr, AIR_STRLEN_MED-1);
    muu->shadeStr[AIR_STRLEN_MED-1] = 0;
!   nrrdAxisInfoGet_nva(muu->nsin, nrrdAxisInfoSize, muu->hctx->volSize);
!   nrrdAxisInfoGet_nva(muu->nsin, nrrdAxisInfoSpacing, muu->hctx->volSpacing);
    muu->hctx->user = muu;
    muu->hctx->renderBegin = (hooverRenderBegin_t *)miteRenderBegin;
--- 156,165 ----
    strncpy(muu->shadeStr, shadeStr, AIR_STRLEN_MED-1);
    muu->shadeStr[AIR_STRLEN_MED-1] = 0;
!   muu->hctx->volSize[0] = nin->axis[baseDim+0].size;
!   muu->hctx->volSize[1] = nin->axis[baseDim+1].size;
!   muu->hctx->volSize[2] = nin->axis[baseDim+2].size;
!   muu->hctx->volSpacing[0] = nin->axis[baseDim+0].spacing;
!   muu->hctx->volSpacing[1] = nin->axis[baseDim+1].spacing;
!   muu->hctx->volSpacing[2] = nin->axis[baseDim+2].spacing;
    muu->hctx->user = muu;
    muu->hctx->renderBegin = (hooverRenderBegin_t *)miteRenderBegin;

[Teem-commit] teem/src/mite txf.c,1.14,1.15

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

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28315

Modified Files:
	txf.c 
Log Message:
typo in error message

Index: txf.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/txf.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** txf.c	26 Feb 2004 06:26:10 -0000	1.14
--- txf.c	26 Feb 2004 18:41:14 -0000	1.15
***************
*** 103,107 ****
        isp->item = airEnumVal(isp->kind->enm, qstr);
        if (-1 == isp->item) {
! 	sprintf(err, "%s: couldn't parse \"%s\" as a %s varable",
  		me, qstr, isp->kind->name);
  	biffAdd(MITE, err); airMopError(mop); return 1;
--- 103,107 ----
        isp->item = airEnumVal(isp->kind->enm, qstr);
        if (-1 == isp->item) {
! 	sprintf(err, "%s: couldn't parse \"%s\" as a %s variable",
  		me, qstr, isp->kind->name);
  	biffAdd(MITE, err); airMopError(mop); return 1;

[Teem-commit] teem/src/bin miter.c,1.23,1.24

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16530/bin

Modified Files:
	miter.c 
Log Message:
fixed stupid warning message about "cant use 1 threads; only using 1"

Index: miter.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/miter.c,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** miter.c	26 Feb 2004 06:26:49 -0000	1.23
--- miter.c	26 Feb 2004 06:45:23 -0000	1.24
***************
*** 151,155 ****
    muu->hctx->renderEnd = (hooverRenderEnd_t *)miteRenderEnd;
  
!   if (!airThreadCapable) {
      fprintf(stderr, "%s: This teem not compiled with "
  	    "multi-threading support.\n", me);
--- 151,155 ----
    muu->hctx->renderEnd = (hooverRenderEnd_t *)miteRenderEnd;
  
!   if (!airThreadCapable && 1 != muu->hctx->numThreads) {
      fprintf(stderr, "%s: This teem not compiled with "
  	    "multi-threading support.\n", me);

[Teem-commit] teem/src/mite shade.c,NONE,1.1 kindnot.c,NONE,1.1

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

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15761

Added Files:
	shade.c kindnot.c 
Log Message:
new to mite

--- NEW FILE: shade.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 "mite.h"
#include "privateMite.h"

miteShadeSpec *
miteShadeSpecNew(void) {
  miteShadeSpec *shpec;

  shpec = (miteShadeSpec *)calloc(1, sizeof(miteShadeSpec));
  if (shpec) {
    shpec->method = miteShadeMethodUnknown;
    shpec->vec0 = gageItemSpecNew();
    shpec->vec1 = gageItemSpecNew();
    shpec->scl0 = gageItemSpecNew();
    shpec->scl1 = gageItemSpecNew();
    if (!( shpec->vec0 && shpec->vec1 && 
	   shpec->scl0 && shpec->scl1 )) {
      return NULL;
    }
  }
  return shpec;
}

miteShadeSpec *
miteShadeSpecNix(miteShadeSpec *shpec) {

  if (shpec) {
    shpec->vec0 = gageItemSpecNix(shpec->vec0);
    shpec->vec1 = gageItemSpecNix(shpec->vec1);
    shpec->scl0 = gageItemSpecNix(shpec->scl0);
    shpec->scl1 = gageItemSpecNix(shpec->scl1);
    AIR_FREE(shpec);
  }
  return NULL;
}

/*
******** miteShadeSpecParse
**
** set up a miteShadeSpec based on a string.  Valid forms are:
**
**   none
**   phong:<vector>
**   litten:<vector>,<vector>,<scalar>,<scalar>
**
** where <vector> and <scalar> are specifications of 3-vector and scalar
** parsable by miteVariableParse
*/
int
miteShadeSpecParse(miteShadeSpec *shpec, char *shadeStr) {
  char me[]="miteShadeSpecParse", err[AIR_STRLEN_MED],
    *buff, *qstr, *tok, *state;
  airArray *mop;
  int ansLength;

  mop = airMopNew();
  if (!( shpec && airStrlen(shadeStr) )) {
    sprintf(err, "%s: got NULL pointer and/or empty string", me);
    biffAdd(MITE, err); airMopError(mop); return 1;
  }
  buff = airToLower(airStrdup(shadeStr));
  if (!buff) {
    sprintf(err, "%s: couldn't strdup shading spec", me);
    biffAdd(MITE, err); airMopError(mop); return 1;
  }
  airMopAdd(mop, buff, airFree, airMopAlways);
  shpec->method = miteShadeMethodUnknown;
  if (!strcmp("none", buff)) {
    shpec->method = miteShadeMethodNone;
  } else if (buff == strstr(buff, "phong:")) {
    shpec->method = miteShadeMethodPhong;
    qstr = buff + strlen("phong:");
    if (miteVariableParse(shpec->vec0, qstr)) {
      sprintf(err, "%s: couldn't parse \"%s\" as shading vector", me, qstr);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    ansLength = shpec->vec0->kind->table[shpec->vec0->item].answerLength;
    if (3 != ansLength) {
      sprintf(err, "%s: \"%s\" isn't a vector (answer length is %d, not 3)",
	      me, qstr, ansLength);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    shpec->method = miteShadeMethodPhong;
  } else if (buff == strstr(buff, "litten:")) {
    qstr = buff + strlen("litten:");
    /* ---- first vector */
    tok = airStrtok(qstr, ",", &state);
    if (miteVariableParse(shpec->vec0, tok)) {
      sprintf(err, "%s: couldn't parse \"%s\" as first lit-tensor vector",
	      me, tok);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    ansLength = shpec->vec0->kind->table[shpec->vec0->item].answerLength;
    if (3 != ansLength) {
      sprintf(err, "%s: \"%s\" isn't a vector (answer length is %d, not 3)",
	      me, qstr, ansLength);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    /* ---- second vector */
    tok = airStrtok(qstr, ",", &state);
    if (miteVariableParse(shpec->vec1, tok)) {
      sprintf(err, "%s: couldn't parse \"%s\" as second lit-tensor vector",
	      me, tok);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    ansLength = shpec->vec1->kind->table[shpec->vec1->item].answerLength;
    if (3 != ansLength) {
      sprintf(err, "%s: \"%s\" isn't a vector (answer length is %d, not 3)",
	      me, qstr, ansLength);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    /* ---- first scalar */
    tok = airStrtok(qstr, ",", &state);
    if (miteVariableParse(shpec->scl0, tok)) {
      sprintf(err, "%s: couldn't parse \"%s\" as first lit-tensor scalar",
	      me, tok);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    ansLength = shpec->scl0->kind->table[shpec->scl0->item].answerLength;
    if (1 != ansLength) {
      sprintf(err, "%s: \"%s\" isn't a scalar (answer length is %d, not 1)",
	      me, qstr, ansLength);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    /* ---- second scalar */
    tok = airStrtok(qstr, ",", &state);
    if (miteVariableParse(shpec->scl1, tok)) {
      sprintf(err, "%s: couldn't parse \"%s\" as second lit-tensor scalar",
	      me, tok);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    ansLength = shpec->scl1->kind->table[shpec->scl1->item].answerLength;
    if (1 != ansLength) {
      sprintf(err, "%s: \"%s\" isn't a scalar (answer length is %d, not 1)",
	      me, qstr, ansLength);
      biffAdd(MITE, err); airMopError(mop); return 1;
    }
    shpec->method = miteShadeMethodLitTen;
  } else {
    sprintf(err, "%s: shading specification \"%s\" not understood",
	    me, shadeStr);
    biffAdd(MITE, err); airMopError(mop); return 1;
  }
  airMopOkay(mop);
  return 0;
}

void
miteShadeSpecPrint(char *buff, const miteShadeSpec *shpec) {
  char me[]="miteShadeSpecPrint", var[4][AIR_STRLEN_MED];

  if (buff && shpec) {
    switch(shpec->method) {
    case miteShadeMethodNone:
      sprintf(buff, "none");
      break;
    case miteShadeMethodPhong:
      miteVariablePrint(var[0], shpec->vec0);
      sprintf(buff, "phong:%s", var[0]);
      break;
    case miteShadeMethodLitTen:
      miteVariablePrint(var[0], shpec->vec0);
      miteVariablePrint(var[1], shpec->vec1);
      miteVariablePrint(var[2], shpec->scl0);
      miteVariablePrint(var[3], shpec->scl1);
      sprintf(buff, "litten:%s,%s,%s,%s", var[0], var[1], var[2], var[3]);
      break;
    default:
      sprintf(buff, "%s: unknown shade method!", me);
      break;
    }
  }
  return;
}

void
miteShadeSpecQueryAdd(gageQuery queryScl, 
		      gageQuery queryVec, 
		      gageQuery queryTen, miteShadeSpec *shpec) {
  if (shpec) {
    switch(shpec->method) {
    case miteShadeMethodNone:
      /* no queries to add */
      break;
    case miteShadeMethodPhong:
      miteQueryAdd(queryScl, queryVec, queryTen, shpec->vec0);
      break;
    case miteShadeMethodLitTen:
      miteQueryAdd(queryScl, queryVec, queryTen, shpec->vec0);
      miteQueryAdd(queryScl, queryVec, queryTen, shpec->vec1);
      miteQueryAdd(queryScl, queryVec, queryTen, shpec->scl0);
      miteQueryAdd(queryScl, queryVec, queryTen, shpec->scl1);
      break;
    default:
      break;
    }
  }
  return;
}


--- NEW FILE: kindnot.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 "mite.h"
#include "privateMite.h"

char
_miteValStr[][AIR_STRLEN_SMALL] = {
  "(unknown miteVal)",
  "Xw",
  "Xi",
  "Yw",
  "Yi",
  "Zw",
  "Zi",
  "Tw",
  "Ti",
  "NdotV",
  "NdotL",
  "GTdotV",
  "VrefN",
  "VdefT",
  "VdefTdotV"
};

int
_miteValVal[] = {
  miteValUnknown,
  miteValXw,
  miteValXi,
  miteValYw,
  miteValYi,
  miteValZw,
  miteValZi,
  miteValTw,
  miteValTi,
  miteValNdotV,
  miteValNdotL,
  miteValGTdotV,
  miteValVrefN,
  miteValVdefT,
  miteValVdefTdotV
};

char
_miteValStrEqv[][AIR_STRLEN_SMALL] = {
  "xw",
  "xi",
  "yw",
  "yi",
  "zw",
  "zi",
  "tw",
  "ti",
  "ndotv", "vdotn",
  "ndotl", "ldotn",
  "gtdotv",
  "vrefn",
  "vdeft",
  "vdeftdotv"
  ""
};

int
_miteValValEqv[] = {
  miteValXw,
  miteValXi,
  miteValYw,
  miteValYi,
  miteValZw,
  miteValZi,
  miteValTw,
  miteValTi,
  miteValNdotV, miteValNdotV,
  miteValNdotL, miteValNdotL,
  miteValGTdotV,
  miteValVrefN,
  miteValVdefT,
  miteValVdefTdotV
};

airEnum
_miteVal = {
  "miteVal",
  MITE_VAL_ITEM_MAX+1,
  _miteValStr, _miteValVal,
  NULL,
  _miteValStrEqv, _miteValValEqv,
  AIR_FALSE
};
airEnum *
miteVal = &_miteVal;

/*
** again, this is not a true gageKind- mainly because these items
** depend on items in different gageKinds (scalar and vector).  So,
** the prerequisites here are all blank.  Go look in _miteQueryAdd()
** to see these items' true prereqs
*/
gageItemEntry
_miteValTable[MITE_VAL_ITEM_MAX+1] = {
  /* enum value        len,deriv,  prereqs,                                       parent item, index*/
  {miteValXw,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValXi,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValYw,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValYi,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValZw,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValZi,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValTw,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValTi,            1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValNdotV,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValNdotL,         1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValGTdotV,        1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValVrefN,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValVdefT,         3,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
  {miteValVdefTdotV,     1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1}
};


gageKind
_miteValGageKind = {
  "mite",
  &_miteVal,
  -1,
  -1,
  MITE_VAL_ITEM_MAX,
  _miteValTable,
  NULL,
  NULL,
  NULL
};

gageKind *
miteValGageKind = &_miteValGageKind;

[Teem-commit] teem/src GNUmakefile,1.51,1.52

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

Update of /cvsroot/teem/teem/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13602

Modified Files:
	GNUmakefile 
Log Message:
begin valgrind debugging of new miter: bigger, better, stronger, slower

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/GNUmakefile,v
retrieving revision 1.51
retrieving revision 1.52
diff -C2 -d -r1.51 -r1.52
*** GNUmakefile	19 Feb 2004 03:57:52 -0000	1.51
--- GNUmakefile	26 Feb 2004 06:27:32 -0000	1.52
***************
*** 96,105 ****
  ## {R}NUM/LIBS: used for craziness below
  ##
! #LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten mite
! #NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E   F
! #RNUMS = F   E    D    C    B    A    9    8    7    6    5    4     3    2    1   0
! LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten
! NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E  
! RNUMS = F   E    D    C    B    A    9    8    7    6    5    4     3    2    1  
  NUM/LIBS = $(join $(NUMS),$(LIBS:%=/%))
  RNUM/LIBS = $(join $(RNUMS),$(LIBS:%=/%))
--- 96,105 ----
  ## {R}NUM/LIBS: used for craziness below
  ##
! LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten mite
! NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E   F
! RNUMS = F   E    D    C    B    A    9    8    7    6    5    4     3    2    1   0
! #LIBS = air hest biff nrrd ell unrrdu dye moss gage bane limn hoover alan echo ten
! #NUMS =  0   1    2    3    4    5    6    7    8    9    A    B     C    D    E  
! #RNUMS = F   E    D    C    B    A    9    8    7    6    5    4     3    2    1  
  NUM/LIBS = $(join $(NUMS),$(LIBS:%=/%))
  RNUM/LIBS = $(join $(RNUMS),$(LIBS:%=/%))

[Teem-commit] teem/src/bin GNUmakefile,1.30,1.31 miter.c,1.22,1.23

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

Update of /cvsroot/teem/teem/src/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13475

Modified Files:
	GNUmakefile miter.c 
Log Message:
begin valgrind debugging of new miter: bigger, better, stronger, slower

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/GNUmakefile,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** GNUmakefile	19 Feb 2004 03:57:52 -0000	1.30
--- GNUmakefile	26 Feb 2004 06:26:49 -0000	1.31
***************
*** 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 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 ungantry ilk tend spots
  
  ## _binD(bins): list of development locations for given bins

Index: miter.c
===================================================================
RCS file: /cvsroot/teem/teem/src/bin/miter.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** miter.c	13 Feb 2004 23:01:12 -0000	1.22
--- miter.c	26 Feb 2004 06:26:49 -0000	1.23
***************
*** 34,38 ****
    hestParm *hparm=NULL;
    miteUser *muu;
!   char *me, *errS, *outS;
    int renorm;
    int E, Ecode;
--- 34,38 ----
    hestParm *hparm=NULL;
    miteUser *muu;
!   char *me, *errS, *outS, *shadeStr;
    int renorm;
    int E, Ecode;
***************
*** 48,53 ****
    
    hparm->respFileEnable = AIR_TRUE;
!   hestOptAdd(&hopt, "i", "nsin", airTypeOther, 1, 1, &(muu->nsin), NULL,
  	     "input scalar volume to render", NULL, NULL, nrrdHestNrrd);
    hestOptAdd(&hopt, "txf", "nin", airTypeOther, 1, -1, &(muu->ntxf), NULL,
  	     "one or more transfer functions",
--- 48,57 ----
    
    hparm->respFileEnable = AIR_TRUE;
!   hestOptAdd(&hopt, "i", "nsin", airTypeOther, 1, 1, &(muu->nsin), "",
  	     "input scalar volume to render", NULL, NULL, nrrdHestNrrd);
+   hestOptAdd(&hopt, "vi", "nvin", airTypeOther, 1, 1, &(muu->nvin), "",
+ 	     "input vector volume to render", NULL, NULL, nrrdHestNrrd);
+   hestOptAdd(&hopt, "ti", "ntin", airTypeOther, 1, 1, &(muu->ntin), "",
+ 	     "input tensor volume to render", NULL, NULL, nrrdHestNrrd);
    hestOptAdd(&hopt, "txf", "nin", airTypeOther, 1, -1, &(muu->ntxf), NULL,
  	     "one or more transfer functions",
***************
*** 79,82 ****
--- 83,88 ----
  	     "cubicdd:1,0",  "second derivative kernel",
  	     NULL, NULL, nrrdHestKernelSpec);
+   hestOptAdd(&hopt, "ss", "shading spec", airTypeString, 1, 1, &shadeStr,
+ 	     "phong:gage(scalar:n)", "how to do shading");
    hestOptAdd(&hopt, "ns", "normal side", airTypeInt, 1, 1, &(muu->normalSide),
  	     "1", "how to interpret gradients as normals:\n "
***************
*** 90,97 ****
  	     "\"Accurate\" kernels don't need this; doing it always "
  	     "makes things go slower");
-   hestOptAdd(&hopt, "sum", NULL, airTypeBool, 0, 0, &(muu->justSum), NULL,
- 	     "Ignore opacity and composite simply by summing");
-   hestOptAdd(&hopt, "nolight", NULL, airTypeBool, 0, 0, &(muu->noDirLight),
- 	     NULL, "Ignore directional lights, use ambient only");
    hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc, "0.0",
  	     "For curvature-based transfer functions, set curvature to "
--- 96,99 ----
***************
*** 102,106 ****
  	     "0.01", "\"reference\" step size (world space) for doing "
  	     "opacity correction in compositing");
!   hestOptAdd(&hopt, "n1", "near1", airTypeDouble, 1, 1, &(muu->near1),
  	     "0.99", "opacity close enough to 1.0 to terminate ray");
    hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1,
--- 104,108 ----
  	     "0.01", "\"reference\" step size (world space) for doing "
  	     "opacity correction in compositing");
!   hestOptAdd(&hopt, "n1", "near1", airTypeDouble, 1, 1, &(muu->opacNear1),
  	     "0.99", "opacity close enough to 1.0 to terminate ray");
    hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1,
***************
*** 136,140 ****
      return 1;
    }
! 
    nrrdAxisInfoGet_nva(muu->nsin, nrrdAxisInfoSize, muu->hctx->volSize);
    nrrdAxisInfoGet_nva(muu->nsin, nrrdAxisInfoSpacing, muu->hctx->volSpacing);
--- 138,143 ----
      return 1;
    }
!   strncpy(muu->shadeStr, shadeStr, AIR_STRLEN_MED-1);
!   muu->shadeStr[AIR_STRLEN_MED-1] = 0;
    nrrdAxisInfoGet_nva(muu->nsin, nrrdAxisInfoSize, muu->hctx->volSize);
    nrrdAxisInfoGet_nva(muu->nsin, nrrdAxisInfoSpacing, muu->hctx->volSpacing);

[Teem-commit] teem/src/mite GNUmakefile,1.15,1.16 mite.h,1.26,1.27 privateMite.h,1.4,1.5 ray.c,1.17,1.18 renderMite.c,1.10,1.11 thread.c,1.9,1.10 txf.c,1.13,1.14 user.c,1.14,1.15

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

Update of /cvsroot/teem/teem/src/mite
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13401

Modified Files:
	GNUmakefile mite.h privateMite.h ray.c renderMite.c thread.c 
	txf.c user.c 
Log Message:
begin valgrind debugging of new miter: bigger, better, stronger, slower

Index: GNUmakefile
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/GNUmakefile,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** GNUmakefile	13 Feb 2004 22:58:40 -0000	1.15
--- GNUmakefile	26 Feb 2004 06:26:10 -0000	1.16
***************
*** 47,51 ****
  $(L).PUBLIC_HEADERS = mite.h
  $(L).PRIVATE_HEADERS = privateMite.h
! $(L).OBJS = defaultsMite.o kindnot.o renderMite.o thread.o ray.o txf.o user.o
  ####
  ####
--- 47,52 ----
  $(L).PUBLIC_HEADERS = mite.h
  $(L).PRIVATE_HEADERS = privateMite.h
! $(L).OBJS = defaultsMite.o kindnot.o txf.o shade.o \
!             user.o renderMite.o thread.o ray.o
  ####
  ####

Index: mite.h
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/mite.h,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** mite.h	19 Feb 2004 03:52:47 -0000	1.26
--- mite.h	26 Feb 2004 06:26:10 -0000	1.27
***************
*** 110,127 ****
      *nvin,               /* 3-vector volume being rendered */
      *ntin,               /* tensor volume being rendered */
!     **ntxf,              /* array of nrrds containing transfer functions,
! 			    these are never altered (in contrast to ntxf
! 			    in miteRender) */
      *nout;               /* output image container, for five-channel output
  			    RGBAZ.  We'll nrrdMaybeAlloc all the image data
  			    and put it in here, but we won't nrrdNuke(nout),
! 			    just like we won't nrrdNuke nsin, ntin, or any of
! 			    the ntxf[i] */
    int ntxfNum;           /* allocated and valid length of ntxf[] */
    char shadeStr[AIR_STRLEN_MED];  /* how to do shading */
    /* for each possible element of the txf range, what value should it
!      start at prior to multiplying by the values (if any) learned from
!      the txf.  Mainly needed to store non-unity values for the
!      quantities not covered by a transfer function */
    mite_t rangeInit[MITE_RANGE_NUM]; 
    double refStep,        /* length of "unity" for doing opacity correction */
--- 110,127 ----
      *nvin,               /* 3-vector volume being rendered */
      *ntin,               /* tensor volume being rendered */
!     **ntxf,              /* array of pointers to nrrds containing transfer
! 			    functions, these are never altered (the ntxf
! 			    in miteRender, however, is created and altered
! 			    based on this ntxf) */
      *nout;               /* output image container, for five-channel output
  			    RGBAZ.  We'll nrrdMaybeAlloc all the image data
  			    and put it in here, but we won't nrrdNuke(nout),
! 			    just like we won't nrrdNuke nsin, nvin, ntin, or
! 			    any of the ntxf[i] */
    int ntxfNum;           /* allocated and valid length of ntxf[] */
    char shadeStr[AIR_STRLEN_MED];  /* how to do shading */
    /* for each possible element of the txf range, what value should it
!      start at prior to rendering. Mainly needed to store non-unity values
!      for the quantities not covered by a transfer function */
    mite_t rangeInit[MITE_RANGE_NUM]; 
    double refStep,        /* length of "unity" for doing opacity correction */
***************
*** 144,152 ****
    int normalSide,        /* determines direction of gradient that is used
  			    as normal for shading:
! 			    1: normal points to lower values
                                 (higher values are more "inside"); 
                              0: "two-sided": dot-products are abs()'d
                              -1: normal points to higher values
!                                (lower values more "inside") */
      verbUi, verbVi;      /* pixel coordinate for which to turn on verbosity */
    airArray *umop;        /* for things allocated which are used across
--- 144,155 ----
    int normalSide,        /* determines direction of gradient that is used
  			    as normal for shading:
! 			    1: the standard way: normal points to lower values
                                 (higher values are more "inside"); 
                              0: "two-sided": dot-products are abs()'d
                              -1: normal points to higher values
!                                (lower values more "inside")
! 			    Setting up the values this way allows for idioms
! 			    like "if (muu->normalSide) ...", meaning, if the
! 			    lighting is one-sided */
      verbUi, verbVi;      /* pixel coordinate for which to turn on verbosity */
    airArray *umop;        /* for things allocated which are used across
***************
*** 154,158 ****
    /* output information from last rendering */
    double rendTime,       /* rendering time, in seconds */
!     sampRate;            /* rate (KHz) at which sampler callback was called */
  } miteUser;
  
--- 157,161 ----
    /* output information from last rendering */
    double rendTime,       /* rendering time, in seconds */
!     sampRate;            /* rate (KHz) at which samples were rendered */
  } miteUser;
  
***************
*** 167,172 ****
    miteShadeMethodUnknown,
    miteShadeMethodNone,        /* 1: no direction shading based on anything
! 				 in the miteShadeSpec: just ambient 
! 				 (though still using over operator) */
    miteShadeMethodPhong,       /* 2: what mite has been doing all along */
    miteShadeMethodLitTen,      /* 3: (tensor-based) lit-tensors */
--- 170,177 ----
    miteShadeMethodUnknown,
    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 */
    miteShadeMethodPhong,       /* 2: what mite has been doing all along */
    miteShadeMethodLitTen,      /* 3: (tensor-based) lit-tensors */
***************
*** 184,189 ****
  */
  typedef struct {
!   int shadeMethod;            /* from miteShadeMethod* enum */
!   gageQuerySpec *vec0, *vec1,
      *scl0, *scl1;             /* things to use for shading.  How these are
  				 interpreted is determined by shadeMethod:
--- 189,194 ----
  */
  typedef struct {
!   int method;                 /* from miteShadeMethod* enum */
!   gageItemSpec *vec0, *vec1,
      *scl0, *scl1;             /* things to use for shading.  How these are
  				 interpreted is determined by shadeMethod:
***************
*** 197,201 ****
  **
  ** rendering-parameter-set-specific (but non-thread-specific) state,
! ** used internally by mite
  */
  typedef struct {
--- 202,208 ----
  **
  ** rendering-parameter-set-specific (but non-thread-specific) state,
! ** used internally by mite.  The primary role here is to store information
! ** derived from the miteUser, in a form which is more immediately useful
! ** for rendering.  
  */
  typedef struct {
***************
*** 207,210 ****
--- 214,221 ----
  				 type mite_t */
    int ntxfNum;                /* allocated and valid length of ntxf[] */
+   int sclPvlIdx, vecPvlIdx,
+     tenPvlIdx;                /* indices of the different gageKinds of 
+ 				 volumes in the gageContext's array of
+ 				 gagePerVolumes.  Probably a hack */
    miteShadeSpec *shpec;       /* information based on muu->shadeStr */
    double time0;               /* rendering start time */
***************
*** 228,233 ****
  enum {
    miteStageOpUnknown,
!   miteStageOpAdd,
    miteStageOpMax,
    miteStageOpMultiply,
    miteStageOpLast
--- 239,245 ----
  enum {
    miteStageOpUnknown,
!   miteStageOpMin,
    miteStageOpMax,
+   miteStageOpAdd,
    miteStageOpMultiply,
    miteStageOpLast
***************
*** 238,242 ****
  				   gage or by mite.  This points into the 
  				   answer vector in one of the thread's
! 				   pervolumes */
    int size,                     /* number of entries along this txf axis */
      op,                         /* from miteStageOp* enum.  Note that this
--- 250,256 ----
  				   gage or by mite.  This points into the 
  				   answer vector in one of the thread's
! 				   pervolumes, or into ansMiteVal in the
! 				   miteThread.  It can be either a scalar
! 				   or a vector */
    int size,                     /* number of entries along this txf axis */
      op,                         /* from miteStageOp* enum.  Note that this
***************
*** 244,254 ****
  				   adjusted by this txf (can't add color while
  				   multiplying opacity) */
!     (*qn)(gage_t *);            /* callback for doing vector quantization of
! 				   vector-valued txf domain variables, or
! 				   NULL if this is a scalar variable */
!   double min, max;              /* min, max (copied from nrrd axis) */
    mite_t *data;                 /* pointer to txf data.  If non-NULL, the
! 				   rest of the variables are meaningful */
!   int rangeIdx[MITE_RANGE_NUM], /* indices into miteThread's range */
      rangeNum;                   /* number of range variables set by the txf
  				   == number of pointers in range[] to use */
--- 258,271 ----
  				   adjusted by this txf (can't add color while
  				   multiplying opacity) */
!     (*qn)(gage_t *);            /* if non-NULL: callback for doing vector
! 				   quantization of vector-valued txf domain
! 				   variables */
!   double min, max;              /* quantization range of values which is 
! 				   covered by this axis of the txf; copied
! 				   from corresponding axis of the nrrd */
    mite_t *data;                 /* pointer to txf data.  If non-NULL, the
! 				   following fields are meaningful */
!   int rangeIdx[MITE_RANGE_NUM], /* indices into miteThread's range, so that
! 				   we know which quantities to update */
      rangeNum;                   /* number of range variables set by the txf
  				   == number of pointers in range[] to use */
***************
*** 267,284 ****
  enum {
    miteValUnknown=-1,    /* -1: nobody knows */
!   miteValXw,            /*  0: "Xw", X position, world space (*gage_t) */
!   miteValXi,            /*  1: "Xi", X     "   , index   "   (*gage_t) */
!   miteValYw,            /*  2: "Yw", Y     "   , world   "   (*gage_t) */
!   miteValYi,            /*  3: "Yi", Y     "   , index   "   (*gage_t) */
!   miteValZw,            /*  4: "Zw", Z     "   , world   "   (*gage_t) */
!   miteValZi,            /*  5: "Zi", Z     "   , index   "   (*gage_t) */
!   miteValTw,            /*  6: "Tw", ray position (*gage_t) */
!   miteValTi,            /*  7: "Ti", ray index (ray sample #) (*gage_t) */
    miteValNdotV,         /*  8: "NdotV", surface normal dotted w/ view vector
! 			        (towards eye) (*gage_t) */
    miteValNdotL,         /*  9: "NdotL", surface normal dotted w/ light vector
! 			        (towards the light source) (*gage_t) */
!   miteValGTdotV,        /* 10: "GTdotV", normal curvature in view direction 
! 			        (*gage_t) */
    miteValVrefN,         /* 11: "VrefN", view vector (towards eye) reflected
  			       across surface normal (gage_t[3]) */
--- 284,302 ----
  enum {
    miteValUnknown=-1,    /* -1: nobody knows */
!   miteValXw,            /*  0: "Xw", X position, world space (gage_t[1]) */
!   miteValXi,            /*  1: "Xi", X     "   , index   "   (gage_t[1]) */
!   miteValYw,            /*  2: "Yw", Y     "   , world   "   (gage_t[1]) */
!   miteValYi,            /*  3: "Yi", Y     "   , index   "   (gage_t[1]) */
!   miteValZw,            /*  4: "Zw", Z     "   , world   "   (gage_t[1]) */
!   miteValZi,            /*  5: "Zi", Z     "   , index   "   (gage_t[1]) */
!   miteValTw,            /*  6: "Tw", ray position (gage_t[1]) */
!   miteValTi,            /*  7: "Ti", ray index (ray sample #) (gage_t[1]) */
    miteValNdotV,         /*  8: "NdotV", surface normal dotted w/ view vector
! 			        (towards eye) (gage_t[1]) */
    miteValNdotL,         /*  9: "NdotL", surface normal dotted w/ light vector
! 			        (towards the light source) (gage_t[1]) */
!   miteValGTdotV,        /* 10: "GTdotV", normal curvature in view direction,
! 			        the contraction of the geometry tensor along
! 				the view vector (gage_t[1]) */
    miteValVrefN,         /* 11: "VrefN", view vector (towards eye) reflected
  			       across surface normal (gage_t[3]) */
***************
*** 287,295 ****
    miteValVdefTdotV,     /* 13: "VdefTdotV", VdefT dotted back with V, not the
  			       same as the tensor contraction along V,
! 			       (*gage_t) */
    miteValLast
  };
! #define MITE_VAL_MAX       13
! #define MITE_VAL_TOTAL_ANS_LENGTH   18
  
  /*
--- 305,312 ----
    miteValVdefTdotV,     /* 13: "VdefTdotV", VdefT dotted back with V, not the
  			       same as the tensor contraction along V,
! 			       (gage_t[1]) */
    miteValLast
  };
! #define MITE_VAL_ITEM_MAX  13
  
  /*
***************
*** 300,312 ****
  typedef struct miteThread_t {
    gageContext *gctx;            /* per-thread context */
!   gage_t *ansScl,               /* shortcut to scalar answer vector */
!     *ansVec,                    /* shortcut to vector answer vector */
!     *ansTen,                    /* shortcut to tensor answer vector */
!     *vec0, *vec1, *scl0, *scl1, /* shortcuts vectors/scalars used for 
! 				   shading; explained with miteShadeSpec */
!     ansMiteVal[MITE_VAL_TOTAL_ANS_LENGTH];  /* room for all the miteVal */
!   int verbose,                  /* blah blah blah */
      thrid,                      /* thread ID */
!     ui, vi,                     /* image coords */
      samples;                    /* number of samples handled so far by
  				   this thread */
--- 317,332 ----
  typedef struct miteThread_t {
    gageContext *gctx;            /* per-thread context */
!   gage_t *ansScl,               /* pointer to gageKindScl answer vector */
!     *ansVec,                    /* pointer to gageKindVec answer vector */
!     *ansTen,                    /* pointer to tenGageKind answer vector */
!     *ansMiteVal,                /* room for all the miteVal answers, which
! 				   unlike ans{Scl,Vec,Ten} is allocated by
! 				   mite instead of by gage */
!     *shadeVec0, *shadeVec1, 
!     *shadeScl0, *shadeScl1;     /* pointers into the ans* arrays above,
! 				   used for shading */
!   int verbose,                  /* blah, blah, blah */
      thrid,                      /* thread ID */
!     ui, vi,                     /* image coords of current ray */
      samples;                    /* number of samples handled so far by
  				   this thread */
***************
*** 336,342 ****
  /* txf.c */
  TEEM_API char miteRangeChar[MITE_RANGE_NUM];
! TEEM_API void miteVariablePrint(char *buff, const gageQuerySpec *qsp);
! TEEM_API int miteVariableParse(gageQuerySpec *qsp, const char *label);
  TEEM_API int miteNtxfCheck(const Nrrd *ntxf);
  
  /* user.c */
--- 356,366 ----
  /* txf.c */
  TEEM_API char miteRangeChar[MITE_RANGE_NUM];
! TEEM_API int miteVariableParse(gageItemSpec *isp, const char *label);
! TEEM_API void miteVariablePrint(char *buff, const gageItemSpec *isp);
  TEEM_API int miteNtxfCheck(const Nrrd *ntxf);
+ TEEM_API void miteQueryAdd(gageQuery queryScl, 
+ 			   gageQuery queryVec, 
+ 			   gageQuery queryTen, gageItemSpec *isp);
+ 
  
  /* user.c */
***************
*** 344,355 ****
  TEEM_API miteUser *miteUserNix(miteUser *muu);
  
! /* renderMite.c */
  TEEM_API miteShadeSpec *miteShadeSpecNew();
  TEEM_API miteShadeSpec *miteShadeSpecNix(miteShadeSpec *);
! TEEM_API int miteShadeParse(miteShadeSpec *shpec, char *shadeStr);
  TEEM_API int miteRenderBegin(miteRender **mrrP, miteUser *muu);
  TEEM_API int miteRenderEnd(miteRender *mrr, miteUser *muu);
  
  /* thread.c */
  TEEM_API int miteThreadBegin(miteThread **mttP, miteRender *mrr, miteUser *muu,
  			     int whichThread);
--- 368,387 ----
  TEEM_API miteUser *miteUserNix(miteUser *muu);
  
! /* shade.c */
  TEEM_API miteShadeSpec *miteShadeSpecNew();
  TEEM_API miteShadeSpec *miteShadeSpecNix(miteShadeSpec *);
! TEEM_API int miteShadeSpecParse(miteShadeSpec *shpec, char *shadeStr);
! TEEM_API void miteShadeSpecPrint(char *buff, const miteShadeSpec *shpec);
! TEEM_API void miteShadeSpecQueryAdd(gageQuery queryScl, 
! 				    gageQuery queryVec, 
! 				    gageQuery queryTen, miteShadeSpec *shpec);
! 
! /* renderMite.c */
  TEEM_API int miteRenderBegin(miteRender **mrrP, miteUser *muu);
  TEEM_API int miteRenderEnd(miteRender *mrr, miteUser *muu);
  
  /* thread.c */
+ TEEM_API miteThread *miteThreadNew();
+ TEEM_API miteThread *miteThreadNix(miteThread *mtt);
  TEEM_API int miteThreadBegin(miteThread **mttP, miteRender *mrr, miteUser *muu,
  			     int whichThread);

Index: privateMite.h
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/privateMite.h,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** privateMite.h	13 Feb 2004 22:58:40 -0000	1.4
--- privateMite.h	26 Feb 2004 06:26:10 -0000	1.5
***************
*** 32,38 ****
  
  /* txf.c */
! extern void _miteQuery(unsigned int *queryScl, 
! 		       unsigned int *queryVec, 
! 		       unsigned int *queryTen, gageQuerySpec *qsp);
  extern int _miteNtxfAlphaAdjust(miteRender *mrr, miteUser *muu);
  extern int _miteStageSet(miteThread *mtt, miteRender *mrr);
--- 32,36 ----
  
  /* txf.c */
! extern gage_t *_miteAnswerPointer(miteThread *mtt, gageItemSpec *isp);
  extern int _miteNtxfAlphaAdjust(miteRender *mrr, miteUser *muu);
  extern int _miteStageSet(miteThread *mtt, miteRender *mrr);

Index: ray.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/ray.c,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** ray.c	13 Feb 2004 22:58:40 -0000	1.17
--- ray.c	26 Feb 2004 06:26:10 -0000	1.18
***************
*** 62,71 ****
    ks = mtt->range[miteRangeKs];
    ELL_3V_SCALE(ad, ka, muu->lit->amb);
!   if (miteShadeMethodPhong == mrr->shpec->shadeMethod) {
      if (kd || ks) {
        if (muu->normalSide) {
! 	ELL_3V_SCALE(N, -muu->normalSide, mtt->vec0);
        } else {
! 	ELL_3V_COPY(N, mtt->vec0);
        }
        if (kd) {
--- 62,77 ----
    ks = mtt->range[miteRangeKs];
    ELL_3V_SCALE(ad, ka, muu->lit->amb);
!   switch (mrr->shpec->method) {
!   case miteShadeMethodNone:
!     /* nothing to do */
!     break;
!   case miteShadeMethodPhong:
!     /* this is dicey- we're *writing* to the answer buffer */
      if (kd || ks) {
+       ELL_3V_NORM(mtt->shadeVec0, mtt->shadeVec0, tmp);
        if (muu->normalSide) {
! 	ELL_3V_SCALE(N, -muu->normalSide, mtt->shadeVec0);
        } else {
! 	ELL_3V_COPY(N, mtt->shadeVec0);
        }
        if (kd) {
***************
*** 75,79 ****
  	}
  	if (LdotN > 0) {
! 	  ELL_3V_SCALE_ADD2(ad, 1.0, ad, LdotN*kd, muu->lit->col[0]);
  	}
        }
--- 81,85 ----
  	}
  	if (LdotN > 0) {
! 	  ELL_3V_SCALE_INCR(ad, LdotN*kd, muu->lit->col[0]);
  	}
        }
***************
*** 92,101 ****
        }
      }
!   } else if (miteShadeMethodLitTen == mrr->shpec->shadeMethod) {
! 
!   } else {
      fprintf(stderr, "!%s: PANIC, shadeMethod %d unimplemented\n", 
! 	    me, mrr->shpec->shadeMethod);
      exit(1);
    }
    *R = (E - 1 + ad[0])*col[0] + s[0];
--- 98,110 ----
        }
      }
!     break;
!   case miteShadeMethodLitTen:
!     fprintf(stderr, "!%s: lit-tensor not yet implemented\n", me);
!     break;
!   default:
      fprintf(stderr, "!%s: PANIC, shadeMethod %d unimplemented\n", 
! 	    me, mrr->shpec->method);
      exit(1);
+     break;
    }
    *R = (E - 1 + ad[0])*col[0] + s[0];
***************
*** 149,163 ****
    mtt->ansMiteVal[miteValTw] = rayT;
    mtt->ansMiteVal[miteValTi] = num;
!   mtt->ansMiteVal[miteValNdotV] = -muu->normalSide*ELL_3V_DOT(mtt->V, mtt->vec0);
!   mtt->ansMiteVal[miteValNdotL] = -muu->normalSide*ELL_3V_DOT(mtt->vec0,
! 							      muu->lit->dir[0]);
    if (!muu->normalSide) {
      mtt->ansMiteVal[miteValNdotV] = AIR_ABS(mtt->ansMiteVal[miteValNdotV]);
      mtt->ansMiteVal[miteValNdotL] = AIR_ABS(mtt->ansMiteVal[miteValNdotL]);
    }
    ELL_3MV_MUL(kn, mtt->nPerp, mtt->V);
    ELL_3V_NORM(kn, kn, len);
    ELL_3MV_MUL(knd, mtt->gten, kn);
    mtt->ansMiteVal[miteValGTdotV] = ELL_3V_DOT(knd, kn);
    
    memcpy(mtt->range, muu->rangeInit, MITE_RANGE_NUM*sizeof(mite_t));
--- 158,183 ----
    mtt->ansMiteVal[miteValTw] = rayT;
    mtt->ansMiteVal[miteValTi] = num;
! #if 0
! 
!   what if shading is none?
! 
!   mtt->ansMiteVal[miteValNdotV] =
!     -muu->normalSide*ELL_3V_DOT(mtt->V, mtt->shadeVec0);
!   mtt->ansMiteVal[miteValNdotL] =
!     -muu->normalSide*ELL_3V_DOT(mtt->shadeVec0, muu->lit->dir[0]);
! #endif
    if (!muu->normalSide) {
      mtt->ansMiteVal[miteValNdotV] = AIR_ABS(mtt->ansMiteVal[miteValNdotV]);
      mtt->ansMiteVal[miteValNdotL] = AIR_ABS(mtt->ansMiteVal[miteValNdotL]);
    }
+ 
+ #if 0
+   this is bullshit
+ 
    ELL_3MV_MUL(kn, mtt->nPerp, mtt->V);
    ELL_3V_NORM(kn, kn, len);
    ELL_3MV_MUL(knd, mtt->gten, kn);
    mtt->ansMiteVal[miteValGTdotV] = ELL_3V_DOT(knd, kn);
+ #endif
    
    memcpy(mtt->range, muu->rangeInit, MITE_RANGE_NUM*sizeof(mite_t));
***************
*** 193,199 ****
    A = 1 - mtt->TT;
    if (A) {
!     ELL_4V_SET(imgData + 4*idx, mtt->RR/A, mtt->GG/A, mtt->BB/A, A);
    } else {
!     ELL_4V_SET(imgData + 4*idx, 0, 0, 0, 0);
    }
    return 0;
--- 213,219 ----
    A = 1 - mtt->TT;
    if (A) {
!     ELL_4V_SET(imgData + 5*idx, mtt->RR/A, mtt->GG/A, mtt->BB/A, A);
    } else {
!     ELL_4V_SET(imgData + 5*idx, 0, 0, 0, 0);
    }
    return 0;

Index: renderMite.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/renderMite.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** renderMite.c	13 Feb 2004 22:58:40 -0000	1.10
--- renderMite.c	26 Feb 2004 06:26:10 -0000	1.11
***************
*** 21,56 ****
  #include "privateMite.h"
  
- miteShadeSpec *
- miteShadeSpecNew(void) {
-   miteShadeSpec *shpec;
- 
-   shpec = (miteShadeSpec *)calloc(1, sizeof(miteShadeSpec));
-   if (shpec) {
-     shpec->shadeMethod = miteShadeMethodUnknown;
-     shpec->vec0 = gageQuerySpecNew();
-     shpec->vec1 = gageQuerySpecNew();
-     shpec->scl0 = gageQuerySpecNew();
-     shpec->scl1 = gageQuerySpecNew();
-     if (!( shpec->vec0 && shpec->vec1 && 
- 	   shpec->scl0 && shpec->scl1 )) {
-       return NULL;
-     }
-   }
-   return shpec;
- }
- 
- miteShadeSpec *
- miteShadeSpecNix(miteShadeSpec *shpec) {
- 
-   if (shpec) {
-     shpec->vec0 = gageQuerySpecNix(shpec->vec0);
-     shpec->vec1 = gageQuerySpecNix(shpec->vec1);
-     shpec->scl0 = gageQuerySpecNix(shpec->scl0);
-     shpec->scl1 = gageQuerySpecNix(shpec->scl1);
-     AIR_FREE(shpec);
-   }
-   return NULL;
- }
- 
  miteRender *
  _miteRenderNew(void) {
--- 21,24 ----
***************
*** 64,68 ****
--- 32,41 ----
        return mrr;
      }
+     mrr->ntxf = NULL;
+     mrr->ntxfNum = 0;
      mrr->shpec = miteShadeSpecNew();
+     mrr->sclPvlIdx = -1;
+     mrr->vecPvlIdx = -1;
+     mrr->tenPvlIdx = -1;
      airMopAdd(mrr->rmop, mrr->shpec,
  	      (airMopper)miteShadeSpecNix, airMopAlways);
***************
*** 81,186 ****
  }
  
- int
- miteShadeParse(miteShadeSpec *shpec, char *shadeStr) {
-   char me[]="miteShadeParse", err[AIR_STRLEN_MED], *buff, *qstr, *tok, *state;
-   airArray *mop;
-   int ansLength;
- 
-   mop = airMopNew();
-   if (!( shpec && airStrlen(shadeStr) )) {
-     sprintf(err, "%s: got NULL pointer and/or empty string", me);
-     biffAdd(MITE, err); airMopError(mop); return 1;
-   }
-   buff = airToLower(airStrdup(shadeStr));
-   if (!buff) {
-     sprintf(err, "%s: couldn't strdup shading spec", me);
-     biffAdd(MITE, err); airMopError(mop); return 1;
-   }
-   airMopAdd(mop, buff, airFree, airMopAlways);
-   if (!strcmp("none", buff)) {
-     shpec->shadeMethod = miteShadeMethodNone;
-   } else if (buff == strstr("phong:", buff)) {
-     qstr = buff + strlen("phong:");
-     if (miteVariableParse(shpec->vec0, qstr)) {
-       sprintf(err, "%s: couldn't parse \"%s\" as shading vector", me, qstr);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     ansLength = shpec->vec0->kind->ansLength[shpec->vec0->query];
-     if (3 != ansLength) {
-       sprintf(err, "%s: \"%s\" isn't a vector (answer length is %d, not 3)",
- 	      me, qstr, ansLength);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     fprintf(stderr, "!%s: got phong:%s(%s)\n", me,
- 	    shpec->vec0->kind->name, 
- 	    airEnumStr(shpec->vec0->kind->enm, shpec->vec0->query));
-   } else if (buff == strstr("litten:", buff)) {
-     qstr = buff + strlen("litten:");
-     /* ---- first vector */
-     tok = airStrtok(qstr, ",", &state);
-     if (miteVariableParse(shpec->vec0, tok)) {
-       sprintf(err, "%s: couldn't parse \"%s\" as lit-tensor vector", me, tok);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     ansLength = shpec->vec0->kind->ansLength[shpec->vec0->query];
-     if (3 != ansLength) {
-       sprintf(err, "%s: \"%s\" isn't a vector (answer length is %d, not 3)",
- 	      me, qstr, ansLength);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     /* ---- second vector */
-     tok = airStrtok(qstr, ",", &state);
-     if (miteVariableParse(shpec->vec1, tok)) {
-       sprintf(err, "%s: couldn't parse \"%s\" as lit-tensor vector", me, tok);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     ansLength = shpec->vec1->kind->ansLength[shpec->vec1->query];
-     if (3 != ansLength) {
-       sprintf(err, "%s: \"%s\" isn't a vector (answer length is %d, not 3)",
- 	      me, qstr, ansLength);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     /* ---- first scalar */
-     tok = airStrtok(qstr, ",", &state);
-     if (miteVariableParse(shpec->scl0, tok)) {
-       sprintf(err, "%s: couldn't parse \"%s\" as lit-tensor scalar", me, tok);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     ansLength = shpec->scl0->kind->ansLength[shpec->scl0->query];
-     if (1 != ansLength) {
-       sprintf(err, "%s: \"%s\" isn't a scalar (answer length is %d, not 1)",
- 	      me, qstr, ansLength);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     /* ---- second scalar */
-     tok = airStrtok(qstr, ",", &state);
-     if (miteVariableParse(shpec->scl1, tok)) {
-       sprintf(err, "%s: couldn't parse \"%s\" as lit-tensor scalar", me, tok);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     ansLength = shpec->scl1->kind->ansLength[shpec->scl1->query];
-     if (1 != ansLength) {
-       sprintf(err, "%s: \"%s\" isn't a scalar (answer length is %d, not 1)",
- 	      me, qstr, ansLength);
-       biffAdd(MITE, err); airMopError(mop); return 1;
-     }
-     fprintf(stderr, "!%s: got litten:%s(%s),\n", me,
- 	    shpec->vec0->kind->name, 
- 	    airEnumStr(shpec->vec0->kind->enm, shpec->vec0->query));
-   } else {
-     sprintf(err, "%s: shading specification \"%s\" not understood",
- 	    me, shadeStr);
-     biffAdd(MITE, err); airMopError(mop); return 1;
-   }
-   airMopOkay(mop);
-   return 0;
- }
- 
  int 
  miteRenderBegin(miteRender **mrrP, miteUser *muu) {
    char me[]="miteRenderBegin", err[AIR_STRLEN_MED];
    gagePerVolume *pvl;
!   int E, T, thr, axi;
!   unsigned int queryScl, queryVec, queryTen;
   
    if (!(mrrP && muu)) {
--- 54,64 ----
  }
  
  int 
  miteRenderBegin(miteRender **mrrP, miteUser *muu) {
    char me[]="miteRenderBegin", err[AIR_STRLEN_MED];
    gagePerVolume *pvl;
!   int E, T, thr, axi, pvlIdx;
!   gageQuery queryScl, queryVec, queryTen;
!   gageItemSpec isp;
   
    if (!(mrrP && muu)) {
***************
*** 201,226 ****
    }
  
!   queryScl = 0;
!   queryTen = 0;
    for (T=0; T<muu->ntxfNum; T++) {
!     for (axi=1; axi<=muu->ntxf[T]->dim-1; axi++) {
!       _miteNtxfQuery(&queryScl, &queryVec, &queryTen,
! 		     muu->ntxf[T]->axis[axi]->label);
!   }
!   if (!muu->noDirLight) {
!     query |= 1<<gageSclNormal;
    }
!   /*
!   fprintf(stderr, "!%s: gageScl query: \n", me);
!   gageQueryPrint(stderr, gageKindScl, query);
!   */
  
    E = 0;
!   if (!muu->nsin) {
!     sprintf(err, "%s: sorry- can't proceed without scalar volume", me);
!     biffAdd(MITE, err); return 1;
    }
-   if (!E) E |= !(pvl = gagePerVolumeNew(muu->gctx0, muu->nsin, gageKindScl));
-   if (!E) E |= gagePerVolumeAttach(muu->gctx0, pvl);
    if (!E) E |= gageKernelSet(muu->gctx0, gageKernel00,
  			     muu->ksp[gageKernel00]->kernel,
--- 79,114 ----
    }
  
!   GAGE_QUERY_RESET(queryScl);
!   GAGE_QUERY_RESET(queryVec);
!   GAGE_QUERY_RESET(queryTen);
    for (T=0; T<muu->ntxfNum; T++) {
!     for (axi=1; axi<muu->ntxf[T]->dim; axi++) {
!       miteVariableParse(&isp, muu->ntxf[T]->axis[axi].label);
!       miteQueryAdd(queryScl, queryVec, queryTen, &isp);
!     }
    }
!   miteShadeSpecParse((*mrrP)->shpec, muu->shadeStr);
!   miteShadeSpecQueryAdd(queryScl, queryVec, queryTen, (*mrrP)->shpec);
  
    E = 0;
!   pvlIdx = 0;
!   if (muu->nsin) {
!     if (!E) E |= !(pvl = gagePerVolumeNew(muu->gctx0, muu->nsin, gageKindScl));
!     if (!E) E |= gageQuerySet(muu->gctx0, pvl, queryScl);
!     if (!E) E |= gagePerVolumeAttach(muu->gctx0, pvl);
!     if (!E) (*mrrP)->sclPvlIdx = pvlIdx++;
!   }
!   if (muu->nvin) {
!     if (!E) E |= !(pvl = gagePerVolumeNew(muu->gctx0, muu->nvin, gageKindVec));
!     if (!E) E |= gageQuerySet(muu->gctx0, pvl, queryVec);
!     if (!E) E |= gagePerVolumeAttach(muu->gctx0, pvl);
!     if (!E) (*mrrP)->vecPvlIdx = pvlIdx++;
!   }
!   if (muu->ntin) {
!     if (!E) E |= !(pvl = gagePerVolumeNew(muu->gctx0, muu->ntin, tenGageKind));
!     if (!E) E |= gageQuerySet(muu->gctx0, pvl, queryTen);
!     if (!E) E |= gagePerVolumeAttach(muu->gctx0, pvl);
!     if (!E) (*mrrP)->tenPvlIdx = pvlIdx++;
    }
    if (!E) E |= gageKernelSet(muu->gctx0, gageKernel00,
  			     muu->ksp[gageKernel00]->kernel,
***************
*** 232,236 ****
  			     muu->ksp[gageKernel22]->kernel,
  			     muu->ksp[gageKernel22]->parm);
-   if (!E) E |= gageQuerySet(muu->gctx0, pvl, query);
    if (!E) E |= gageUpdate(muu->gctx0);
    if (E) {
--- 120,123 ----
***************
*** 241,245 ****
  	  me, GAGE_FD(muu->gctx0));
    
!   if (nrrdMaybeAlloc(muu->nout, mite_nt, 3, 4,
  		     muu->hctx->imgSize[0], muu->hctx->imgSize[1])) {
      sprintf(err, "%s: nrrd trouble", me);
--- 128,132 ----
  	  me, GAGE_FD(muu->gctx0));
    
!   if (nrrdMaybeAlloc(muu->nout, mite_nt, 3, 5 /* RGBAZ */ ,
  		     muu->hctx->imgSize[0], muu->hctx->imgSize[1])) {
      sprintf(err, "%s: nrrd trouble", me);
***************
*** 255,260 ****
  
    for (thr=0; thr<muu->hctx->numThreads; thr++) {
!     (*mrrP)->tt[thr] = (miteThread *)calloc(1, sizeof(miteThread));
!     airMopAdd((*mrrP)->rmop, (*mrrP)->tt[thr], airFree, airMopAlways);
    }
  
--- 142,152 ----
  
    for (thr=0; thr<muu->hctx->numThreads; thr++) {
!     (*mrrP)->tt[thr] = miteThreadNew();
!     if (!((*mrrP)->tt[thr])) {
!       sprintf(err, "%s: couldn't allocate thread[%d]", me, thr);
!       biffAdd(MITE, err); return 1;
!     }
!     airMopAdd((*mrrP)->rmop, (*mrrP)->tt[thr],
! 	      (airMopper)miteThreadNix, airMopAlways);
    }
  

Index: thread.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/thread.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** thread.c	13 Feb 2004 22:58:40 -0000	1.9
--- thread.c	26 Feb 2004 06:26:10 -0000	1.10
***************
*** 21,28 ****
  #include "privateMite.h"
  
  /*
  ******** miteThreadBegin()
  **
! ** this has the body of what would be miteThreadInit
  */
  int 
--- 21,63 ----
  #include "privateMite.h"
  
+ miteThread *
+ miteThreadNew() {
+   miteThread *mtt;
+   
+   mtt = (miteThread *)calloc(1, sizeof(miteThread));
+   if (!mtt) {
+     return NULL;
+   }
+ 
+   mtt->gctx = NULL;
+   mtt->ansScl = mtt->ansVec = mtt->ansTen = NULL;
+   mtt->shadeVec0 = mtt->shadeVec1 = NULL;
+   mtt->shadeScl0 = mtt->shadeScl1 = NULL;
+   mtt->ansMiteVal = 
+     (gage_t *)calloc(gageKindTotalAnswerLength(miteValGageKind), 
+ 		     sizeof(gage_t));
+   mtt->verbose = 0;
+   mtt->thrid = -1;
+   mtt->ui = mtt->vi = -1;
+   mtt->samples = 0;
+   mtt->stage = NULL;
+   /* mtt->range[], rayStep, V, RR, GG, BB, TT  initialized in 
+      miteRayBegin or in miteSample */
+   
+   return mtt;
+ }
+ 
+ miteThread *
+ miteThreadNix(miteThread *mtt) {
+ 
+   AIR_FREE(mtt->ansMiteVal);
+   AIR_FREE(mtt);
+   return NULL;
+ }
+ 
  /*
  ******** miteThreadBegin()
  **
! ** this has some of the body of what would be miteThreadInit
  */
  int 
***************
*** 30,36 ****
  		miteUser *muu, int whichThread) {
    char me[]="miteThreadBegin", err[AIR_STRLEN_MED];
!   int msi;
!   
    (*mttP) = mrr->tt[whichThread];
    if (!whichThread) {
      /* this is the first thread- it just points to the parent gageContext */
--- 65,72 ----
  		miteUser *muu, int whichThread) {
    char me[]="miteThreadBegin", err[AIR_STRLEN_MED];
! 
!   /* all the miteThreads have already been allocated */
    (*mttP) = mrr->tt[whichThread];
+ 
    if (!whichThread) {
      /* this is the first thread- it just points to the parent gageContext */
***************
*** 44,58 ****
      }
    }
!   (*mttP)->ansScl = (*mttP)->gctx->pvl[0]->ans;
!   (*mttP)->norm = (*mttP)->ans + gageKindScl->ansOffset[gageSclNormal];
    (*mttP)->nPerp = (*mttP)->ans + gageKindScl->ansOffset[gageSclNPerp];
    (*mttP)->gten = (*mttP)->ans + gageKindScl->ansOffset[gageSclGeomTens];
!   for (msi=0; msi<=MITE_SCL_MAX; msi++) {
!     (*mttP)->mscl[msi] = 0.0;
!   }
    (*mttP)->thrid = whichThread;
    (*mttP)->samples = 0;
    (*mttP)->verbose = 0;
!   _miteStageSet(*mttP, mrr, gageKindScl);
    return 0;
  }
--- 80,128 ----
      }
    }
! 
!   (*mttP)->ansScl = (-1 != mrr->sclPvlIdx
! 		     ? (*mttP)->gctx->pvl[mrr->sclPvlIdx]->answer
! 		     : NULL);
!   (*mttP)->ansVec = (-1 != mrr->vecPvlIdx
! 		     ? (*mttP)->gctx->pvl[mrr->vecPvlIdx]->answer
! 		     : NULL);
!   (*mttP)->ansTen = (-1 != mrr->tenPvlIdx
! 		     ? (*mttP)->gctx->pvl[mrr->tenPvlIdx]->answer
! 		     : NULL);
! 
! #if 0
    (*mttP)->nPerp = (*mttP)->ans + gageKindScl->ansOffset[gageSclNPerp];
    (*mttP)->gten = (*mttP)->ans + gageKindScl->ansOffset[gageSclGeomTens];
! #endif
! 
    (*mttP)->thrid = whichThread;
    (*mttP)->samples = 0;
    (*mttP)->verbose = 0;
!   
!   /* set up shading answers */
!   switch(mrr->shpec->method) {
!   case miteShadeMethodNone:
!     /* nothing to do */
!     break;
!   case miteShadeMethodPhong:
!     (*mttP)->shadeVec0 = _miteAnswerPointer(*mttP, mrr->shpec->vec0);
!     break;
!   case miteShadeMethodLitTen:
!     (*mttP)->shadeVec0 = _miteAnswerPointer(*mttP, mrr->shpec->vec0);
!     (*mttP)->shadeVec1 = _miteAnswerPointer(*mttP, mrr->shpec->vec1);
!     (*mttP)->shadeScl0 = _miteAnswerPointer(*mttP, mrr->shpec->scl0);
!     (*mttP)->shadeScl1 = _miteAnswerPointer(*mttP, mrr->shpec->scl1);
!     break;
!   default:
!     sprintf(err, "%s: shade method %d not implemented!",
! 	    me, mrr->shpec->method);
!     biffAdd(MITE, err); return 1;
!     break;
!   }
! 
!   if (_miteStageSet(*mttP, mrr)) {
!     sprintf(err, "%s: trouble setting up stage array", me);
!     biffAdd(MITE, err); return 1;
!   }
    return 0;
  }

Index: txf.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/txf.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** txf.c	13 Feb 2004 22:58:41 -0000	1.13
--- txf.c	26 Feb 2004 06:26:10 -0000	1.14
***************
*** 29,64 ****
  miteRangeChar[MITE_RANGE_NUM] = "ARGBEadsp";
  
- void
- miteVariablePrint(char *buff, const gageQuerySpec *qsp) {
-   char me[]="miteVariablePrint";
-   
-   if (gageKindScl == qsp->kind
-       || gageKindVec == qsp->kind
-       || tenGageKind == qsp->kind) {
-     sprintf(buff, "gage(%s:%s)", qsp->kind->name, 
- 	    airEnumStr(qsp->kind->enm, qsp->query));
-   } else if (miteValGageKind == qsp->kind) {
-     sprintf(buff, "%s(%s)", qsp->kind->name, 
- 	    airEnumStr(qsp->kind->enm, qsp->query));
-   } else {
-     sprintf(buff, "(%s: unknown variable!)", me);
-   }
-   return;
- }
- 
- 
  /*
  ******** miteVariableParse()
  **
  ** takes a string (usually the label from a nrrd axis) and parses it
! ** to determine the gageQuerySpec from it (which means finding the
! ** kind and query).  The valid formats are (currently):
  **
! **   <query>              : miteValGageKind (DEPRECATED)
! **   gage(<query>)        : gageKindScl (DEPRECATED)
! **   gage(scalar:<query>) : gageKindScl (preferred)
! **   gage(vector:<query>) : gageKindVec
! **   gage(tensor:<query>) : tenGageKind
! **   mite(<query>)        : miteValGageKind
  **
  ** Notice that "scalar", "vector", and "tensor" to NOT refer to the type 
--- 29,45 ----
  miteRangeChar[MITE_RANGE_NUM] = "ARGBEadsp";
  
  /*
  ******** miteVariableParse()
  **
  ** takes a string (usually the label from a nrrd axis) and parses it
! ** to determine the gageItemSpec from it (which means finding the
! ** kind and item).  The valid formats are:
  **
! **   <item>              : miteValGageKind (DEPRECATED)
! **   mite(<item>)        : miteValGageKind
! **   gage(<item>)        : gageKindScl (DEPRECATED)
! **   gage(scalar:<item>) : gageKindScl
! **   gage(vector:<item>) : gageKindVec
! **   gage(tensor:<item>) : tenGageKind
  **
  ** Notice that "scalar", "vector", and "tensor" to NOT refer to the type 
***************
*** 67,76 ****
  */
  int
! miteVariableParse(gageQuerySpec *qsp, const char *label) {
    char me[]="miteVariableParse", err[AIR_STRLEN_MED], *buff, *endparen,
      *kqstr, *col, *kstr, *qstr;
    airArray *mop;
    
!   if (!( qsp && label )) {
      sprintf(err, "%s: got NULL pointer", me);
      biffAdd(MITE, err); return 1;
--- 48,57 ----
  */
  int
! miteVariableParse(gageItemSpec *isp, const char *label) {
    char me[]="miteVariableParse", err[AIR_STRLEN_MED], *buff, *endparen,
      *kqstr, *col, *kstr, *qstr;
    airArray *mop;
    
!   if (!( isp && label )) {
      sprintf(err, "%s: got NULL pointer", me);
      biffAdd(MITE, err); return 1;
***************
*** 91,98 ****
      *endparen = 0;
      kqstr = buff + strlen("gage(");
!     /* first see if its a gageKindScl specification */
!     qsp->query = airEnumVal(gageScl, kqstr);
!     if (-1 != qsp->query) {
!       qsp->kind = gageKindScl;
        fprintf(stderr, "\n%s: WARNING: deprecated use of txf domain "
  	      "\"gage(%s)\" without explicit gage kind specification; "
--- 72,79 ----
      *endparen = 0;
      kqstr = buff + strlen("gage(");
!     /* first see if its a (deprecated) gageKindScl specification */
!     isp->item = airEnumVal(gageScl, kqstr);
!     if (-1 != isp->item) {
!       isp->kind = gageKindScl;
        fprintf(stderr, "\n%s: WARNING: deprecated use of txf domain "
  	      "\"gage(%s)\" without explicit gage kind specification; "
***************
*** 100,108 ****
  	      me, kqstr, gageKindScl->name, kqstr);
      } else {
!       /* should be of form "<kind>:<query>" */
        col = strstr(kqstr, ":");
        if (!col) {
  	sprintf(err, "%s: didn't see \":\" seperator between gage "
! 		"kind and query", me);
  	biffAdd(MITE, err); airMopError(mop); return 1;
        }
--- 81,89 ----
  	      me, kqstr, gageKindScl->name, kqstr);
      } else {
!       /* should be of form "<kind>:<item>" */
        col = strstr(kqstr, ":");
        if (!col) {
  	sprintf(err, "%s: didn't see \":\" seperator between gage "
! 		"kind and item", me);
  	biffAdd(MITE, err); airMopError(mop); return 1;
        }
***************
*** 111,127 ****
        qstr = col+1;
        if (!strcmp(gageKindScl->name, kstr)) {
! 	qsp->kind = gageKindScl;
        } else if (!strcmp(gageKindVec->name, kstr)) {
! 	qsp->kind = gageKindVec;
        } else if (!strcmp(tenGageKind->name, kstr)) {
! 	qsp->kind = tenGageKind;
        } else {
  	sprintf(err, "%s: don't recognized \"%s\" gage kind", me, kstr);
  	biffAdd(MITE, err); airMopError(mop); return 1;
        }
!       qsp->query = airEnumVal(qsp->kind->enm, qstr);
!       if (-1 == qsp->query) {
  	sprintf(err, "%s: couldn't parse \"%s\" as a %s varable",
! 		me, qstr, qsp->kind->name);
  	biffAdd(MITE, err); airMopError(mop); return 1;
        }
--- 92,108 ----
        qstr = col+1;
        if (!strcmp(gageKindScl->name, kstr)) {
! 	isp->kind = gageKindScl;
        } else if (!strcmp(gageKindVec->name, kstr)) {
! 	isp->kind = gageKindVec;
        } else if (!strcmp(tenGageKind->name, kstr)) {
! 	isp->kind = tenGageKind;
        } else {
  	sprintf(err, "%s: don't recognized \"%s\" gage kind", me, kstr);
  	biffAdd(MITE, err); airMopError(mop); return 1;
        }
!       isp->item = airEnumVal(isp->kind->enm, qstr);
!       if (-1 == isp->item) {
  	sprintf(err, "%s: couldn't parse \"%s\" as a %s varable",
! 		me, qstr, isp->kind->name);
  	biffAdd(MITE, err); airMopError(mop); return 1;
        }
***************
*** 134,151 ****
      }
      *endparen = 0;
!     kqstr = buff + strlen("mite(");
!     qsp->query = airEnumVal(miteVal, kqstr);
!     if (-1 == qsp->query) {
        sprintf(err, "%s: couldn't parse \"%s\" as a miteVal variable",
! 	      me, kqstr);
        biffAdd(MITE, err); airMopError(mop); return 1;
      }
!     qsp->kind = miteValGageKind;
    } else {
      /* didn't start with "gage(" or "mite(" */
!     qsp->query = airEnumVal(miteVal, label);
!     if (-1 != qsp->query) {
        /* its measured by mite */
!       qsp->kind = miteValGageKind;
        fprintf(stderr, "\n%s: WARNING: deprecated use of txf domain "
  	      "\"%s\"; should use \"mite(%s)\" instead\n\n",
--- 115,132 ----
      }
      *endparen = 0;
!     qstr = buff + strlen("mite(");
!     isp->item = airEnumVal(miteVal, qstr);
!     if (-1 == isp->item) {
        sprintf(err, "%s: couldn't parse \"%s\" as a miteVal variable",
! 	      me, qstr);
        biffAdd(MITE, err); airMopError(mop); return 1;
      }
!     isp->kind = miteValGageKind;
    } else {
      /* didn't start with "gage(" or "mite(" */
!     isp->item = airEnumVal(miteVal, label);
!     if (-1 != isp->item) {
        /* its measured by mite */
!       isp->kind = miteValGageKind;
        fprintf(stderr, "\n%s: WARNING: deprecated use of txf domain "
  	      "\"%s\"; should use \"mite(%s)\" instead\n\n",
***************
*** 160,167 ****
  }
  
  int
  miteNtxfCheck(const Nrrd *ntxf) {
!   char me[]="miteNtxfCheck", err[AIR_STRLEN_MED], *range, *domS;
!   gageQuerySpec qsp;
    int rii, axi;
  
--- 141,166 ----
  }
  
+ void
+ miteVariablePrint(char *buff, const gageItemSpec *isp) {
+   char me[]="miteVariablePrint";
+   
+   if (gageKindScl == isp->kind
+       || gageKindVec == isp->kind
+       || tenGageKind == isp->kind) {
+     sprintf(buff, "gage(%s:%s)", isp->kind->name, 
+ 	    airEnumStr(isp->kind->enm, isp->item));
+   } else if (miteValGageKind == isp->kind) {
+     sprintf(buff, "%s(%s)", isp->kind->name, 
+ 	    airEnumStr(isp->kind->enm, isp->item));
+   } else {
+     sprintf(buff, "(%s: unknown gageKind!)", me);
+   }
+   return;
+ }
+ 
  int
  miteNtxfCheck(const Nrrd *ntxf) {
!   char me[]="miteNtxfCheck", err[AIR_STRLEN_MED], *rangeStr, *domStr;
!   gageItemSpec isp;
    int rii, axi;
  
***************
*** 185,203 ****
      biffAdd(MITE, err); return 1;
    }
!   range = ntxf->axis[0].label;
!   if (0 == airStrlen(range)) {
      sprintf(err, "%s: axis[0]'s label doesn't specify txf range", me);
      biffAdd(MITE, err); return 1;
    }
!   if (airStrlen(range) != ntxf->axis[0].size) {
      sprintf(err, "%s: axis[0]'s size is %d, but label specifies %d values",
! 	    me, ntxf->axis[0].size, (int)airStrlen(range));
      biffAdd(MITE, err); return 1;
    }
!   for (rii=0; rii<airStrlen(range); rii++) {
!     if (!strchr(miteRangeChar, range[rii])) {
        sprintf(err, "%s: char %d of axis[0]'s label (\"%c\") isn't a valid "
  	      "transfer function range specifier (not in \"%s\")",
! 	      me, rii, range[rii], miteRangeChar);
        biffAdd(MITE, err); return 1;
      }
--- 184,202 ----
      biffAdd(MITE, err); return 1;
    }
!   rangeStr = ntxf->axis[0].label;
!   if (0 == airStrlen(rangeStr)) {
      sprintf(err, "%s: axis[0]'s label doesn't specify txf range", me);
      biffAdd(MITE, err); return 1;
    }
!   if (airStrlen(rangeStr) != ntxf->axis[0].size) {
      sprintf(err, "%s: axis[0]'s size is %d, but label specifies %d values",
! 	    me, ntxf->axis[0].size, (int)airStrlen(rangeStr));
      biffAdd(MITE, err); return 1;
    }
!   for (rii=0; rii<airStrlen(rangeStr); rii++) {
!     if (!strchr(miteRangeChar, rangeStr[rii])) {
        sprintf(err, "%s: char %d of axis[0]'s label (\"%c\") isn't a valid "
  	      "transfer function range specifier (not in \"%s\")",
! 	      me, rii, rangeStr[rii], miteRangeChar);
        biffAdd(MITE, err); return 1;
      }
***************
*** 218,239 ****
        biffAdd(MITE, err); return 1;
      }
!     domS = ntxf->axis[axi].label;
!     if (0 == airStrlen(domS)) {
        sprintf(err, "%s: axis[%d] of txf didn't specify a domain variable",
  	      me, axi);
        biffAdd(MITE, err); return 1;
      }
!     if (miteVariableParse(&qsp, domS)) {
        sprintf(err, "%s: couldn't parse txf domain \"%s\" for axis %d\n", 
! 	      me, domS, axi);
        biffAdd(MITE, err); return 1;
      }
!     if (!( 1 == qsp.kind->ansLength[qsp.query] ||
! 	   3 == qsp.kind->ansLength[qsp.query] )) {
        sprintf(err, "%s: %s not a scalar or vector: can't be a txf "
! 	      "domain variable", me, domS);
        biffAdd(MITE, err); return 1;
      }
!     if (3 == qsp.kind->ansLength[qsp.query]) {
        /* has to be right length for one of the quantization schemes */
        if (!( limnQNBins[limnQN16checker] == ntxf->axis[axi].size ||
--- 217,238 ----
        biffAdd(MITE, err); return 1;
      }
!     domStr = ntxf->axis[axi].label;
!     if (0 == airStrlen(domStr)) {
        sprintf(err, "%s: axis[%d] of txf didn't specify a domain variable",
  	      me, axi);
        biffAdd(MITE, err); return 1;
      }
!     if (miteVariableParse(&isp, domStr)) {
        sprintf(err, "%s: couldn't parse txf domain \"%s\" for axis %d\n", 
! 	      me, domStr, axi);
        biffAdd(MITE, err); return 1;
      }
!     if (!( 1 == isp.kind->table[isp.item].answerLength ||
! 	   3 == isp.kind->table[isp.item].answerLength )) {
        sprintf(err, "%s: %s not a scalar or vector: can't be a txf "
! 	      "domain variable", me, domStr);
        biffAdd(MITE, err); return 1;
      }
!     if (3 == isp.kind->table[isp.item].answerLength) {
        /* has to be right length for one of the quantization schemes */
        if (!( limnQNBins[limnQN16checker] == ntxf->axis[axi].size ||
***************
*** 241,245 ****
  	     limnQNBins[limnQN12checker] == ntxf->axis[axi].size )) {
  	sprintf(err, "%s: vector %s can be quantized into %d, %d, or %d bins "
! 		"but not %d", me, domS, limnQNBins[limnQN16checker],
  		limnQNBins[limnQN14checker], limnQNBins[limnQN12checker],
  		ntxf->axis[axi].size);
--- 240,244 ----
  	     limnQNBins[limnQN12checker] == ntxf->axis[axi].size )) {
  	sprintf(err, "%s: vector %s can be quantized into %d, %d, or %d bins "
! 		"but not %d", me, domStr, limnQNBins[limnQN16checker],
  		limnQNBins[limnQN14checker], limnQNBins[limnQN12checker],
  		ntxf->axis[axi].size);
***************
*** 253,264 ****
  
  /*
! ** _miteQuery()
  **
! ** This looks a given gageQuerySpec and sets the bits in the
  ** gageKindScl and tenGageKind queries that are required to calculate
  ** the quantity
  **
! ** NOTE: This does NOT initialize the *query{Scl,Vec,Ten}: it
! ** just bit-wise or's on new stuff
  **
  ** HEY: this is really unfortunate: each new gage type use for
--- 252,263 ----
  
  /*
! ******** miteQueryAdd()
  **
! ** This looks a given gageItemSpec and sets the bits in the
  ** gageKindScl and tenGageKind queries that are required to calculate
  ** the quantity
  **
! ** NOTE: This does NOT initialize the query{Scl,Vec,Ten}: it
! ** just adds on new items to the existing queries
  **
  ** HEY: this is really unfortunate: each new gage type use for
***************
*** 266,306 ****
  ** arguments here, which is part of the reason that mite may end
  ** up explicitly depending on the libraries supplying those gageKinds
! ** (like how new mite depends on ten)
  */
  void
! _miteQuery(unsigned int *queryScl, 
! 	   unsigned int *queryVec, 
! 	   unsigned int *queryTen, gageQuerySpec *qsp) {
!   char me[]="_miteQuery";
    
!   /*
!   for (i=1; i<ntxf->dim; i++) {
!     miteVariableParse(qsp, ntxf->axis[i].label);
!   */
!   if (gageKindScl == qsp->kind) {
!     *queryScl |= 1 << qsp->query;
!   } else if (gageKindVec == qsp->kind) {
!     *queryVec |= 1 << qsp->query;
!   } else if (tenGageKind == qsp->kind) {
!     *queryTen |= 1 << qsp->query;
!   } else if (miteValGageKind == qsp->kind) {
!     /* HEY: the first of these two have useful analogs for tensor
!        data, but I won't be able to express them ... */
!     switch(qsp->query) {
      case miteValNdotV: 
!       *queryScl |= 1 << gageSclNormal;
        break;
      case miteValNdotL:
!       *queryScl |= 1 << gageSclNormal;
        break;
      case miteValGTdotV:
!       *queryScl |= 1 << gageSclGeomTens;
        break;
      case miteValVrefN:
!       *queryScl |= 1 << gageSclNormal;
        break;
      case miteValVdefT:
      case miteValVdefTdotV:
!       *queryTen |= 1 << tenGageTensor;
        break;
      }
--- 265,305 ----
  ** arguments here, which is part of the reason that mite may end
  ** up explicitly depending on the libraries supplying those gageKinds
! ** (like how mite now must depend on ten)
  */
  void
! miteQueryAdd(gageQuery queryScl, 
! 	     gageQuery queryVec, 
! 	     gageQuery queryTen, gageItemSpec *isp) {
!   char me[]="miteQueryAdd";
    
!   if (gageKindScl == isp->kind) {
!     GAGE_QUERY_ITEM_ON(queryScl, isp->item);
!   } else if (gageKindVec == isp->kind) {
!     GAGE_QUERY_ITEM_ON(queryVec, isp->item);
!   } else if (tenGageKind == isp->kind) {
!     GAGE_QUERY_ITEM_ON(queryTen, isp->item);
!   } else if (miteValGageKind == isp->kind) {
!     /* HEY: some these have useful analogs for tensor data, but I
!        won't be able to express them.  This means that while Phong
!        shading of *scalar* volumes can be implemented with transfer
!        functions, it is currently not possible in *tensor* volumes
!        (for instance, using the gradient of fractional anisotropy) */
!     switch(isp->item) {
      case miteValNdotV: 
!       GAGE_QUERY_ITEM_ON(queryScl, gageSclNormal);
        break;
      case miteValNdotL:
!       GAGE_QUERY_ITEM_ON(queryScl, gageSclNormal);
        break;
      case miteValGTdotV:
!       GAGE_QUERY_ITEM_ON(queryScl, gageSclGeomTens);
        break;
      case miteValVrefN:
!       GAGE_QUERY_ITEM_ON(queryScl, gageSclNormal);
        break;
      case miteValVdefT:
+       GAGE_QUERY_ITEM_ON(queryTen, tenGageTensor);
      case miteValVdefTdotV:
!       GAGE_QUERY_ITEM_ON(queryTen, tenGageTensor);
        break;
      }
***************
*** 418,421 ****
--- 417,446 ----
  }
  
+ gage_t *
+ _miteAnswerPointer(miteThread *mtt, gageItemSpec *isp) {
+   char me[]="_miteAnswerPointer";
+   gage_t *ret;
+ 
+   if (gageKindScl == isp->kind) {
+     ret = mtt->ansScl;
+   } else if (gageKindVec == isp->kind) {
+     ret = mtt->ansVec;
+   } else if (tenGageKind == isp->kind) {
+     ret = mtt->ansTen;
+   } else if (miteValGageKind == isp->kind) {
+     ret = mtt->ansMiteVal;
+   } else {
+     fprintf(stderr, "\nPANIC: %s: unknown gageKind!\n", me);
+     exit(1);
+   }
+   ret += gageKindAnswerOffset(isp->kind, isp->item);
+   return ret;
+ }
+ 
+ /*
+ ** _miteStageSet
+ **
+ ** ALLOCATES and initializes stage array in a miteThread
+ */
  int
  _miteStageSet(miteThread *mtt, miteRender *mrr) {
***************
*** 424,428 ****
    Nrrd *ntxf;
    miteStage *stage;
!   gageQuerySpec qsp;
    char rc;
    
--- 449,453 ----
    Nrrd *ntxf;
    miteStage *stage;
!   gageItemSpec isp;
    char rc;
    
***************
*** 442,460 ****
        stage = mtt->stage + stageIdx;
        _miteStageInit(stage);
!       miteVariableParse(&qsp, ntxf->axis[di].label);
!       if (gageKindScl == qsp.kind) {
! 	stage->val = mtt->ansScl;
!       } else if (gageKindVec == qsp.kind) {
! 	stage->val = mtt->ansVec;
!       } else if (tenGageKind == qsp.kind) {
! 	stage->val = mtt->ansTen;
!       } else if (miteValGageKind == qsp.kind) {
! 	stage->val = mtt->ansMiteVal;
!       } else {
! 	sprintf(err, "%s: don't handle gageKind for \"%s\"",
! 		me, ntxf->axis[di].label);
! 	biffAdd(MITE, err); return 1;
!       }
!       stage->val += qsp.kind->ansOffset[qsp.query];
        /*
        fprintf(stderr, "!%s: ans=%p + offset[%d]=%d == %p\n", me,
--- 467,472 ----
        stage = mtt->stage + stageIdx;
        _miteStageInit(stage);
!       miteVariableParse(&isp, ntxf->axis[di].label);
!       stage->val = _miteAnswerPointer(mtt, &isp);
        /*
        fprintf(stderr, "!%s: ans=%p + offset[%d]=%d == %p\n", me,
***************
*** 469,475 ****
  	stage->data = ntxf->data;
  	stage->op = miteStageOpMultiply;
! 	if (1 == qsp.kind->ansLength[qsp.query]) {
  	  stage->qn = NULL;
! 	} else if (3 == 1 == qsp.kind->ansLength[qsp.query]) {
  	  if (limnQNBins[limnQN16checker] == ntxf->axis[di].size) {
  	    stage->qn = limnVtoQN_GT[limnQN16checker];
--- 481,487 ----
  	stage->data = ntxf->data;
  	stage->op = miteStageOpMultiply;
! 	if (1 == isp.kind->table[isp.item].answerLength) {
  	  stage->qn = NULL;
! 	} else if (3 == isp.kind->table[isp.item].answerLength) {
  	  if (limnQNBins[limnQN16checker] == ntxf->axis[di].size) {
  	    stage->qn = limnVtoQN_GT[limnQN16checker];
***************
*** 487,491 ****
  	  sprintf(err, "%s: %s not scalar or vector (len = %d): can't be "
  		  "a txf domain variable", me,
! 		  ntxf->axis[di].label, qsp.kind->ansLength[qsp.query]);
  	  biffAdd(MITE, err); return 1;
  	}
--- 499,504 ----
  	  sprintf(err, "%s: %s not scalar or vector (len = %d): can't be "
  		  "a txf domain variable", me,
! 		  ntxf->axis[di].label,
! 		  isp.kind->table[isp.item].answerLength);
  	  biffAdd(MITE, err); return 1;
  	}
***************
*** 528,532 ****
        for (rii=0; rii<stage->rangeNum; rii++) {
  	ri = stage->rangeIdx[rii];
! 	mtt->range[ri] *= rangeData[rii];
        }
        finalIdx = 0;
--- 541,559 ----
        for (rii=0; rii<stage->rangeNum; rii++) {
  	ri = stage->rangeIdx[rii];
! 	switch(stage->op) {
! 	case miteStageOpMin:
! 	  mtt->range[ri] = AIR_MIN(mtt->range[ri], rangeData[rii]);
! 	  break;
! 	case miteStageOpMax:
! 	  mtt->range[ri] = AIR_MAX(mtt->range[ri], rangeData[rii]);
! 	  break;
! 	case miteStageOpAdd:
! 	  mtt->range[ri] += rangeData[rii];
! 	  break;
! 	case miteStageOpMultiply:
! 	default:
! 	  mtt->range[ri] *= rangeData[rii];
! 	  break;
! 	}
        }
        finalIdx = 0;

Index: user.c
===================================================================
RCS file: /cvsroot/teem/teem/src/mite/user.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** user.c	13 Feb 2004 22:58:41 -0000	1.14
--- user.c	26 Feb 2004 06:26:10 -0000	1.15
***************
*** 44,48 ****
    muu->refStep = miteDefRefStep;
    muu->rayStep = AIR_NAN;
!   muu->near1 = miteDefNear1;
    muu->hctx = hooverContextNew();
    airMopAdd(muu->umop, muu->hctx, (airMopper)hooverContextNix, airMopAlways);
--- 44,49 ----
    muu->refStep = miteDefRefStep;
    muu->rayStep = AIR_NAN;
!   muu->opacMatters = miteDefOpacMatters;
!   muu->opacNear1 = miteDefOpacNear1;
    muu->hctx = hooverContextNew();
    airMopAdd(muu->umop, muu->hctx, (airMopper)hooverContextNix, airMopAlways);
***************
*** 75,79 ****
  _miteUserCheck(miteUser *muu) {
    char me[]="miteUserCheck", err[AIR_STRLEN_MED];
!   int T, gotOpac;
    
    if (!muu) {
--- 76,84 ----
  _miteUserCheck(miteUser *muu) {
    char me[]="miteUserCheck", err[AIR_STRLEN_MED];
!   int T, axi, gotOpac;
!   gageItemSpec isp;
!   gageQuery queryScl, queryVec, queryTen;
!   miteShadeSpec *shpec;
!   airArray *mop;
    
    if (!muu) {
***************
*** 81,94 ****
      biffAdd(MITE, err); return 1;
    }
    if (!( muu->ntxfNum >= 1 )) {
      sprintf(err, "%s: need at least one transfer function", me);
!     biffAdd(MITE, err); return 1;
    }
    gotOpac = AIR_FALSE;
    for (T=0; T<muu->ntxfNum; T++) {
      if (miteNtxfCheck(muu->ntxf[T])) {
        sprintf(err, "%s: ntxf[%d] (%d of %d) can't be used as a txf",
  	      me, T, T+1, muu->ntxfNum);
!       biffAdd(MITE, err); return 1;
      }
      gotOpac |= !!strchr(muu->ntxf[T]->axis[0].label, 'A');
--- 86,108 ----
      biffAdd(MITE, err); return 1;
    }
+   mop = airMopNew();
    if (!( muu->ntxfNum >= 1 )) {
      sprintf(err, "%s: need at least one transfer function", me);
!     biffAdd(MITE, err); airMopError(mop); return 1;
    }
    gotOpac = AIR_FALSE;
+   GAGE_QUERY_RESET(queryScl);
+   GAGE_QUERY_RESET(queryVec);
+   GAGE_QUERY_RESET(queryTen);
    for (T=0; T<muu->ntxfNum; T++) {
      if (miteNtxfCheck(muu->ntxf[T])) {
        sprintf(err, "%s: ntxf[%d] (%d of %d) can't be used as a txf",
  	      me, T, T+1, muu->ntxfNum);
!       biffAdd(MITE, err); airMopError(mop); return 1;
!     }
!     /* NOTE: no error checking because miteNtxfCheck succeeded */
!     for (axi=1; axi<muu->ntxf[T]->dim; axi++) {
!       miteVariableParse(&isp, muu->ntxf[T]->axis[axi].label);
!       miteQueryAdd(queryScl, queryVec, queryTen, &isp);
      }
      gotOpac |= !!strchr(muu->ntxf[T]->axis[0].label, 'A');
***************
*** 102,125 ****
  	    "************************\n\n\n", me);
    }
    if (!muu->nout) {
      sprintf(err, "%s: rendered image nrrd is NULL", me);
!     biffAdd(MITE, err); return 1;
!   }
!   if (!(muu->nsin || muu->ntin)) {
!     sprintf(err, "%s: got neither scalar nor tensor volume", me);
!     biffAdd(MITE, err); return 1;
    }
    if (muu->nsin) {
      if (gageVolumeCheck(muu->gctx0, muu->nsin, gageKindScl)) {
!       sprintf(err, "%s: trouble with input scalar volume", me);
!       biffMove(MITE, err, GAGE); return 1;
      }
!   } else {
      if (gageVolumeCheck(muu->gctx0, muu->ntin, tenGageKind)) {
!       sprintf(err, "%s: trouble with input tensor volume", me);
!       biffMove(MITE, err, GAGE); return 1;
      }
    }
! 
    return 0;
  }
--- 116,168 ----
  	    "************************\n\n\n", me);
    }
+   shpec = miteShadeSpecNew();
+   airMopAdd(mop, shpec, (airMopper)miteShadeSpecNix, airMopAlways);
+   if (miteShadeSpecParse(shpec, muu->shadeStr)) {
+     sprintf(err, "%s: couldn't parse shading spec \"%s\"", 
+ 	    me, muu->shadeStr);
+     biffAdd(MITE, err); airMopError(mop); return 1;
+   }
+   miteShadeSpecQueryAdd(queryScl, queryVec, queryTen, shpec);
+   if (GAGE_QUERY_NONZERO(queryScl) && !(muu->nsin)) {
+     sprintf(err, "%s: txf or shading require %s volume, but don't have one",
+ 	    me, gageKindScl->name);
+     biffAdd(MITE, err); airMopError(mop); return 1;
+   }
+   if (GAGE_QUERY_NONZERO(queryVec) && !(muu->nvin)) {
+     sprintf(err, "%s: txf or shading require %s volume, but don't have one",
+ 	    me, gageKindVec->name);
+     biffAdd(MITE, err); airMopError(mop); return 1;
+   }
+   if (GAGE_QUERY_NONZERO(queryTen) && !(muu->ntin)) {
+     sprintf(err, "%s: txf or shading require %s volume, but don't have one",
+ 	    me, tenGageKind->name);
+     biffAdd(MITE, err); airMopError(mop); return 1;
+   }
    if (!muu->nout) {
      sprintf(err, "%s: rendered image nrrd is NULL", me);
!     biffAdd(MITE, err); airMopError(mop); return 1;
    }
    if (muu->nsin) {
      if (gageVolumeCheck(muu->gctx0, muu->nsin, gageKindScl)) {
!       sprintf(err, "%s: trouble with input %s volume",
! 	      me, gageKindScl->name);
!       biffMove(MITE, err, GAGE); airMopError(mop); return 1;
      }
!   }
!   if (muu->nvin) {
!     if (gageVolumeCheck(muu->gctx0, muu->nvin, gageKindVec)) {
!       sprintf(err, "%s: trouble with input %s volume", 
! 	      me, gageKindVec->name);
!       biffMove(MITE, err, GAGE); airMopError(mop); return 1;
!     }
!   }
!   if (muu->ntin) {
      if (gageVolumeCheck(muu->gctx0, muu->ntin, tenGageKind)) {
!       sprintf(err, "%s: trouble with input %s volume", 
! 	      me, tenGageK...
 
[truncated message content]

[Teem-commit] teem/src/gage scl.c,1.32,1.33

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

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12647

Modified Files:
	scl.c 
Log Message:
tentatively removed \"n\" as synonim for normalized gradient in gageScl airEnum

Index: scl.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/scl.c,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** scl.c	23 Feb 2004 06:02:19 -0000	1.32
--- scl.c	26 Feb 2004 06:20:25 -0000	1.33
***************
*** 193,197 ****
    "gv", "gvec", "gradvec", "grad vec", "gradient vector",
    "gm", "gmag", "gradmag", "grad mag", "gradient magnitude",
!   "n", "normal", "gnorm", "normg", "norm", "normgrad", \
         "norm grad", "normalized gradient",
    "np", "nperp", 
--- 193,197 ----
    "gv", "gvec", "gradvec", "grad vec", "gradient vector",
    "gm", "gmag", "gradmag", "grad mag", "gradient magnitude",
!   "gn", /* pray "n", */ "normal", "gnorm", "normg", "norm", "normgrad", \
         "norm grad", "normalized gradient",
    "np", "nperp", 
***************
*** 226,230 ****
    GS_GV, GS_GV, GS_GV, GS_GV, GS_GV, 
    GS_GM, GS_GM, GS_GM, GS_GM, GS_GM,
!   GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N,
    GS_NP, GS_NP,
    GS_H, GS_H, GS_H, 
--- 226,230 ----
    GS_GV, GS_GV, GS_GV, GS_GV, GS_GV, 
    GS_GM, GS_GM, GS_GM, GS_GM, GS_GM,
!   GS_N, /* pray GS_N, */ GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N,
    GS_NP, GS_NP,
    GS_H, GS_H, GS_H, 

[Teem-commit] teem/src/gage gage.h,1.60,1.61

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

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12510

Modified Files:
	gage.h 
Log Message:
added GAGE_QUERY_ZERO, re-ordered item and kind in gageItemSpec

Index: gage.h
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/gage.h,v
retrieving revision 1.60
retrieving revision 1.61
diff -C2 -d -r1.60 -r1.61
*** gage.h	19 Feb 2004 03:50:02 -0000	1.60
--- gage.h	26 Feb 2004 06:19:28 -0000	1.61
***************
*** 449,452 ****
--- 449,454 ----
    (p[0] == q[0] && p[1] == q[1] && p[2] == q[2] && p[3] == q[3] \
     && p[4] == q[4] && p[5] == q[5] && p[6] == q[6] && p[7] == q[7])
+ #define GAGE_QUERY_NONZERO(q) \
+   (q[0] | q[1] | q[2] | q[3] | q[4] | q[5] | q[6] | q[7])
  #define GAGE_QUERY_ITEM_TEST(q, i) (q[i/8] & (1 << (i % 8)))
  #define GAGE_QUERY_ITEM_ON(q, i) (q[i/8] |= (1 << (i % 8)))
***************
*** 572,580 ****
  ******** gageItemSpec struct
  **
! ** dumb little way to store an item/kind pair
  */
  typedef struct {
!   int item;                   /* the quantity we care about */
!   gageKind *kind;             /* what kind it comes from */
  } gageItemSpec;
  
--- 574,583 ----
  ******** gageItemSpec struct
  **
! ** dumb little way to store a kind/item pair.  Formerly known
! ** as a gageQuerySpec.  
  */
  typedef struct {
!   gageKind *kind;             /* the kind of the volume to measure */
!   int item;                   /* the quantity to measure */
  } gageItemSpec;
  

[Teem-commit] teem/src/nrrd enumsNrrd.c,1.29,1.30

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

Update of /cvsroot/teem/teem/src/nrrd
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9317

Modified Files:
	enumsNrrd.c 
Log Message:
added stdv as alias for nrrdMeasureSD to nrrdMeasure airEnum

Index: enumsNrrd.c
===================================================================
RCS file: /cvsroot/teem/teem/src/nrrd/enumsNrrd.c,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** enumsNrrd.c	9 Feb 2004 06:49:29 -0000	1.29
--- enumsNrrd.c	23 Feb 2004 18:04:15 -0000	1.30
***************
*** 537,541 ****
    "Linf",
    "variance", "var",
!   "SD",
    "histo-min",
    "histo-max",
--- 537,541 ----
    "Linf",
    "variance", "var",
!   "SD", "stdv",
    "histo-min",
    "histo-max",
***************
*** 564,568 ****
    nrrdMeasureLinf,
    nrrdMeasureVariance, nrrdMeasureVariance,
!   nrrdMeasureSD,
    nrrdMeasureHistoMin,
    nrrdMeasureHistoMax,
--- 564,568 ----
    nrrdMeasureLinf,
    nrrdMeasureVariance, nrrdMeasureVariance,
!   nrrdMeasureSD, nrrdMeasureSD,
    nrrdMeasureHistoMin,
    nrrdMeasureHistoMax,

[Teem-commit] teem/src/ten enumsTen.c,1.16,1.17 ten.h,1.74,1.75 tenGage.c,1.14,1.15

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30125

Modified Files:
	enumsTen.c ten.h tenGage.c 
Log Message:
added P (and its derivatives), the phase of the cubic eigenvalue polynomial, as new quantity in tenGage, and finished preliminary debugging

Index: enumsTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/enumsTen.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** enumsTen.c	23 Feb 2004 02:40:24 -0000	1.16
--- enumsTen.c	23 Feb 2004 06:03:13 -0000	1.17
***************
*** 73,76 ****
--- 73,77 ----
    "FA",
    "R",
+   "P",
  
    "evals",
***************
*** 113,116 ****
--- 114,121 ----
    "R normal",
  
+   "P grad vec",
+   "P grad mag",
+   "P normal",
+ 
    "anisotropies"
  };
***************
*** 127,130 ****
--- 132,136 ----
    "FA",
    "R",
+   "P",
    "3 eigenvalues",
    "eigenvalue 0",
***************
*** 157,160 ****
--- 163,169 ----
    "R grad mag",
    "R normal",
+   "P grad vec",
+   "P grad mag",
+   "P normal",
    "anisotropies"
  };
***************
*** 163,205 ****
  _tenGageVal[] = {
    tenGageUnknown,
!   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] */
!   tenGageEval,          /*  8: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /*  9: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /* 10: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* 11: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* 12: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* 13: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* 14: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 15: "evec2", minor eigenvectors of tensor: GT[3] */
!   tenGageTensorGrad,    /* 16: "tg, all tensor component gradients: GT[21] */
!   tenGageTraceGradVec,  /* 17: "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* 18: "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* 19: "trn": normal of trace: GT[3] */
!   tenGageBGradVec,      /* 20: "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* 21: "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* 22: "bn", normal of B: GT[3] */
!   tenGageDetGradVec,    /* 23: "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* 24: "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* 25: "detn", normal of Det: GT[3] */
!   tenGageSGradVec,      /* 26: "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* 27: "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* 28: "sn", normal of S: GT[3] */
!   tenGageQGradVec,      /* 29: "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 30: "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 31: "qn", normalized gradient of Q: GT[3] */
!   tenGageFAGradVec,     /* 32: "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* 33: "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* 34: "fan", normalized gradient of FA: GT[3] */
!   tenGageRGradVec,      /* 35: "rgv", gradient vector of Q: GT[3] */
!   tenGageRGradMag,      /* 36: "rgm", gradient magnitude of Q: GT[1] */
!   tenGageRNormal,       /* 37: "rn", normalized gradient of Q: GT[3] */
!   tenGageAniso          /* 38: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
  };
  
--- 172,218 ----
  _tenGageVal[] = {
    tenGageUnknown,
!   tenGageTensor,        /* "t", the reconstructed tensor: GT[7] */
!   tenGageTrace,         /* "tr", trace of tensor: GT[1] */
!   tenGageB,             /* "b": GT[1] */
!   tenGageDet,           /* "det", determinant of tensor: GT[1] */
!   tenGageS,             /* "s", square of frobenius norm: GT[1] */
!   tenGageQ,             /* "q", (S - B)/9: GT[1] */
!   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] */
!   tenGageEval1,         /* "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* "evec2", minor eigenvectors of tensor: GT[3] */
!   tenGageTensorGrad,    /* "tg, all tensor component gradients: GT[21] */
!   tenGageTraceGradVec,  /* "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* "trn": normal of trace: GT[3] */
!   tenGageBGradVec,      /* "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* "bn", normal of B: GT[3] */
!   tenGageDetGradVec,    /* "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* "detn", normal of Det: GT[3] */
!   tenGageSGradVec,      /* "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* "sn", normal of S: GT[3] */
!   tenGageQGradVec,      /* "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* "qn", normalized gradient of Q: GT[3] */
!   tenGageFAGradVec,     /* "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* "fan", normalized gradient of FA: GT[3] */
!   tenGageRGradVec,      /* "rgv", gradient vector of Q: GT[3] */
!   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] */
  };
  
***************
*** 214,217 ****
--- 227,231 ----
    "fa",
    "r",
+   "p",
    "eval",
    "eval0",
***************
*** 244,247 ****
--- 258,264 ----
    "rgm", "r grad mag",
    "rn", "r normal",
+   "pgv", "p grad vec",
+   "pgm", "p grad mag",
+   "pn", "p normal",
    "an", "aniso", "anisotropies",
    ""
***************
*** 258,261 ****
--- 275,279 ----
    tenGageFA,
    tenGageR,
+   tenGageP,
    tenGageEval,
    tenGageEval0,
***************
*** 288,291 ****
--- 306,312 ----
    tenGageRGradMag, tenGageRGradMag,
    tenGageRNormal, tenGageRNormal,
+   tenGagePGradVec, tenGagePGradVec,
+   tenGagePGradMag, tenGagePGradMag,
+   tenGagePNormal, tenGagePNormal,
    tenGageAniso, tenGageAniso, tenGageAniso
  };

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.74
retrieving revision 1.75
diff -C2 -d -r1.74 -r1.75
*** ten.h	23 Feb 2004 02:40:24 -0000	1.74
--- ten.h	23 Feb 2004 06:03:13 -0000	1.75
***************
*** 151,155 ****
  ** R = (9*A*B - 2*A^3 - 27*C)/54 
       = (5*A*B - 2*A*S - 27*C)/54 = thirdmoment({v1,v2,v3})/2
! ** (phase in cubic solution = arccos(R/sqrt(Q)^3))
  */
  enum {
--- 151,155 ----
  ** 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
  */
  enum {
***************
*** 164,212 ****
    tenGageFA,            /*  6: "fa", fractional anisotropy: GT[1] */
    tenGageR,             /*  7: "r", 9*A*B - 2*A^3 - 27*C: GT[1] */
  
!   tenGageEval,          /*  8: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /*  9: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /* 10: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* 11: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* 12: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* 13: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* 14: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 15: "evec2", minor eigenvectors of tensor: GT[3] */
  
!   tenGageTensorGrad,    /* 16: "tg, all tensor component gradients, starting
  			       with the confidence gradient: GT[21] */
  
!   tenGageTraceGradVec,  /* 17: "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* 18: "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* 19: "trn": normal of trace: GT[3] */
    
!   tenGageBGradVec,      /* 20: "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* 21: "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* 22: "bn", normal of B: GT[3] */
  
!   tenGageDetGradVec,    /* 23: "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* 24: "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* 25: "detn", normal of Det: GT[3] */
  
!   tenGageSGradVec,      /* 26: "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* 27: "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* 28: "sn", normal of S: GT[3] */
  
!   tenGageQGradVec,      /* 29: "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 30: "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 31: "qn", normalized gradient of Q: GT[3] */
  
!   tenGageFAGradVec,     /* 32: "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* 33: "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* 34: "fan", normalized gradient of FA: GT[3] */
  
!   tenGageRGradVec,      /* 35: "rgv", gradient vector of Q: GT[3] */
!   tenGageRGradMag,      /* 36: "rgm", gradient magnitude of Q: GT[1] */
!   tenGageRNormal,       /* 37: "rn", normalized gradient of Q: GT[3] */
  
!   tenGageAniso,         /* 38: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  38
  
  /*
--- 164,217 ----
    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
  
  /*

Index: tenGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tenGage.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** tenGage.c	23 Feb 2004 02:40:24 -0000	1.14
--- tenGage.c	23 Feb 2004 06:03:13 -0000	1.15
***************
*** 24,67 ****
  gageItemEntry
  _tenGageTable[TEN_GAGE_ITEM_MAX+1] = {
!   /* enum value              len,deriv,  prereqs,                                       parent item, index*/
!   {tenGageTensor,              7,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {tenGageTrace,               1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageB,                   1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageDet,                 1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageS,                   1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageQ,                   1,  0,  {tenGageS, tenGageB, -1, -1, -1},                        -1,  -1},
!   {tenGageFA,                  1,  0,  {tenGageQ, tenGageS, -1, -1, -1},                        -1,  -1},
!   {tenGageR,                   1,  0,  {tenGageTrace, tenGageB, tenGageDet, tenGageS, -1},      -1,  -1},
!   {tenGageEval,                3,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageEval0,               1,  0,  {tenGageEval, -1, -1, -1, -1},                  tenGageEval,   0},
!   {tenGageEval1,               1,  0,  {tenGageEval, -1, -1, -1, -1},                  tenGageEval,   1},
!   {tenGageEval2,               1,  0,  {tenGageEval, -1, -1, -1, -1},                  tenGageEval,   2},
!   {tenGageEvec,                9,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageEvec0,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                  tenGageEvec,   0},
!   {tenGageEvec1,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                  tenGageEvec,   3},
!   {tenGageEvec2,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                  tenGageEvec,   6},
!   {tenGageTensorGrad,         21,  1,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {tenGageTraceGradVec,        3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageTraceGradMag,        1,  1,  {tenGageTraceGradVec, -1, -1, -1, -1},                   -1,  -1},
!   {tenGageTraceNormal,         3,  1,  {tenGageTraceGradVec, tenGageTraceGradMag, -1, -1, -1},  -1,  -1},
!   {tenGageBGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageBGradMag,            1,  1,  {tenGageBGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageBNormal,             3,  1,  {tenGageBGradVec, tenGageBGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageDetGradVec,          3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageDetGradMag,          1,  1,  {tenGageDetGradVec, -1, -1, -1, -1},                     -1,  -1},
!   {tenGageDetNormal,           3,  1,  {tenGageDetGradVec, tenGageDetGradMag, -1, -1, -1},      -1,  -1},
!   {tenGageSGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageSGradMag,            1,  1,  {tenGageSGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageSNormal,             3,  1,  {tenGageSGradVec, tenGageSGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageQGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageQGradMag,            1,  1,  {tenGageQGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageQNormal,             3,  1,  {tenGageQGradVec, tenGageQGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageFAGradVec,           3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageFAGradMag,           1,  1,  {tenGageFAGradVec, -1, -1, -1, -1},                      -1,  -1},
!   {tenGageFANormal,            3,  1,  {tenGageFAGradVec, tenGageFAGradMag, -1, -1, -1},        -1,  -1},
!   {tenGageRGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageRGradMag,            1,  1,  {tenGageRGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageRNormal,             3,  1,  {tenGageRGradVec, tenGageRGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageAniso, TEN_ANISO_MAX+1,  0,  {tenGageEval0, tenGageEval1, tenGageEval2, -1, -1},      -1,  -1}
  };
  
--- 24,83 ----
  gageItemEntry
  _tenGageTable[TEN_GAGE_ITEM_MAX+1] = {
!   /* enum value              len,deriv,  prereqs,                                                                     parent item, index*/
!   {tenGageTensor,              7,  0,  {-1, -1, -1, -1, -1},                                                                  -1,  -1},
! 
!   {tenGageTrace,               1,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
!   {tenGageB,                   1,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
!   {tenGageDet,                 1,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
!   {tenGageS,                   1,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
!   {tenGageQ,                   1,  0,  {tenGageS, tenGageB, -1, -1, -1},                                                      -1,  -1},
!   {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},
!   {tenGageEval0,               1,  0,  {tenGageEval, -1, -1, -1, -1},                                                tenGageEval,   0},
!   {tenGageEval1,               1,  0,  {tenGageEval, -1, -1, -1, -1},                                                tenGageEval,   1},
!   {tenGageEval2,               1,  0,  {tenGageEval, -1, -1, -1, -1},                                                tenGageEval,   2},
!   {tenGageEvec,                9,  0,  {tenGageTensor, -1, -1, -1, -1},                                                       -1,  -1},
!   {tenGageEvec0,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                                                tenGageEvec,   0},
!   {tenGageEvec1,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                                                tenGageEvec,   3},
!   {tenGageEvec2,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                                                tenGageEvec,   6},
! 
!   {tenGageTensorGrad,         21,  1,  {-1, -1, -1, -1, -1},                                                                  -1,  -1},
! 
!   {tenGageTraceGradVec,        3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},                                        -1,  -1},
!   {tenGageTraceGradMag,        1,  1,  {tenGageTraceGradVec, -1, -1, -1, -1},                                                 -1,  -1},
!   {tenGageTraceNormal,         3,  1,  {tenGageTraceGradVec, tenGageTraceGradMag, -1, -1, -1},                                -1,  -1},
! 
!   {tenGageBGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},                                        -1,  -1},
!   {tenGageBGradMag,            1,  1,  {tenGageBGradVec, -1, -1, -1, -1},                                                     -1,  -1},
!   {tenGageBNormal,             3,  1,  {tenGageBGradVec, tenGageBGradMag, -1, -1, -1},                                        -1,  -1},
! 
!   {tenGageDetGradVec,          3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},                                        -1,  -1},
!   {tenGageDetGradMag,          1,  1,  {tenGageDetGradVec, -1, -1, -1, -1},                                                   -1,  -1},
!   {tenGageDetNormal,           3,  1,  {tenGageDetGradVec, tenGageDetGradMag, -1, -1, -1},                                    -1,  -1},
! 
!   {tenGageSGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},                                        -1,  -1},
!   {tenGageSGradMag,            1,  1,  {tenGageSGradVec, -1, -1, -1, -1},                                                     -1,  -1},
!   {tenGageSNormal,             3,  1,  {tenGageSGradVec, tenGageSGradMag, -1, -1, -1},                                        -1,  -1},
! 
!   {tenGageQGradVec,            3,  1,  {tenGageSGradVec, tenGageBGradVec, -1, -1, -1},                                        -1,  -1},
!   {tenGageQGradMag,            1,  1,  {tenGageQGradVec, -1, -1, -1, -1},                                                     -1,  -1},
!   {tenGageQNormal,             3,  1,  {tenGageQGradVec, tenGageQGradMag, -1, -1, -1},                                        -1,  -1},
! 
!   {tenGageFAGradVec,           3,  1,  {tenGageQGradVec, tenGageSGradVec, tenGageFA, -1, -1},                                 -1,  -1},
!   {tenGageFAGradMag,           1,  1,  {tenGageFAGradVec, -1, -1, -1, -1},                                                    -1,  -1},
!   {tenGageFANormal,            3,  1,  {tenGageFAGradVec, tenGageFAGradMag, -1, -1, -1},                                      -1,  -1},
! 
!   {tenGageRGradVec,            3,  1,  {tenGageTraceGradVec, tenGageBGradVec, tenGageDetGradVec, tenGageSGradVec, -1},        -1,  -1},
!   {tenGageRGradMag,            1,  1,  {tenGageRGradVec, -1, -1, -1, -1},                                                     -1,  -1},
!   {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}
  };
  
***************
*** 127,137 ****
  _tenGageAnswer (gageContext *ctx, gagePerVolume *pvl) {
    /* char me[]="_tenGageAnswer"; */
!   gage_t *tenAns, *evalAns, *evecAns, *vecTmp=NULL, magTmp=0,
!     tmp0, tmp1,
!     dtConf=0, dtA=0, dtB=0, dtC=0, dtD=0, dtE=0, dtF=0,
      *gradDtA=NULL, *gradDtB=NULL, *gradDtC=NULL,
      *gradDtD=NULL, *gradDtE=NULL, *gradDtF=NULL,
!     gradCbA[3], *gradCbS=NULL, *gradCbB=NULL, *gradCbQ=NULL,
!     cbQ=0, cbA=0, cbB=0, cbC=0, cbS=0;
  
  #if !GAGE_TYPE_FLOAT
--- 143,155 ----
  _tenGageAnswer (gageContext *ctx, gagePerVolume *pvl) {
    /* char me[]="_tenGageAnswer"; */
!   double epsilon=1.0E-13;
!   gage_t *tenAns, *evalAns, *evecAns, *vecTmp=NULL,
      *gradDtA=NULL, *gradDtB=NULL, *gradDtC=NULL,
      *gradDtD=NULL, *gradDtE=NULL, *gradDtF=NULL,
!     *gradCbS=NULL, *gradCbB=NULL, *gradCbQ=NULL, *gradCbR=NULL;
!   double tmp0, tmp1, magTmp=0,
!     gradCbA[3], gradCbC[3],
!     dtA=0, dtB=0, dtC=0, dtD=0, dtE=0, dtF=0,
!     cbQQQ=0, cbQ=0, cbR=0, cbA=0, cbB=0, cbC=0, cbS=0;
  
  #if !GAGE_TYPE_FLOAT
***************
*** 145,149 ****
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensor)) {
      /* done if doV */
-     dtConf = tenAns[0];
      dtA = tenAns[1];
      dtB = tenAns[2];
--- 163,166 ----
***************
*** 177,184 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFA)) {
!     pvl->directAnswer[tenGageFA][0] = 3*sqrt(cbQ/cbS);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageR)) {
!     pvl->directAnswer[tenGageR][0] = (5*cbA*cbB - 27*cbC - 2*cbA*cbS)/54;
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvec)) {
--- 194,207 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFA)) {
!     pvl->directAnswer[tenGageFA][0] = 3*sqrt(cbQ/(epsilon + cbS));
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageR)) {
!     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)) {
***************
*** 224,228 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageTraceNormal], 1.0/magTmp, vecTmp);
    }
    /* --- B --- */
--- 247,252 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageTraceNormal],
! 		 1.0/(epsilon + magTmp), vecTmp);
    }
    /* --- B --- */
***************
*** 241,245 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageBNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageBNormal], 1.0/magTmp, vecTmp);
    }
    /* --- Det --- */
--- 265,270 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageBNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageBNormal],
! 		 1.0/(epsilon + magTmp), vecTmp);
    }
    /* --- Det --- */
***************
*** 253,256 ****
--- 278,282 ----
  		      2*(dtB*dtC - dtA*dtE), gradDtE,
  		      dtA*dtD - dtB*dtB, gradDtF);
+     ELL_3V_SCALE(gradCbC, -1, vecTmp);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDetGradMag)) {
***************
*** 258,262 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDetNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageDetNormal], 1.0/magTmp, vecTmp);
    }
    /* --- S --- */
--- 284,289 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDetNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageDetNormal],
! 		 1.0/(epsilon + magTmp), vecTmp);
    }
    /* --- S --- */
***************
*** 275,279 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageSNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageSNormal], 1.0/magTmp, vecTmp);
    }
    /* --- Q --- */
--- 302,307 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageSNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageSNormal],
! 		 1.0/(epsilon + magTmp), vecTmp);
    }
    /* --- Q --- */
***************
*** 288,298 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageQNormal], 1.0/magTmp, vecTmp);
    }
    /* --- FA --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFAGradVec)) {
      vecTmp = pvl->directAnswer[tenGageFAGradVec];
!     tmp0 = 9.0/(2*pvl->directAnswer[tenGageFA][0]*cbS);
!     tmp1 = -tmp0*cbQ/cbS;
      ELL_3V_SCALE_ADD2(vecTmp,
  		      tmp0, gradCbQ, 
--- 316,327 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageQNormal],
! 		 1.0/(epsilon + magTmp), vecTmp);
    }
    /* --- FA --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFAGradVec)) {
      vecTmp = pvl->directAnswer[tenGageFAGradVec];
!     tmp0 = 9.0/(epsilon + 2*pvl->directAnswer[tenGageFA][0]*cbS);
!     tmp1 = -tmp0*cbQ/(epsilon + cbS);
      ELL_3V_SCALE_ADD2(vecTmp,
  		      tmp0, gradCbQ, 
***************
*** 303,314 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFANormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageFANormal], 1.0/magTmp, vecTmp);
    }
    /* --- R --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRGradVec)) {
!     vecTmp = pvl->directAnswer[tenGageRGradVec];
      ELL_3V_SCALE_ADD4(vecTmp,
  		      (5*cbB - 2*cbS)/54.0, gradCbA,
! 		      1.0/2.0, pvl->directAnswer[tenGageDetGradVec],
  		      5.0*cbA/54.0, gradCbB,
  		      -cbA/27.0, gradCbS);
--- 332,345 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFANormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageFANormal],
! 		 1.0/(epsilon + magTmp), vecTmp);
    }
    /* --- R --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRGradVec)) {
!     gradCbR = vecTmp = pvl->directAnswer[tenGageRGradVec];
!     tmp0 = 1.0/(epsilon + 2*sqrt(cbQ*cbQ*cbQ));
      ELL_3V_SCALE_ADD4(vecTmp,
  		      (5*cbB - 2*cbS)/54.0, gradCbA,
! 		      -1.0/2.0, gradCbC,
  		      5.0*cbA/54.0, gradCbB,
  		      -cbA/27.0, gradCbS);
***************
*** 318,322 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageRNormal], 1.0/magTmp, vecTmp);
    }
    /* --- Aniso --- */
--- 349,372 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageRNormal],
! 		 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));
!     tmp1 = 1.0/(epsilon + tmp1);
!     tmp0 = tmp1*3*cbR/(epsilon + 2*cbQ);
!     ELL_3V_SCALE_ADD2(vecTmp,
! 		      tmp0, gradCbQ,
! 		      -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);
    }
    /* --- Aniso --- */

[Teem-commit] teem/src/gage scl.c,1.31,1.32

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

Update of /cvsroot/teem/teem/src/gage
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30002

Modified Files:
	scl.c 
Log Message:
made gageScl airEnum strings for gradient vector and gradient vector more consistent with those that are used in tenGage

Index: scl.c
===================================================================
RCS file: /cvsroot/teem/teem/src/gage/scl.c,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** scl.c	19 Feb 2004 03:50:02 -0000	1.31
--- scl.c	23 Feb 2004 06:02:19 -0000	1.32
***************
*** 191,196 ****
  _gageSclStrEqv[][AIR_STRLEN_SMALL] = {
    "v", "val", "value", 
!   "grad", "gvec", "gradvec", "grad vec", "gradient vector",
!   "g", "gm", "gmag", "gradmag", "grad mag", "gradient magnitude",
    "n", "normal", "gnorm", "normg", "norm", "normgrad", \
         "norm grad", "normalized gradient",
--- 191,196 ----
  _gageSclStrEqv[][AIR_STRLEN_SMALL] = {
    "v", "val", "value", 
!   "gv", "gvec", "gradvec", "grad vec", "gradient vector",
!   "gm", "gmag", "gradmag", "grad mag", "gradient magnitude",
    "n", "normal", "gnorm", "normg", "norm", "normgrad", \
         "norm grad", "normalized gradient",
***************
*** 225,229 ****
    GS_V, GS_V, GS_V,
    GS_GV, GS_GV, GS_GV, GS_GV, GS_GV, 
!   GS_GM, GS_GM, GS_GM, GS_GM, GS_GM, GS_GM,
    GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N,
    GS_NP, GS_NP,
--- 225,229 ----
    GS_V, GS_V, GS_V,
    GS_GV, GS_GV, GS_GV, GS_GV, GS_GV, 
!   GS_GM, GS_GM, GS_GM, GS_GM, GS_GM,
    GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N, GS_N,
    GS_NP, GS_NP,

[Teem-commit] teem/src/ell ellMacros.h,1.38,1.39

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

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28431

Modified Files:
	ellMacros.h 
Log Message:
fixed typos in ELL_3V macros

Index: ellMacros.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/ellMacros.h,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** ellMacros.h	23 Feb 2004 02:38:59 -0000	1.38
--- ellMacros.h	23 Feb 2004 02:54:22 -0000	1.39
***************
*** 158,173 ****
     (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2])
  
! #define ELL_3V_SCALE_ADD4(v3, s0, v0, s1, v1, s2, v2, s3, v3)           \
!   ((v3)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0] + (s3)*(v3)[0], \
!    (v3)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1] + (s3)*(v3)[1], \
!    (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2] + (s3)*(v3)[2])
  
! #define ELL_3V_SCALE_ADD6(v3, s0, v0, s1, v1, s2, v2,     \
                                s3, v3, s4, v4, s5, v5)     \
!   ((v3)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0]   \
             + (s3)*(v3)[0] + (s4)*(v4)[0] + (s5)*(v5)[0],  \
!    (v3)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1]   \
             + (s3)*(v3)[1] + (s4)*(v4)[1] + (s5)*(v5)[1],  \
!    (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2]   \
             + (s3)*(v3)[2] + (s4)*(v4)[2] + (s5)*(v5)[2])
  
--- 158,173 ----
     (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2])
  
! #define ELL_3V_SCALE_ADD4(v4, s0, v0, s1, v1, s2, v2, s3, v3)           \
!   ((v4)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0] + (s3)*(v3)[0], \
!    (v4)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1] + (s3)*(v3)[1], \
!    (v4)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2] + (s3)*(v3)[2])
  
! #define ELL_3V_SCALE_ADD6(v6, s0, v0, s1, v1, s2, v2,     \
                                s3, v3, s4, v4, s5, v5)     \
!   ((v6)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0]   \
             + (s3)*(v3)[0] + (s4)*(v4)[0] + (s5)*(v5)[0],  \
!    (v6)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1]   \
             + (s3)*(v3)[1] + (s4)*(v4)[1] + (s5)*(v5)[1],  \
!    (v6)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2]   \
             + (s3)*(v3)[2] + (s4)*(v4)[2] + (s5)*(v5)[2])
  

[Teem-commit] teem/src/ten aniso.c,1.25,1.26 enumsTen.c,1.15,1.16 ten.h,1.73,1.74 tenGage.c,1.13,1.14 tensor.c,1.26,1.27

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

Update of /cvsroot/teem/teem/src/ten
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26294

Modified Files:
	aniso.c enumsTen.c ten.h tenGage.c tensor.c 
Log Message:
debugging tenGageKind

Index: aniso.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/aniso.c,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** aniso.c	7 Jan 2004 15:34:31 -0000	1.25
--- aniso.c	23 Feb 2004 02:40:18 -0000	1.26
***************
*** 185,189 ****
    in = nin->data;
    for (I=0; I<=N-1; I++) {
!     /* tenVerbose = (I == 1882); */
      tensor = in + I*7;
      if (tensor[0] < thresh) {
--- 185,189 ----
    in = nin->data;
    for (I=0; I<=N-1; I++) {
!     /* tenVerbose = (I == 911327); */
      tensor = in + I*7;
      if (tensor[0] < thresh) {

Index: enumsTen.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/enumsTen.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** enumsTen.c	19 Feb 2004 11:14:09 -0000	1.15
--- enumsTen.c	23 Feb 2004 02:40:24 -0000	1.16
***************
*** 64,87 ****
  _tenGageStr[][AIR_STRLEN_SMALL] = {
    "(unknown tenGage)",
    "tensor",
    "trace",
!   "frob",
!   "eigenvalues",
!   "eigenvalue0",
!   "eigenvalue1",
!   "eigenvalue2",
!   "eigenvectors",
!   "eigenvector0",
!   "eigenvector1",
!   "eigenvector2",
!   "tensor gradient",
!   "Q anisotropy",
!   "Q gradient vector",
!   "Q gradient magnitude",
!   "normalized Q gradient",
!   "multigrad",
!   "fro(multigrad)",
!   "multigrad eigenvalues",
!   "multigrad eigenvectors",
    "anisotropies"
  };
--- 64,116 ----
  _tenGageStr[][AIR_STRLEN_SMALL] = {
    "(unknown tenGage)",
+ 
    "tensor",
    "trace",
!   "B",
!   "det",
!   "S",
!   "Q",
!   "FA",
!   "R",
! 
!   "evals",
!   "eval0",
!   "eval1",
!   "eval2",
!   "evecs",
!   "evec0",
!   "evec1",
!   "evec2",
! 
!   "tensor grad",
! 
!   "trace grad vec",
!   "trace grad mag",
!   "trace normal",
! 
!   "B grad vec",
!   "B grad mag",
!   "B normal",
! 
!   "det grad vec",
!   "det grad mag",
!   "det normal",
! 
!   "S grad vec",
!   "S grad mag",
!   "S normal",
! 
!   "Q grad vec",
!   "Q grad mag",
!   "Q normal",
! 
!   "FA grad vec",
!   "FA grad mag",
!   "FA normal",
! 
!   "R grad vec",
!   "R grad mag",
!   "R normal",
! 
    "anisotropies"
  };
***************
*** 89,113 ****
  char
  _tenGageDesc[][AIR_STRLEN_MED] = {
!   "unknown tenGage query",
!   "reconstructed tensor",
!   "tensor trace",
!   "frob(tensor)",
!   "3 tensor eigenvalues",
!   "tensor eigenvalue 0",
!   "tensor eigenvalue 1",
!   "tensor eigenvalue 2",
!   "3 tensor eigenvectors",
!   "tensor eigenvector 0",
!   "tensor eigenvector 1",
!   "tensor eigenvector 2",
!   "tensor gradient",
!   "Q anisotropy",
!   "Q gradient vector",
!   "Q gradient magnitude",
!   "normalized Q gradient",
!   "multigrad",
!   "frob(multigrad)",
!   "multigrad eigenvalues",
!   "multigrad eigenvectors",
    "anisotropies"
  };
--- 118,160 ----
  char
  _tenGageDesc[][AIR_STRLEN_MED] = {
!   "(unknown tenGage item)",
!   "tensor",
!   "trace",
!   "B",
!   "determinant",
!   "S",
!   "Q",
!   "FA",
!   "R",
!   "3 eigenvalues",
!   "eigenvalue 0",
!   "eigenvalue 1",
!   "eigenvalue 2",
!   "3 eigenvectors",
!   "eigenvector 0",
!   "eigenvector 1",
!   "eigenvector 2",
!   "tensor gradients",
!   "trace grad vec",
!   "trace grad mag",
!   "trace normal",
!   "B grad vec",
!   "B grad mag",
!   "B normal",
!   "determinant grad vec",
!   "determinant grad mag",
!   "determinant normal",
!   "S grad vec",
!   "S grad mag",
!   "S normal",
!   "Q grad vec",
!   "Q grad mag",
!   "Q normal",
!   "FA grad vec",
!   "FA grad mag",
!   "FA normal",
!   "R grad vec",
!   "R grad mag",
!   "R normal",
    "anisotropies"
  };
***************
*** 116,186 ****
  _tenGageVal[] = {
    tenGageUnknown,
!   tenGageTensor,
!   tenGageTrace,
!   tenGageFrobTensor,
!   tenGageEval,
!   tenGageEval0,
!   tenGageEval1,
!   tenGageEval2,
!   tenGageEvec,
!   tenGageEvec0,
!   tenGageEvec1,
!   tenGageEvec2,
!   tenGageTensorGrad,
!   tenGageQ,
!   tenGageQGradVec,
!   tenGageQGradMag,
!   tenGageQNormal,
!   tenGageMultiGrad,
!   tenGageFrobMG,
!   tenGageMGEval,
!   tenGageMGEvec,
!   tenGageAniso
  };
  
- #define TG_T    tenGageTensor
- #define TG_TR   tenGageTrace
- #define TG_FT   tenGageFrobTensor
- #define TG_AL   tenGageEval
- #define TG_AL0   tenGageEval0
- #define TG_AL1   tenGageEval1
- #define TG_AL2   tenGageEval2
- #define TG_EC   tenGageEvec
- #define TG_EC0   tenGageEvec0
- #define TG_EC1   tenGageEvec1
- #define TG_EC2   tenGageEvec2
- #define TG_TG   tenGageTensorGrad
- #define TG_Q    tenGageQ
- #define TG_QGV  tenGageQGradVec
- #define TG_QGM  tenGageQGradMag
- #define TG_QGN  tenGageQNormal
- #define TG_MG   tenGageMultiGrad
- #define TG_FMG  tenGageFrobMG
- #define TG_MGA  tenGageMGEval
- #define TG_MGE  tenGageMGEvec
- #define TG_AN   tenGageAniso
- 
  char
  _tenGageStrEqv[][AIR_STRLEN_SMALL] = {
!   "t", "ten", "tensor",
    "tr", "trace",
!   "frt", "fro", "frob", "frobt",
!   "eval", "eigenvalue",
!   "eval0", "eigenvalue0",
!   "eval1", "eigenvalue1",
!   "eval2", "eigenvalue2",
!   "evec", "eigenvector",
!   "evec0", "eigenvector0",
!   "evec1", "eigenvector1",
!   "evec2", "eigenvector2",
!   "tg", "tgrad", "t grad", "tensor gradient",
    "q",
!   "qv", "qgrad", "q grad", "q gradient vector",
!   "qg", "qgmag", "q gmag", "q gradient magnitude",
!   "qn", "qnorm", "q norm", "normalized q gradient",
!   "mg", "multigrad",
!   "frmg", "frobmg", "frob mg",
!   "mgeval", "mg eval", "multigrad eigenvalues",
!   "mgevec", "mg evec", "multigrad eigenvectors",
    "an", "aniso", "anisotropies",
    ""
--- 163,247 ----
  _tenGageVal[] = {
    tenGageUnknown,
!   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] */
!   tenGageEval,          /*  8: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /*  9: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /* 10: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* 11: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* 12: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* 13: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* 14: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 15: "evec2", minor eigenvectors of tensor: GT[3] */
!   tenGageTensorGrad,    /* 16: "tg, all tensor component gradients: GT[21] */
!   tenGageTraceGradVec,  /* 17: "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* 18: "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* 19: "trn": normal of trace: GT[3] */
!   tenGageBGradVec,      /* 20: "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* 21: "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* 22: "bn", normal of B: GT[3] */
!   tenGageDetGradVec,    /* 23: "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* 24: "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* 25: "detn", normal of Det: GT[3] */
!   tenGageSGradVec,      /* 26: "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* 27: "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* 28: "sn", normal of S: GT[3] */
!   tenGageQGradVec,      /* 29: "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 30: "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 31: "qn", normalized gradient of Q: GT[3] */
!   tenGageFAGradVec,     /* 32: "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* 33: "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* 34: "fan", normalized gradient of FA: GT[3] */
!   tenGageRGradVec,      /* 35: "rgv", gradient vector of Q: GT[3] */
!   tenGageRGradMag,      /* 36: "rgm", gradient magnitude of Q: GT[1] */
!   tenGageRNormal,       /* 37: "rn", normalized gradient of Q: GT[3] */
!   tenGageAniso          /* 38: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
  };
  
  char
  _tenGageStrEqv[][AIR_STRLEN_SMALL] = {
!   "t", "tensor",
    "tr", "trace",
!   "b",
!   "det",
!   "s",
    "q",
!   "fa",
!   "r",
!   "eval",
!   "eval0",
!   "eval1",
!   "eval2",
!   "evec",
!   "evec0",
!   "evec1",
!   "evec2",
!   "tg", "tensor grad",
!   "trgv", "tracegv", "trace grad vec",
!   "trgm", "tracegm", "trace grad mag",
!   "trn", "tracen", "trace normal",
!   "bgv", "b grad vec",
!   "bgm", "b grad mag",
!   "bn", "b normal",
!   "detgv", "det grad vec",
!   "detgm", "det grad mag",
!   "detn", "det normal",
!   "sgv", "s grad vec",
!   "sgm", "s grad mag",
!   "sn", "s normal",
!   "qgv", "q grad vec",
!   "qgm", "q grad mag",
!   "qn", "q normal",
!   "fagv", "fa grad vec",
!   "fagm", "fa grad mag",
!   "fan", "fa normal",
!   "rgv", "r grad vec",
!   "rgm", "r grad mag",
!   "rn", "r normal",
    "an", "aniso", "anisotropies",
    ""
***************
*** 189,213 ****
  int
  _tenGageValEqv[] = {
!   TG_T, TG_T, TG_T,
!   TG_TR, TG_TR,
!   TG_FT, TG_FT, TG_FT, TG_FT,
!   TG_AL, TG_AL,
!   TG_AL0, TG_AL0,
!   TG_AL1, TG_AL1,
!   TG_AL2, TG_AL2,
!   TG_EC, TG_EC,
!   TG_EC0, TG_EC0,
!   TG_EC1, TG_EC1,
!   TG_EC2, TG_EC2,
!   TG_TG, TG_TG, TG_TG, TG_TG,
!   TG_Q,
!   TG_QGV, TG_QGV, TG_QGV, TG_QGV,
!   TG_QGM, TG_QGM, TG_QGM, TG_QGM,
!   TG_QGN, TG_QGN, TG_QGN, TG_QGN,
!   TG_MG, TG_MG,
!   TG_FMG, TG_FMG, TG_FMG,
!   TG_MGA, TG_MGA, TG_MGA,
!   TG_MGE, TG_MGE, TG_MGE,
!   TG_AN, TG_AN, TG_AN
  };
  
--- 250,292 ----
  int
  _tenGageValEqv[] = {
!   tenGageTensor, tenGageTensor,
!   tenGageTrace, tenGageTrace,
!   tenGageB,
!   tenGageDet,
!   tenGageS,
!   tenGageQ,
!   tenGageFA,
!   tenGageR,
!   tenGageEval,
!   tenGageEval0,
!   tenGageEval1,
!   tenGageEval2,
!   tenGageEvec,
!   tenGageEvec0,
!   tenGageEvec1,
!   tenGageEvec2,
!   tenGageTensorGrad, tenGageTensorGrad,
!   tenGageTraceGradVec, tenGageTraceGradVec, tenGageTraceGradVec,
!   tenGageTraceGradMag, tenGageTraceGradMag, tenGageTraceGradMag,
!   tenGageTraceNormal, tenGageTraceNormal, tenGageTraceNormal,
!   tenGageBGradVec, tenGageBGradVec,
!   tenGageBGradMag, tenGageBGradMag,
!   tenGageBNormal, tenGageBNormal,
!   tenGageDetGradVec, tenGageDetGradVec,
!   tenGageDetGradMag, tenGageDetGradMag,
!   tenGageDetNormal, tenGageDetNormal,
!   tenGageSGradVec, tenGageSGradVec,
!   tenGageSGradMag, tenGageSGradMag,
!   tenGageSNormal, tenGageSNormal,
!   tenGageQGradVec, tenGageQGradVec,
!   tenGageQGradMag, tenGageQGradMag,
!   tenGageQNormal, tenGageQNormal,
!   tenGageFAGradVec, tenGageFAGradVec,
!   tenGageFAGradMag, tenGageFAGradMag,
!   tenGageFANormal, tenGageFANormal,
!   tenGageRGradVec, tenGageRGradVec,
!   tenGageRGradMag, tenGageRGradMag,
!   tenGageRNormal, tenGageRNormal,
!   tenGageAniso, tenGageAniso, tenGageAniso
  };
  

Index: ten.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/ten.h,v
retrieving revision 1.73
retrieving revision 1.74
diff -C2 -d -r1.73 -r1.74
*** ten.h	19 Feb 2004 11:14:09 -0000	1.73
--- ten.h	23 Feb 2004 02:40:24 -0000	1.74
***************
*** 141,176 ****
  ** 
  ** all the possible queries supported in the tenGage gage kind
  */
  enum {
    tenGageUnknown = -1,  /* -1: nobody knows */
    tenGageTensor,        /*  0: "t", the reconstructed tensor: GT[7] */
    tenGageTrace,         /*  1: "tr", trace of tensor: GT[1] */
!   tenGageFrobTensor,    /*  2: "fro", frobenius norm of tensor: GT[1] */
!   tenGageEval,          /*  3: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /*  4: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /*  5: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /*  6: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /*  7: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /*  8: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /*  9: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 10: "evec2", minor eigenvectors of tensor: GT[3] */
!   tenGageTensorGrad,    /* 11: "tg", all tensor component gradients, starting
! 			       with the confidence value gradient: GT[21] */
!   tenGageQ,             /* 12: "q", Q anisotropy (or 9 times it): GT[1] */
!   tenGageQGradVec,      /* 13: "qv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 14: "qg", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 15: "qn", normalized gradient of Q GT[3] */
!   tenGageMultiGrad,     /* 16: "mg", sum of outer products of gradients of 
! 			       tensor elements, correctly counting the
! 			       off-diagonal entries twice, but not counting
! 			       the confidence value: GT[9] */
!   tenGageFrobMG,        /* 17: "frmg", frob. norm of multi gradient: GT[1] */
!   tenGageMGEval,        /* 18: "mgeval", eigenvalues of multi gradient: GT[3]*/
!   tenGageMGEvec,        /* 19: "mgevec", eigenvectors of multi
! 			       gradient: GT[9] */
!   tenGageAniso,         /* 20: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  20
  
  /*
--- 141,212 ----
  ** 
  ** all the possible queries supported in the tenGage gage kind
+ ** various properties of the quantities below (eigenvalues = v1, v2, v3):
+ ** eigenvalue cubic equation: v^3 + A*v^2 + B*v + C = 0
+ ** Trace = v1 + v2 + v3 = -A
+ ** B = v1*v2 + v1*v3 + v2*v3
+ ** Det = v1*v2*v3 = -C
+ ** S = v1*v1 + v2*v2 + v3*v3
+ ** Q = (S-B)/9 = variance({v1,v2,v3})/2 = (RootRadius/2)^2
+ ** FA = 3*sqrt(Q/S)
+ ** R = (9*A*B - 2*A^3 - 27*C)/54 
+      = (5*A*B - 2*A*S - 27*C)/54 = thirdmoment({v1,v2,v3})/2
+ ** (phase in cubic solution = arccos(R/sqrt(Q)^3))
  */
  enum {
    tenGageUnknown = -1,  /* -1: nobody knows */
+ 
    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] */
! 
!   tenGageEval,          /*  8: "eval", all eigenvalues of tensor : GT[3] */
!   tenGageEval0,         /*  9: "eval0", major eigenvalue of tensor : GT[1] */
!   tenGageEval1,         /* 10: "eval1", medium eigenvalue of tensor : GT[1] */
!   tenGageEval2,         /* 11: "eval2", minor eigenvalue of tensor : GT[1] */
!   tenGageEvec,          /* 12: "evec", major eigenvectors of tensor: GT[9] */
!   tenGageEvec0,         /* 13: "evec0", major eigenvectors of tensor: GT[3] */
!   tenGageEvec1,         /* 14: "evec1", medium eigenvectors of tensor: GT[3] */
!   tenGageEvec2,         /* 15: "evec2", minor eigenvectors of tensor: GT[3] */
! 
!   tenGageTensorGrad,    /* 16: "tg, all tensor component gradients, starting
! 			       with the confidence gradient: GT[21] */
! 
!   tenGageTraceGradVec,  /* 17: "trgv": gradient (vector) of trace: GT[3] */
!   tenGageTraceGradMag,  /* 18: "trgm": gradient magnitude of trace: GT[1] */
!   tenGageTraceNormal,   /* 19: "trn": normal of trace: GT[3] */
!   
!   tenGageBGradVec,      /* 20: "bgv", gradient (vector) of B: GT[3] */
!   tenGageBGradMag,      /* 21: "bgm", gradient magnitude of B: GT[1] */
!   tenGageBNormal,       /* 22: "bn", normal of B: GT[3] */
! 
!   tenGageDetGradVec,    /* 23: "detgv", gradient (vector) of Det: GT[3] */
!   tenGageDetGradMag,    /* 24: "detgm", gradient magnitude of Det: GT[1] */
!   tenGageDetNormal,     /* 25: "detn", normal of Det: GT[3] */
! 
!   tenGageSGradVec,      /* 26: "sgv", gradient (vector) of S: GT[3] */
!   tenGageSGradMag,      /* 27: "sgm", gradient magnitude of S: GT[1] */
!   tenGageSNormal,       /* 28: "sn", normal of S: GT[3] */
! 
!   tenGageQGradVec,      /* 29: "qgv", gradient vector of Q: GT[3] */
!   tenGageQGradMag,      /* 30: "qgm", gradient magnitude of Q: GT[1] */
!   tenGageQNormal,       /* 31: "qn", normalized gradient of Q: GT[3] */
! 
!   tenGageFAGradVec,     /* 32: "fagv", gradient vector of FA: GT[3] */
!   tenGageFAGradMag,     /* 33: "fagm", gradient magnitude of FA: GT[1] */
!   tenGageFANormal,      /* 34: "fan", normalized gradient of FA: GT[3] */
! 
!   tenGageRGradVec,      /* 35: "rgv", gradient vector of Q: GT[3] */
!   tenGageRGradMag,      /* 36: "rgm", gradient magnitude of Q: GT[1] */
!   tenGageRNormal,       /* 37: "rn", normalized gradient of Q: GT[3] */
! 
!   tenGageAniso,         /* 38: "an", all anisotropies: GT[TEN_ANISO_MAX+1] */
    tenGageLast
  };
! #define TEN_GAGE_ITEM_MAX  38
  
  /*

Index: tenGage.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tenGage.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** tenGage.c	19 Feb 2004 11:14:09 -0000	1.13
--- tenGage.c	23 Feb 2004 02:40:24 -0000	1.14
***************
*** 27,31 ****
    {tenGageTensor,              7,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {tenGageTrace,               1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageFrobTensor,          1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
    {tenGageEval,                3,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
    {tenGageEval0,               1,  0,  {tenGageEval, -1, -1, -1, -1},                  tenGageEval,   0},
--- 27,36 ----
    {tenGageTensor,              7,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {tenGageTrace,               1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageB,                   1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageDet,                 1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageS,                   1,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
!   {tenGageQ,                   1,  0,  {tenGageS, tenGageB, -1, -1, -1},                        -1,  -1},
!   {tenGageFA,                  1,  0,  {tenGageQ, tenGageS, -1, -1, -1},                        -1,  -1},
!   {tenGageR,                   1,  0,  {tenGageTrace, tenGageB, tenGageDet, tenGageS, -1},      -1,  -1},
    {tenGageEval,                3,  0,  {tenGageTensor, -1, -1, -1, -1},                         -1,  -1},
    {tenGageEval0,               1,  0,  {tenGageEval, -1, -1, -1, -1},                  tenGageEval,   0},
***************
*** 37,48 ****
    {tenGageEvec2,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                  tenGageEvec,   6},
    {tenGageTensorGrad,         21,  1,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {tenGageQ,                   1,  0,  {-1, -1, -1, -1, -1},                                    -1,  -1},
    {tenGageQGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
    {tenGageQGradMag,            1,  1,  {tenGageQGradVec, -1, -1, -1, -1},                       -1,  -1},
    {tenGageQNormal,             3,  1,  {tenGageQGradVec, tenGageQGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageMultiGrad,           9,  1,  {tenGageTensorGrad, -1, -1, -1, -1},                     -1,  -1},
!   {tenGageFrobMG,              1,  1,  {tenGageMultiGrad, -1, -1, -1, -1},                      -1,  -1},
!   {tenGageMGEval,              3,  1,  {tenGageMultiGrad, -1, -1, -1, -1},                      -1,  -1},
!   {tenGageMGEvec,              9,  1,  {tenGageMultiGrad, -1, -1, -1, -1},                      -1,  -1},
    {tenGageAniso, TEN_ANISO_MAX+1,  0,  {tenGageEval0, tenGageEval1, tenGageEval2, -1, -1},      -1,  -1}
  };
--- 42,66 ----
    {tenGageEvec2,               3,  0,  {tenGageEvec, -1, -1, -1, -1},                  tenGageEvec,   6},
    {tenGageTensorGrad,         21,  1,  {-1, -1, -1, -1, -1},                                    -1,  -1},
!   {tenGageTraceGradVec,        3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageTraceGradMag,        1,  1,  {tenGageTraceGradVec, -1, -1, -1, -1},                   -1,  -1},
!   {tenGageTraceNormal,         3,  1,  {tenGageTraceGradVec, tenGageTraceGradMag, -1, -1, -1},  -1,  -1},
!   {tenGageBGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageBGradMag,            1,  1,  {tenGageBGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageBNormal,             3,  1,  {tenGageBGradVec, tenGageBGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageDetGradVec,          3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageDetGradMag,          1,  1,  {tenGageDetGradVec, -1, -1, -1, -1},                     -1,  -1},
!   {tenGageDetNormal,           3,  1,  {tenGageDetGradVec, tenGageDetGradMag, -1, -1, -1},      -1,  -1},
!   {tenGageSGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageSGradMag,            1,  1,  {tenGageSGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageSNormal,             3,  1,  {tenGageSGradVec, tenGageSGradMag, -1, -1, -1},          -1,  -1},
    {tenGageQGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
    {tenGageQGradMag,            1,  1,  {tenGageQGradVec, -1, -1, -1, -1},                       -1,  -1},
    {tenGageQNormal,             3,  1,  {tenGageQGradVec, tenGageQGradMag, -1, -1, -1},          -1,  -1},
!   {tenGageFAGradVec,           3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageFAGradMag,           1,  1,  {tenGageFAGradVec, -1, -1, -1, -1},                      -1,  -1},
!   {tenGageFANormal,            3,  1,  {tenGageFAGradVec, tenGageFAGradMag, -1, -1, -1},        -1,  -1},
!   {tenGageRGradVec,            3,  1,  {tenGageTensor, tenGageTensorGrad, -1, -1, -1},          -1,  -1},
!   {tenGageRGradMag,            1,  1,  {tenGageRGradVec, -1, -1, -1, -1},                       -1,  -1},
!   {tenGageRNormal,             3,  1,  {tenGageRGradVec, tenGageRGradMag, -1, -1, -1},          -1,  -1},
    {tenGageAniso, TEN_ANISO_MAX+1,  0,  {tenGageEval0, tenGageEval1, tenGageEval2, -1, -1},      -1,  -1}
  };
***************
*** 109,114 ****
  _tenGageAnswer (gageContext *ctx, gagePerVolume *pvl) {
    /* char me[]="_tenGageAnswer"; */
!   gage_t *tenAns, *tgradAns, *QgradAns, *evalAns, *evecAns, tmptmp=0,
!     dtA=0, dtB=0, dtC=0, dtD=0, dtE=0, dtF=0, cbA, cbB;
  
  #if !GAGE_TYPE_FLOAT
--- 127,137 ----
  _tenGageAnswer (gageContext *ctx, gagePerVolume *pvl) {
    /* char me[]="_tenGageAnswer"; */
!   gage_t *tenAns, *evalAns, *evecAns, *vecTmp=NULL, magTmp=0,
!     tmp0, tmp1,
!     dtConf=0, dtA=0, dtB=0, dtC=0, dtD=0, dtE=0, dtF=0,
!     *gradDtA=NULL, *gradDtB=NULL, *gradDtC=NULL,
!     *gradDtD=NULL, *gradDtE=NULL, *gradDtF=NULL,
!     gradCbA[3], *gradCbS=NULL, *gradCbB=NULL, *gradCbQ=NULL,
!     cbQ=0, cbA=0, cbB=0, cbC=0, cbS=0;
  
  #if !GAGE_TYPE_FLOAT
***************
*** 118,127 ****
  
    tenAns = pvl->directAnswer[tenGageTensor];
-   tgradAns = pvl->directAnswer[tenGageTensorGrad];
-   QgradAns = pvl->directAnswer[tenGageQGradVec];
    evalAns = pvl->directAnswer[tenGageEval];
    evecAns = pvl->directAnswer[tenGageEvec];
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensor)) {
      /* done if doV */
      dtA = tenAns[1];
      dtB = tenAns[2];
--- 141,149 ----
  
    tenAns = pvl->directAnswer[tenGageTensor];
    evalAns = pvl->directAnswer[tenGageEval];
    evecAns = pvl->directAnswer[tenGageEvec];
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensor)) {
      /* done if doV */
+     dtConf = tenAns[0];
      dtA = tenAns[1];
      dtB = tenAns[2];
***************
*** 136,145 ****
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTrace)) {
!     pvl->directAnswer[tenGageTrace][0] = dtA + dtD + dtF;
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFrobTensor)) {
!     pvl->directAnswer[tenGageFrobTensor][0] = sqrt(dtA*dtA + 2*dtB*dtB 
! 						   + 2*dtC*dtC + dtD*dtD
! 						   + 2*dtE*dtE + dtF*dtF);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvec)) {
--- 158,184 ----
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTrace)) {
!     cbA = -(pvl->directAnswer[tenGageTrace][0] = dtA + dtD + dtF);
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageB)) {
!     cbB = pvl->directAnswer[tenGageB][0] = 
!       dtA*dtD + dtA*dtF + dtD*dtF - dtB*dtB - dtC*dtC - dtE*dtE;
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDet)) {
!     cbC = -(pvl->directAnswer[tenGageDet][0] = 
! 	    2*dtB*dtC*dtE + dtA*dtD*dtF 
! 	    - dtC*dtC*dtD - dtA*dtE*dtE - dtB*dtB*dtF);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageS)) {
!     cbS = (pvl->directAnswer[tenGageS][0] = 
! 	   dtA*dtA + dtD*dtD + dtF*dtF + 2*dtB*dtB + 2*dtC*dtC + 2*dtE*dtE);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQ)) {
!     cbQ = pvl->directAnswer[tenGageQ][0] = (cbS - cbB)/9;
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFA)) {
!     pvl->directAnswer[tenGageFA][0] = 3*sqrt(cbQ/cbS);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageR)) {
!     pvl->directAnswer[tenGageR][0] = (5*cbA*cbB - 27*cbC - 2*cbA*cbS)/54;
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvec)) {
***************
*** 166,198 ****
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensorGrad)) {
      /* done if doD1 */
    }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQ)) {
!     cbA = -(dtA + dtD + dtF);
!     cbB = dtA*dtD - dtB*dtB + dtA*dtF - dtC*dtC + dtD*dtF - dtE*dtE;
!     /*
!     cbC = -(dtA*dtD*dtF + 2*dtB*dtE*dtC
! 	    - dtC*dtC*dtD - dtB*dtB*dtF - dtA*dtE*dtE);
!     */
!     pvl->directAnswer[tenGageQ][0] = cbA*cbA - 3*cbB;
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQGradVec)) {
!     ELL_3V_SET(QgradAns, 0, 0, 0);
!     ELL_3V_SCALE_INCR(QgradAns,   dtA, tgradAns + 1*3);
!     ELL_3V_SCALE_INCR(QgradAns, 2*dtB, tgradAns + 2*3);
!     ELL_3V_SCALE_INCR(QgradAns, 2*dtC, tgradAns + 3*3);
!     ELL_3V_SCALE_INCR(QgradAns,   dtD, tgradAns + 4*3);
!     ELL_3V_SCALE_INCR(QgradAns, 2*dtE, tgradAns + 5*3);
!     ELL_3V_SCALE_INCR(QgradAns,   dtF, tgradAns + 6*3);
!     tmptmp = -(dtA + dtD + dtF)/3;
!     ELL_3V_SCALE_INCR(QgradAns, tmptmp, tgradAns + 1*3);
!     ELL_3V_SCALE_INCR(QgradAns, tmptmp, tgradAns + 4*3);
!     ELL_3V_SCALE_INCR(QgradAns, tmptmp, tgradAns + 6*3);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQGradMag)) {
!     tmptmp = pvl->directAnswer[tenGageQGradMag][0] = ELL_3V_LEN(QgradAns);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageQNormal], 1.0/tmptmp, QgradAns);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageAniso)) {
  #if GAGE_TYPE_FLOAT
--- 205,324 ----
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensorGrad)) {
      /* done if doD1 */
+     vecTmp = pvl->directAnswer[tenGageTensorGrad];
+     gradDtA = vecTmp + 1*3;
+     gradDtB = vecTmp + 2*3;
+     gradDtC = vecTmp + 3*3;
+     gradDtD = vecTmp + 4*3;
+     gradDtE = vecTmp + 5*3;
+     gradDtF = vecTmp + 6*3;
    }
! 
!   /* --- Trace --- */
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceGradVec)) {
!     vecTmp = pvl->directAnswer[tenGageTraceGradVec];
!     ELL_3V_ADD3(vecTmp, gradDtA, gradDtD, gradDtF);
!     ELL_3V_SCALE(gradCbA, -1, vecTmp);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceGradMag)) {
!     magTmp = pvl->directAnswer[tenGageTraceGradMag][0] = ELL_3V_LEN(vecTmp);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTraceNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageTraceNormal], 1.0/magTmp, vecTmp);
!   }
!   /* --- B --- */
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageBGradVec)) {
!     gradCbB = vecTmp = pvl->directAnswer[tenGageBGradVec];
!     ELL_3V_SCALE_ADD6(vecTmp, 
! 		      dtD + dtF, gradDtA,
! 		      -2*dtB, gradDtB,
! 		      -2*dtC, gradDtC,
! 		      dtA + dtF, gradDtD,
! 		      -2*dtE, gradDtE,
! 		      dtA + dtD, gradDtF);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageBGradMag)) {
!     magTmp = pvl->directAnswer[tenGageBGradMag][0] = ELL_3V_LEN(vecTmp);
!   }
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageBNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageBNormal], 1.0/magTmp, vecTmp);
!   }
!   /* --- Det --- */
!   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDetGradVec)) {
!     vecTmp = pvl->directAnswer[tenGageDetGradVec];
!     ELL_3V_SCALE_ADD6(vecTmp,
! 		      dtD*dtF - dtE*dtE, gradDtA,
! 		      2*(dtC*dtE - dtB*dtF), gradDtB,
! 		      2*(dtB*dtE - dtC*dtD), gradDtC,
! 		      dtA*dtF - dtC*dtC, gradDtD,
! 		      2*(dtB*dtC - dtA*dtE), gradDtE,
! 		      dtA*dtD - dtB*dtB, gradDtF);
    }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDetGradMag)) {
+     magTmp = pvl->directAnswer[tenGageDetGradMag][0] = ELL_3V_LEN(vecTmp);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageDetNormal)) {
+     ELL_3V_SCALE(pvl->directAnswer[tenGageDetNormal], 1.0/magTmp, vecTmp);
+   }
+   /* --- S --- */
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageSGradVec)) {
+     gradCbS = vecTmp = pvl->directAnswer[tenGageSGradVec];
+     ELL_3V_SCALE_ADD6(vecTmp,
+ 		      2*dtA, gradDtA,
+ 		      4*dtB, gradDtB,
+ 		      4*dtC, gradDtC,
+ 		      2*dtD, gradDtD,
+ 		      4*dtE, gradDtE,
+ 		      2*dtF, gradDtF);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageSGradMag)) {
+     magTmp = pvl->directAnswer[tenGageSGradMag][0] = ELL_3V_LEN(vecTmp);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageSNormal)) {
+     ELL_3V_SCALE(pvl->directAnswer[tenGageSNormal], 1.0/magTmp, vecTmp);
+   }
+   /* --- Q --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQGradVec)) {
!     gradCbQ = vecTmp = pvl->directAnswer[tenGageQGradVec];
!     ELL_3V_SCALE_ADD2(vecTmp,
! 		      1.0/9.0, gradCbS, 
! 		      -1.0/9.0, gradCbB);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQGradMag)) {
!     magTmp = pvl->directAnswer[tenGageQGradMag][0] = ELL_3V_LEN(vecTmp);
    }
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageQNormal)) {
!     ELL_3V_SCALE(pvl->directAnswer[tenGageQNormal], 1.0/magTmp, vecTmp);
    }
+   /* --- FA --- */
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFAGradVec)) {
+     vecTmp = pvl->directAnswer[tenGageFAGradVec];
+     tmp0 = 9.0/(2*pvl->directAnswer[tenGageFA][0]*cbS);
+     tmp1 = -tmp0*cbQ/cbS;
+     ELL_3V_SCALE_ADD2(vecTmp,
+ 		      tmp0, gradCbQ, 
+ 		      tmp1, gradCbS);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFAGradMag)) {
+     magTmp = pvl->directAnswer[tenGageFAGradMag][0] = ELL_3V_LEN(vecTmp);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFANormal)) {
+     ELL_3V_SCALE(pvl->directAnswer[tenGageFANormal], 1.0/magTmp, vecTmp);
+   }
+   /* --- R --- */
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRGradVec)) {
+     vecTmp = pvl->directAnswer[tenGageRGradVec];
+     ELL_3V_SCALE_ADD4(vecTmp,
+ 		      (5*cbB - 2*cbS)/54.0, gradCbA,
+ 		      1.0/2.0, pvl->directAnswer[tenGageDetGradVec],
+ 		      5.0*cbA/54.0, gradCbB,
+ 		      -cbA/27.0, gradCbS);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRGradMag)) {
+     magTmp = pvl->directAnswer[tenGageRGradMag][0] = ELL_3V_LEN(vecTmp);
+   }
+   if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRNormal)) {
+     ELL_3V_SCALE(pvl->directAnswer[tenGageRNormal], 1.0/magTmp, vecTmp);
+   }
+   /* --- Aniso --- */
    if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageAniso)) {
  #if GAGE_TYPE_FLOAT

Index: tensor.c
===================================================================
RCS file: /cvsroot/teem/teem/src/ten/tensor.c,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** tensor.c	7 Jan 2004 15:34:31 -0000	1.26
--- tensor.c	23 Feb 2004 02:40:24 -0000	1.27
***************
*** 200,204 ****
    if (_evec) {
      ret = ell_3m_eigensolve_d(eval, evec, m, AIR_TRUE);
!     if (ell_cubic_root_three != ret && tenVerbose) {
        fprintf(stderr, "---- cubic ret = %d\n", ret);
        fprintf(stderr, "tensor = {\n");
--- 200,204 ----
    if (_evec) {
      ret = ell_3m_eigensolve_d(eval, evec, m, AIR_TRUE);
!     if (tenVerbose) {
        fprintf(stderr, "---- cubic ret = %d\n", ret);
        fprintf(stderr, "tensor = {\n");
***************
*** 209,213 ****
        fprintf(stderr, "    % 15.7f,\n", t[5]);
        fprintf(stderr, "    % 15.7f}\n", t[6]);
!       fprintf(stderr, "roots = \n");
        fprintf(stderr, "    % 31.15f\n", trc + eval[0]);
        fprintf(stderr, "    % 31.15f\n", trc + eval[1]);
--- 209,213 ----
        fprintf(stderr, "    % 15.7f,\n", t[5]);
        fprintf(stderr, "    % 15.7f}\n", t[6]);
!       fprintf(stderr, "roots = %d:\n", ret);
        fprintf(stderr, "    % 31.15f\n", trc + eval[0]);
        fprintf(stderr, "    % 31.15f\n", trc + eval[1]);

[Teem-commit] teem/src/ell ellMacros.h,1.37,1.38

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

Update of /cvsroot/teem/teem/src/ell
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26020

Modified Files:
	ellMacros.h 
Log Message:
added some more ELL_3V macros

Index: ellMacros.h
===================================================================
RCS file: /cvsroot/teem/teem/src/ell/ellMacros.h,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** ellMacros.h	7 Jan 2004 15:34:29 -0000	1.37
--- ellMacros.h	23 Feb 2004 02:38:59 -0000	1.38
***************
*** 138,141 ****
--- 138,146 ----
     (v2)[2] = (a)*(v1)[2])
  
+ #define ELL_3V_SCALE_INCR(v2, s0, v0) \
+   ((v2)[0] += (s0)*(v0)[0], \
+    (v2)[1] += (s0)*(v0)[1], \
+    (v2)[2] += (s0)*(v0)[2])
+ 
  #define ELL_3V_SCALE_ADD2(v2, s0, v0, s1, v1) \
    ((v2)[0] = (s0)*(v0)[0] + (s1)*(v1)[0],     \
***************
*** 143,156 ****
     (v2)[2] = (s0)*(v0)[2] + (s1)*(v1)[2])
  
! #define ELL_3V_SCALE_INCR(v2, s0, v0) \
!   ((v2)[0] += (s0)*(v0)[0], \
!    (v2)[1] += (s0)*(v0)[1], \
!    (v2)[2] += (s0)*(v0)[2])
  
! #define ELL_3V_SCALE_ADD3(v3, s0, v0, s1, v1, s2, v2)        \
!   ((v3)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0],    \
!    (v3)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1],    \
     (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2])
  
  #define ELL_3V_LEN(v) (sqrt(ELL_3V_DOT((v),(v))))
  
--- 148,180 ----
     (v2)[2] = (s0)*(v0)[2] + (s1)*(v1)[2])
  
! #define ELL_3V_SCALE_INCR2(v2, s0, v0, s1, v1) \
!   ((v2)[0] += (s0)*(v0)[0] + (s1)*(v1)[0],     \
!    (v2)[1] += (s0)*(v0)[1] + (s1)*(v1)[1],     \
!    (v2)[2] += (s0)*(v0)[2] + (s1)*(v1)[2])
  
! #define ELL_3V_SCALE_ADD3(v3, s0, v0, s1, v1, s2, v2)     \
!   ((v3)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0],  \
!    (v3)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1],  \
     (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2])
  
+ #define ELL_3V_SCALE_ADD4(v3, s0, v0, s1, v1, s2, v2, s3, v3)           \
+   ((v3)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0] + (s3)*(v3)[0], \
+    (v3)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1] + (s3)*(v3)[1], \
+    (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2] + (s3)*(v3)[2])
+ 
+ #define ELL_3V_SCALE_ADD6(v3, s0, v0, s1, v1, s2, v2,     \
+                               s3, v3, s4, v4, s5, v5)     \
+   ((v3)[0] = (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0]   \
+            + (s3)*(v3)[0] + (s4)*(v4)[0] + (s5)*(v5)[0],  \
+    (v3)[1] = (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1]   \
+            + (s3)*(v3)[1] + (s4)*(v4)[1] + (s5)*(v5)[1],  \
+    (v3)[2] = (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2]   \
+            + (s3)*(v3)[2] + (s4)*(v4)[2] + (s5)*(v5)[2])
+ 
+ #define ELL_3V_SCALE_INCR3(v3, s0, v0, s1, v1, s2, v2)     \
+   ((v3)[0] += (s0)*(v0)[0] + (s1)*(v1)[0] + (s2)*(v2)[0],  \
+    (v3)[1] += (s0)*(v0)[1] + (s1)*(v1)[1] + (s2)*(v2)[1],  \
+    (v3)[2] += (s0)*(v0)[2] + (s1)*(v1)[2] + (s2)*(v2)[2])
+ 
  #define ELL_3V_LEN(v) (sqrt(ELL_3V_DOT((v),(v))))