void
ell_3m_mul_d(double m3[9], const double _m1[9], const double _m2[9]) {
double m1[9], m2[9];
ELL_3M_COPY(m1, _m1);
ELL_3M_COPY(m2, _m2);
ELL_3M_MUL(m3, m1, m2);
}
void
ell_3m_mul_f(float m3[9], const float _m1[9], const float _m2[9]) {
float m1[9], m2[9];
ELL_3M_COPY(m1, _m1);
ELL_3M_COPY(m2, _m2);
ELL_3M_MUL(m3, m1, m2);
}
/*
******** ell_3m_svd_d
**
** singular value decomposition:
** mat = uu * diag(sval) * vv
**
** singular values are square roots of eigenvalues of mat * mat^T
** columns of uu are eigenvectors of mat * mat^T
** rows of vv are eigenvectors of mat^T * mat
**
** returns info about singular values according to ellCubeRoot enum
**
** HEY: I think this does the wrong thing when given a symmetric
** matrix with negative eigenvalues . . .
*/
int
ell_3m_svd_d(double uu[9], double sval[3], double vv[9],
const double mat[9], const int newton) {
double trn[9], msqr[9], eval[3], evec[9];
int roots;
ELL_3M_TRANSPOSE(trn, mat);
ELL_3M_MUL(msqr, mat, trn);
roots = ell_3m_eigensolve_d(eval, evec, msqr, newton);
sval[0] = sqrt(eval[0]);
sval[1] = sqrt(eval[1]);
sval[2] = sqrt(eval[2]);
ELL_3M_TRANSPOSE(uu, evec);
ELL_3M_MUL(msqr, trn, mat);
_ell_3m_evecs_d(vv, eval, roots, msqr);
return roots;
}
void
tend_helixDoit(Nrrd *nout, double bnd,
double orig[3], double i2w[9], double mf[9],
double r, double R, double S, double angle, int incrtwist,
double ev[3], double bgEval) {
int sx, sy, sz, xi, yi, zi;
double th, t0, t1, t2, t3, v1, v2,
wpos[3], vpos[3], mfT[9],
W2H[9], H2W[9], H2C[9], C2H[9], fv[3], rv[3], uv[3], mA[9], mB[9], inside,
tmp[3], len;
float *out;
sx = nout->axis[1].size;
sy = nout->axis[2].size;
sz = nout->axis[3].size;
out = (float*)nout->data;
ELL_3M_TRANSPOSE(mfT, mf);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "zi = %d/%d\n", zi, sz);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
ELL_3V_SET(tmp, xi, yi, zi);
ELL_3MV_MUL(vpos, i2w, tmp);
ELL_3V_INCR(vpos, orig);
#define WPOS(pos, th) ELL_3V_SET((pos),R*cos(th), R*sin(th), S*(th)/(2*AIR_PI))
#define VAL(th) (WPOS(wpos, th), ELL_3V_DIST(wpos, vpos))
#define RR 0.61803399
#define CC (1.0-RR)
#define SHIFT3(a,b,c,d) (a)=(b); (b)=(c); (c)=(d)
#define SHIFT2(a,b,c) (a)=(b); (b)=(c)
th = atan2(vpos[1], vpos[0]);
th += 2*AIR_PI*floor(0.5 + vpos[2]/S - th/(2*AIR_PI));
if (S*th/(2*AIR_PI) > vpos[2]) {
t0 = th - AIR_PI; t3 = th;
} else {
t0 = th; t3 = th + AIR_PI;
}
t1 = RR*t0 + CC*t3;
t2 = CC*t0 + RR*t3;
v1 = VAL(t1);
v2 = VAL(t2);
while ( t3-t0 > 0.000001*(AIR_ABS(t1)+AIR_ABS(t2)) ) {
if (v1 < v2) {
SHIFT3(t3, t2, t1, CC*t0 + RR*t2);
SHIFT2(v2, v1, VAL(t1));
} else {
SHIFT3(t0, t1, t2, RR*t1 + CC*t3);
SHIFT2(v1, v2, VAL(t2));
}
}
/* t1 (and t2) are now the th for which the point on the helix
(R*cos(th), R*sin(th), S*(th)/(2*AIR_PI)) is closest to vpos */
WPOS(wpos, t1);
ELL_3V_SUB(wpos, vpos, wpos);
ELL_3V_SET(fv, -R*sin(t1), R*cos(t1), S/AIR_PI); /* helix tangent */
ELL_3V_NORM(fv, fv, len);
ELL_3V_COPY(rv, wpos);
ELL_3V_NORM(rv, rv, len);
len = ELL_3V_DOT(rv, fv);
ELL_3V_SCALE(tmp, -len, fv);
ELL_3V_ADD2(rv, rv, tmp);
ELL_3V_NORM(rv, rv, len); /* rv now normal to helix, closest to
pointing to vpos */
ELL_3V_CROSS(uv, rv, fv);
ELL_3V_NORM(uv, uv, len); /* (rv,fv,uv) now right-handed frame */
ELL_3MV_ROW0_SET(W2H, uv); /* as is (uv,rv,fv) */
ELL_3MV_ROW1_SET(W2H, rv);
ELL_3MV_ROW2_SET(W2H, fv);
ELL_3M_TRANSPOSE(H2W, W2H);
inside = 0.5 - 0.5*airErf((ELL_3V_LEN(wpos)-r)/(bnd + 0.0001));
if (incrtwist) {
th = angle*ELL_3V_LEN(wpos)/r;
} else {
th = angle;
}
ELL_3M_ROTATE_Y_SET(H2C, th);
ELL_3M_TRANSPOSE(C2H, H2C);
ELL_3M_SCALE_SET(mA,
AIR_LERP(inside, bgEval, ev[1]),
AIR_LERP(inside, bgEval, ev[2]),
AIR_LERP(inside, bgEval, ev[0]));
ELL_3M_MUL(mB, mA, H2C);
ELL_3M_MUL(mA, mB, W2H);
ELL_3M_MUL(mB, mA, mf);
ELL_3M_MUL(mA, C2H, mB);
ELL_3M_MUL(mB, H2W, mA);
ELL_3M_MUL(mA, mfT, mB);
TEN_M2T_TT(out, float, mA);
out[0] = 1.0;
out += 7;
}
}
}
return;
}
int
tend_helixMain(int argc, char **argv, char *me, hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
int size[3], nit;
Nrrd *nout;
double R, r, S, bnd, angle, ev[3], ip[3], iq[4], mp[3], mq[4], tmp[9],
orig[3], i2w[9], rot[9], mf[9], spd[4][3], bge;
char *outS;
hestOptAdd(&hopt, "s", "size", airTypeInt, 3, 3, size, NULL,
"sizes along fast, medium, and slow axes of the sampled volume, "
"often called \"X\", \"Y\", and \"Z\". It is best to use "
"slightly different sizes here, to expose errors in interpreting "
"axis ordering (e.g. \"-s 39 40 41\")");
hestOptAdd(&hopt, "ip", "image orientation", airTypeDouble, 3, 3, ip,
"0 0 0",
"quaternion quotient space orientation of image");
hestOptAdd(&hopt, "mp", "measurement orientation", airTypeDouble, 3, 3, mp,
"0 0 0",
"quaternion quotient space orientation of measurement frame");
hestOptAdd(&hopt, "b", "boundary", airTypeDouble, 1, 1, &bnd, "10",
"parameter governing how fuzzy the boundary between high and "
"low anisotropy is. Use \"-b 0\" for no fuzziness");
hestOptAdd(&hopt, "r", "little radius", airTypeDouble, 1, 1, &r, "30",
"(minor) radius of cylinder tracing helix");
hestOptAdd(&hopt, "R", "big radius", airTypeDouble, 1, 1, &R, "50",
"(major) radius of helical turns");
hestOptAdd(&hopt, "S", "spacing", airTypeDouble, 1, 1, &S, "100",
"spacing between turns of helix (along its axis)");
hestOptAdd(&hopt, "a", "angle", airTypeDouble, 1, 1, &angle, "60",
"maximal angle of twist of tensors along path. There is no "
"twist at helical core of path, and twist increases linearly "
"with radius around this path. Positive twist angle with "
"positive spacing resulting in a right-handed twist around a "
"right-handed helix. ");
hestOptAdd(&hopt, "nit", NULL, airTypeInt, 0, 0, &nit, NULL,
"changes behavior of twist angle as function of distance from "
"center of helical core: instead of increasing linearly as "
"describe above, be at a constant angle");
hestOptAdd(&hopt, "ev", "eigenvalues", airTypeDouble, 3, 3, ev,
"0.006 0.002 0.001",
"eigenvalues of tensors (in order) along direction of coil, "
"circumferential around coil, and radial around coil. ");
hestOptAdd(&hopt, "bg", "background", airTypeDouble, 1, 1, &bge, "0.5",
"eigenvalue of isotropic background");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output file");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_helixInfoL);
JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7),
AIR_CAST(size_t, size[0]),
AIR_CAST(size_t, size[1]),
AIR_CAST(size_t, size[2]))) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating output:\n%s\n", me, err);
airMopError(mop); return 1;
}
ELL_4V_SET(iq, 1.0, ip[0], ip[1], ip[2]);
ell_q_to_3m_d(rot, iq);
ELL_3V_SET(orig,
-2*R + 2*R/size[0],
-2*R + 2*R/size[1],
-2*R + 2*R/size[2]);
ELL_3M_ZERO_SET(i2w);
ELL_3M_DIAG_SET(i2w, 4*R/size[0], 4*R/size[1], 4*R/size[2]);
ELL_3MV_MUL(tmp, rot, orig);
ELL_3V_COPY(orig, tmp);
ELL_3M_MUL(tmp, rot, i2w);
ELL_3M_COPY(i2w, tmp);
ELL_4V_SET(mq, 1.0, mp[0], mp[1], mp[2]);
ell_q_to_3m_d(mf, mq);
tend_helixDoit(nout, bnd,
orig, i2w, mf,
r, R, S, angle*AIR_PI/180, !nit, ev, bge);
nrrdSpaceSet(nout, nrrdSpaceRightAnteriorSuperior);
nrrdSpaceOriginSet(nout, orig);
ELL_3V_SET(spd[0], AIR_NAN, AIR_NAN, AIR_NAN);
ELL_3MV_COL0_GET(spd[1], i2w);
ELL_3MV_COL1_GET(spd[2], i2w);
ELL_3MV_COL2_GET(spd[3], i2w);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoSpaceDirection,
spd[0], spd[1], spd[2], spd[3]);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoCenter,
nrrdCenterUnknown, nrrdCenterCell,
nrrdCenterCell, nrrdCenterCell);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoKind,
nrrdKind3DMaskedSymMatrix, nrrdKindSpace,
nrrdKindSpace, nrrdKindSpace);
nout->measurementFrame[0][0] = mf[0];
nout->measurementFrame[1][0] = mf[1];
nout->measurementFrame[2][0] = mf[2];
nout->measurementFrame[0][1] = mf[3];
nout->measurementFrame[1][1] = mf[4];
nout->measurementFrame[2][1] = mf[5];
nout->measurementFrame[0][2] = mf[6];
nout->measurementFrame[1][2] = mf[7];
nout->measurementFrame[2][2] = mf[8];
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;
}
void
_gageVecAnswer(gageContext *ctx, gagePerVolume *pvl) {
char me[]="_gageVecAnswer";
double cmag, tmpMat[9], mgevec[9], mgeval[3];
double symm[9], asym[9], tran[9], eval[3], tmpVec[3], norm;
gage_t *vecAns, *normAns, *jacAns, *curlAns, *hesAns, *curlGradAns,
*helGradAns, *dirHelDirAns, *curlnormgradAns;
/* int asw; */
vecAns = pvl->directAnswer[gageVecVector];
normAns = pvl->directAnswer[gageVecNormalized];
jacAns = pvl->directAnswer[gageVecJacobian];
curlAns = pvl->directAnswer[gageVecCurl];
hesAns = pvl->directAnswer[gageVecHessian];
curlGradAns = pvl->directAnswer[gageVecCurlGradient];
curlnormgradAns = pvl->directAnswer[gageVecCurlNormGrad];
helGradAns = pvl->directAnswer[gageVecHelGradient];
dirHelDirAns = pvl->directAnswer[gageVecDirHelDeriv];
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecVector)) {
/* done if doV */
if (ctx->verbose) {
fprintf(stderr, "vec = ");
ell_3v_PRINT(stderr, vecAns);
}
}
/* done if doV
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecVector{0,1,2})) {
}
*/
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecLength)) {
pvl->directAnswer[gageVecLength][0] = AIR_CAST(gage_t, ELL_3V_LEN(vecAns));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecNormalized)) {
if (pvl->directAnswer[gageVecLength][0]) {
ELL_3V_SCALE_TT(normAns, gage_t,
1.0/pvl->directAnswer[gageVecLength][0], vecAns);
} else {
ELL_3V_COPY(normAns, gageZeroNormal);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecJacobian)) {
/* done if doD1 */
/*
0:dv_x/dx 1:dv_x/dy 2:dv_x/dz
3:dv_y/dx 4:dv_y/dy 5:dv_y/dz
6:dv_z/dx 7:dv_z/dy 8:dv_z/dz
*/
if (ctx->verbose) {
fprintf(stderr, "%s: jac = \n", me);
ell_3m_PRINT(stderr, jacAns);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecDivergence)) {
pvl->directAnswer[gageVecDivergence][0] = jacAns[0] + jacAns[4] + jacAns[8];
if (ctx->verbose) {
fprintf(stderr, "%s: div = %g + %g + %g = %g\n", me,
jacAns[0], jacAns[4], jacAns[8],
pvl->directAnswer[gageVecDivergence][0]);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurl)) {
ELL_3V_SET(curlAns,
jacAns[7] - jacAns[5],
jacAns[2] - jacAns[6],
jacAns[3] - jacAns[1]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurlNorm)) {
pvl->directAnswer[gageVecCurlNorm][0] =
AIR_CAST(gage_t, ELL_3V_LEN(curlAns));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecHelicity)) {
pvl->directAnswer[gageVecHelicity][0] =
ELL_3V_DOT(vecAns, curlAns);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecNormHelicity)) {
cmag = ELL_3V_LEN(curlAns);
pvl->directAnswer[gageVecNormHelicity][0] =
AIR_CAST(gage_t, cmag ? ELL_3V_DOT(normAns, curlAns)/cmag : 0);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecLambda2)) {
ELL_3M_TRANSPOSE(tran, jacAns);
/* symmetric part */
ELL_3M_SCALE_ADD2(symm, 0.5, jacAns, 0.5, tran);
/* antisymmetric part */
ELL_3M_SCALE_ADD2(asym, 0.5, jacAns, -0.5, tran);
/* square symmetric part */
ELL_3M_MUL(tmpMat, symm, symm);
ELL_3M_COPY(symm, tmpMat);
/* square antisymmetric part */
ELL_3M_MUL(tmpMat, asym, asym);
/* sum of both */
ELL_3M_ADD2(symm, symm, tmpMat);
/* get eigenvalues in sorted order */
/* asw = */ ell_3m_eigenvalues_d(eval, symm, AIR_TRUE);
pvl->directAnswer[gageVecLambda2][0] = AIR_CAST(gage_t, eval[1]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecImaginaryPart)) {
pvl->directAnswer[gageVecImaginaryPart][0] =
AIR_CAST(gage_t, gage_imaginary_part_eigenvalues(jacAns));
}
/* 2nd order vector derivative continued */
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecHessian)) {
/* done if doD2 */
/* the ordering is induced by the scalar hessian computation :
0:d2v_x/dxdx 1:d2v_x/dxdy 2:d2v_x/dxdz
3:d2v_x/dydx 4:d2v_x/dydy 5:d2v_x/dydz
6:d2v_x/dzdx 7:d2v_x/dzdy 8:d2v_x/dzdz
9:d2v_y/dxdx [...]
[...]
24:dv2_z/dzdx 25:d2v_z/dzdy 26:d2v_z/dzdz
*/
if (ctx->verbose) {
fprintf(stderr, "%s: hes = \n", me);
ell_3m_PRINT(stderr, hesAns); /* ?? */
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecDivGradient)) {
pvl->directAnswer[gageVecDivGradient][0] = hesAns[0] + hesAns[12] + hesAns[24];
pvl->directAnswer[gageVecDivGradient][1] = hesAns[1] + hesAns[13] + hesAns[25];
pvl->directAnswer[gageVecDivGradient][2] = hesAns[2] + hesAns[14] + hesAns[26];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurlGradient)) {
pvl->directAnswer[gageVecCurlGradient][0] = hesAns[21]-hesAns[15];
pvl->directAnswer[gageVecCurlGradient][1] = hesAns[22]-hesAns[16];
pvl->directAnswer[gageVecCurlGradient][2] = hesAns[23]-hesAns[17];
pvl->directAnswer[gageVecCurlGradient][3] = hesAns[ 6]-hesAns[18];
pvl->directAnswer[gageVecCurlGradient][4] = hesAns[ 7]-hesAns[19];
pvl->directAnswer[gageVecCurlGradient][5] = hesAns[ 8]-hesAns[20];
pvl->directAnswer[gageVecCurlGradient][6] = hesAns[ 9]-hesAns[ 1];
pvl->directAnswer[gageVecCurlGradient][7] = hesAns[10]-hesAns[ 2];
pvl->directAnswer[gageVecCurlGradient][8] = hesAns[11]-hesAns[ 3];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecCurlNormGrad)) {
norm = 1./ELL_3V_LEN(curlAns);
tmpVec[0] = hesAns[21] - hesAns[15];
tmpVec[1] = hesAns[ 6] - hesAns[18];
tmpVec[2] = hesAns[ 9] - hesAns[ 3];
pvl->directAnswer[gageVecCurlNormGrad][0]=
AIR_CAST(gage_t, norm*ELL_3V_DOT(tmpVec, curlAns));
tmpVec[0] = hesAns[22] - hesAns[16];
tmpVec[1] = hesAns[ 7] - hesAns[19];
tmpVec[2] = hesAns[10] - hesAns[ 4];
pvl->directAnswer[gageVecCurlNormGrad][1]=
AIR_CAST(gage_t, norm*ELL_3V_DOT(tmpVec, curlAns));
tmpVec[0] = hesAns[23] - hesAns[17];
tmpVec[1] = hesAns[ 8] - hesAns[20];
tmpVec[2] = hesAns[11] - hesAns[ 5];
pvl->directAnswer[gageVecCurlNormGrad][2]=
AIR_CAST(gage_t, norm*ELL_3V_DOT(tmpVec, curlAns));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecNCurlNormGrad)) {
norm = 1./ELL_3V_LEN(curlnormgradAns);
ELL_3V_SCALE_TT(pvl->directAnswer[gageVecNCurlNormGrad], gage_t,
norm, pvl->directAnswer[gageVecCurlNormGrad]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecHelGradient)) {
pvl->directAnswer[gageVecHelGradient][0] =
jacAns[0]*curlAns[0]+
jacAns[3]*curlAns[1]+
jacAns[6]*curlAns[2]+
curlGradAns[0]*vecAns[0]+
curlGradAns[3]*vecAns[1]+
curlGradAns[6]*vecAns[2];
pvl->directAnswer[gageVecHelGradient][1] =
jacAns[1]*curlAns[0]+
jacAns[4]*curlAns[1]+
jacAns[7]*curlAns[2]+
curlGradAns[1]*vecAns[0]+
curlGradAns[4]*vecAns[1]+
curlGradAns[7]*vecAns[2];
pvl->directAnswer[gageVecHelGradient][0] =
jacAns[2]*curlAns[0]+
jacAns[5]*curlAns[1]+
jacAns[8]*curlAns[2]+
curlGradAns[2]*vecAns[0]+
curlGradAns[5]*vecAns[1]+
curlGradAns[8]*vecAns[2];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecDirHelDeriv)) {
pvl->directAnswer[gageVecDirHelDeriv][0] =
ELL_3V_DOT(normAns, helGradAns);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecProjHelGradient)) {
pvl->directAnswer[gageVecDirHelDeriv][0] =
helGradAns[0]-dirHelDirAns[0]*normAns[0];
pvl->directAnswer[gageVecDirHelDeriv][1] =
helGradAns[1]-dirHelDirAns[0]*normAns[1];
pvl->directAnswer[gageVecDirHelDeriv][2] =
helGradAns[2]-dirHelDirAns[0]*normAns[2];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient0)) {
ELL_3V_SET(pvl->directAnswer[gageVecGradient0],
jacAns[0],
jacAns[1],
jacAns[2]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient1)) {
ELL_3V_SET(pvl->directAnswer[gageVecGradient1],
jacAns[3],
jacAns[4],
jacAns[5]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecGradient2)) {
ELL_3V_SET(pvl->directAnswer[gageVecGradient2],
jacAns[6],
jacAns[7],
jacAns[8]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecMultiGrad)) {
ELL_3M_IDENTITY_SET(pvl->directAnswer[gageVecMultiGrad]);
ELL_3MV_OUTER_ADD(pvl->directAnswer[gageVecMultiGrad],
pvl->directAnswer[gageVecGradient0],
pvl->directAnswer[gageVecGradient0]);
ELL_3MV_OUTER_ADD(pvl->directAnswer[gageVecMultiGrad],
pvl->directAnswer[gageVecGradient1],
pvl->directAnswer[gageVecGradient1]);
ELL_3MV_OUTER_ADD(pvl->directAnswer[gageVecMultiGrad],
pvl->directAnswer[gageVecGradient2],
pvl->directAnswer[gageVecGradient2]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecMGFrob)) {
pvl->directAnswer[gageVecMGFrob][0]
= AIR_CAST(gage_t, ELL_3M_FROB(pvl->directAnswer[gageVecMultiGrad]));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecMGEval)) {
ELL_3M_COPY(tmpMat, pvl->directAnswer[gageVecMultiGrad]);
/* HEY: look at the return value for root multiplicity? */
ell_3m_eigensolve_d(mgeval, mgevec, tmpMat, AIR_TRUE);
ELL_3V_COPY_TT(pvl->directAnswer[gageVecMGEval], gage_t, mgeval);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageVecMGEvec)) {
ELL_3M_COPY_TT(pvl->directAnswer[gageVecMGEvec], gage_t, mgevec);
}
return;
}
void
ell_3m_post_mul_d(double _m[9], const double x[9]) {
double m[9];
ELL_3M_MUL(m, x, _m);
ELL_3M_COPY(_m, m);
}
void
ell_3m_post_mul_f(float _m[9], const float x[9]) {
float m[9];
ELL_3M_MUL(m, x, _m);
ELL_3M_COPY(_m, m);
}
void
_gageSclAnswer (gageContext *ctx, gagePerVolume *pvl) {
char me[]="_gageSclAnswer";
double gmag=0, *hess, *norm, *gvec, *gten, *k1, *k2, curv=0,
sHess[9]={0,0,0,0,0,0,0,0,0};
double tmpMat[9], tmpVec[3], hevec[9], heval[3];
double len, gp1[3], gp2[3], *nPerp, ncTen[9], nProj[9]={0,0,0,0,0,0,0,0,0};
double alpha = 0.5;
double beta = 0.5;
double gamma = 5;
double cc = 1e-6;
#define FD_MEDIAN_MAX 16
int fd, nidx, xi, yi, zi;
double *fw, iv3wght[2*FD_MEDIAN_MAX*FD_MEDIAN_MAX*FD_MEDIAN_MAX],
wghtSum, wght;
/* convenience pointers for work below */
hess = pvl->directAnswer[gageSclHessian];
gvec = pvl->directAnswer[gageSclGradVec];
norm = pvl->directAnswer[gageSclNormal];
nPerp = pvl->directAnswer[gageSclNPerp];
gten = pvl->directAnswer[gageSclGeomTens];
k1 = pvl->directAnswer[gageSclK1];
k2 = pvl->directAnswer[gageSclK2];
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclValue)) {
/* done if doV */
if (ctx->verbose) {
fprintf(stderr, "%s: val = % 15.7f\n", me,
(double)(pvl->directAnswer[gageSclValue][0]));
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclGradVec)) {
/* done if doD1 */
if (ctx->verbose) {
fprintf(stderr, "%s: gvec = ", me);
ell_3v_print_d(stderr, gvec);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclGradMag)) {
/* this is the true value of gradient magnitude */
gmag = pvl->directAnswer[gageSclGradMag][0] = sqrt(ELL_3V_DOT(gvec, gvec));
}
/* NB: it would seem that gageParmGradMagMin is completely ignored ... */
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclNormal)) {
if (gmag) {
ELL_3V_SCALE(norm, 1/gmag, gvec);
/* polishing ...
len = sqrt(ELL_3V_DOT(norm, norm));
ELL_3V_SCALE(norm, 1/len, norm);
*/
} else {
ELL_3V_COPY(norm, gageZeroNormal);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclNPerp)) {
/* nPerp = I - outer(norm, norm) */
/* NB: this sets both nPerp and nProj */
ELL_3MV_OUTER(nProj, norm, norm);
ELL_3M_SCALE(nPerp, -1, nProj);
nPerp[0] += 1;
nPerp[4] += 1;
nPerp[8] += 1;
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessian)) {
/* done if doD2 */
if (ctx->verbose) {
fprintf(stderr, "%s: hess = \n", me);
ell_3m_print_d(stderr, hess);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclLaplacian)) {
pvl->directAnswer[gageSclLaplacian][0] = hess[0] + hess[4] + hess[8];
if (ctx->verbose) {
fprintf(stderr, "%s: lapl = %g + %g + %g = %g\n", me,
hess[0], hess[4], hess[8],
pvl->directAnswer[gageSclLaplacian][0]);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessFrob)) {
pvl->directAnswer[gageSclHessFrob][0] = ELL_3M_FROB(hess);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessEval)) {
/* HEY: look at the return value for root multiplicity? */
ell_3m_eigensolve_d(heval, hevec, hess, AIR_TRUE);
ELL_3V_COPY(pvl->directAnswer[gageSclHessEval], heval);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessEvec)) {
ELL_3M_COPY(pvl->directAnswer[gageSclHessEvec], hevec);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessRidgeness)) {
double A, B, S;
if (heval[1] >0 || heval[2]>0) {
pvl->directAnswer[gageSclHessRidgeness][0] = 0;
}
else if (AIR_ABS(heval[1])<1e-10 || AIR_ABS(heval[2])<1e-10) {
pvl->directAnswer[gageSclHessRidgeness][0] = 0;
}
else {
double *ans;
A = AIR_ABS(heval[1])/AIR_ABS(heval[2]);
B = AIR_ABS(heval[0])/sqrt(AIR_ABS(heval[1]*heval[2]));
S = sqrt(heval[0]*heval[0] + heval[1]*heval[1] + heval[2]*heval[2]);
ans = pvl->directAnswer[gageSclHessRidgeness];
ans[0] = (1-exp(-A*A/(2*alpha*alpha))) *
exp(-B*B/(2*beta*beta)) *
(1-exp(-S*S/(2*gamma*gamma))) *
exp(-2*cc*cc/(AIR_ABS(heval[1])*heval[2]*heval[2]));
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessValleyness)) {
double A, B, S;
if (heval[0] <0 || heval[1]<0) {
pvl->directAnswer[gageSclHessValleyness][0] = 0;
}
else if (AIR_ABS(heval[0])<1e-10 || AIR_ABS(heval[1])<1e-10) {
pvl->directAnswer[gageSclHessValleyness][0] = 0;
}
else {
double *ans;
A = AIR_ABS(heval[1])/AIR_ABS(heval[0]);
B = AIR_ABS(heval[2])/sqrt(AIR_ABS(heval[1]*heval[0]));
S = sqrt(heval[0]*heval[0] + heval[1]*heval[1] + heval[2]*heval[2]);
ans = pvl->directAnswer[gageSclHessValleyness];
ans[0] = (1-exp(-A*A/(2*alpha*alpha))) *
exp(-B*B/(2*beta*beta)) *
(1-exp(-S*S/(2*gamma*gamma))) *
exp(-2*cc*cc/(AIR_ABS(heval[1])*heval[0]*heval[0]));
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclHessMode)) {
pvl->directAnswer[gageSclHessMode][0] = airMode3_d(heval);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageScl2ndDD)) {
ELL_3MV_MUL(tmpVec, hess, norm);
pvl->directAnswer[gageScl2ndDD][0] = ELL_3V_DOT(norm, tmpVec);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclGeomTens)) {
if (gmag > ctx->parm.gradMagCurvMin) {
/* parm.curvNormalSide applied here to determine the sense of the
normal when doing all curvature calculations */
ELL_3M_SCALE(sHess, -(ctx->parm.curvNormalSide)/gmag, hess);
/* gten = nPerp * sHess * nPerp */
ELL_3M_MUL(tmpMat, sHess, nPerp);
ELL_3M_MUL(gten, nPerp, tmpMat);
if (ctx->verbose) {
fprintf(stderr, "%s: gten: \n", me);
ell_3m_print_d(stderr, gten);
ELL_3MV_MUL(tmpVec, gten, norm);
len = ELL_3V_LEN(tmpVec);
fprintf(stderr, "%s: should be small: %30.15f\n", me, (double)len);
ell_3v_perp_d(gp1, norm);
ELL_3MV_MUL(tmpVec, gten, gp1);
len = ELL_3V_LEN(tmpVec);
fprintf(stderr, "%s: should be bigger: %30.15f\n", me, (double)len);
ELL_3V_CROSS(gp2, gp1, norm);
ELL_3MV_MUL(tmpVec, gten, gp2);
len = ELL_3V_LEN(tmpVec);
fprintf(stderr, "%s: should (also) be bigger: %30.15f\n",
me, (double)len);
}
} else {
ELL_3M_ZERO_SET(gten);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclTotalCurv)) {
curv = pvl->directAnswer[gageSclTotalCurv][0] = ELL_3M_FROB(gten);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclShapeTrace)) {
pvl->directAnswer[gageSclShapeTrace][0] = (curv
? ELL_3M_TRACE(gten)/curv
: 0);
}
if ( (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclK1)) ||
(GAGE_QUERY_ITEM_TEST(pvl->query, gageSclK2)) ){
double T, N, D;
T = ELL_3M_TRACE(gten);
N = curv;
D = 2*N*N - T*T;
/*
if (D < -0.0000001) {
fprintf(stderr, "%s: %g %g\n", me, T, N);
fprintf(stderr, "%s: !!! D curv determinant % 22.10f < 0.0\n", me, D);
fprintf(stderr, "%s: gten: \n", me);
ell_3m_print_d(stderr, gten);
}
*/
D = AIR_MAX(D, 0);
D = sqrt(D);
k1[0] = 0.5*(T + D);
k2[0] = 0.5*(T - D);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclMeanCurv)) {
pvl->directAnswer[gageSclMeanCurv][0] = (*k1 + *k2)/2;
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclGaussCurv)) {
pvl->directAnswer[gageSclGaussCurv][0] = (*k1)*(*k2);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclShapeIndex)) {
pvl->directAnswer[gageSclShapeIndex][0] =
-(2/AIR_PI)*atan2(*k1 + *k2, *k1 - *k2);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclCurvDir1)) {
/* HEY: this only works when K1, K2, 0 are all well mutually distinct,
since these are the eigenvalues of the geometry tensor, and this
code assumes that the eigenspaces are all one-dimensional */
ELL_3M_COPY(tmpMat, gten);
ELL_3M_DIAG_SET(tmpMat, gten[0] - *k1, gten[4]- *k1, gten[8] - *k1);
ell_3m_1d_nullspace_d(tmpVec, tmpMat);
ELL_3V_COPY(pvl->directAnswer[gageSclCurvDir1], tmpVec);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclCurvDir2)) {
/* HEY: this only works when K1, K2, 0 are all well mutually distinct,
since these are the eigenvalues of the geometry tensor, and this
code assumes that the eigenspaces are all one-dimensional */
ELL_3M_COPY(tmpMat, gten);
ELL_3M_DIAG_SET(tmpMat, gten[0] - *k2, gten[4] - *k2, gten[8] - *k2);
ell_3m_1d_nullspace_d(tmpVec, tmpMat);
ELL_3V_COPY(pvl->directAnswer[gageSclCurvDir2], tmpVec);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclFlowlineCurv)) {
if (gmag >= ctx->parm.gradMagCurvMin) {
/* because of the gageSclGeomTens prerequisite, sHess, nPerp, and
nProj are all already set */
/* ncTen = nPerp * sHess * nProj */
ELL_3M_MUL(tmpMat, sHess, nProj);
ELL_3M_MUL(ncTen, nPerp, tmpMat);
} else {
ELL_3M_ZERO_SET(ncTen);
}
/* there used to be a wrong extra sqrt() here */
pvl->directAnswer[gageSclFlowlineCurv][0] = ELL_3M_FROB(ncTen);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, gageSclMedian)) {
/* this item is currently a complete oddball in that it does not
benefit from anything done in the "filter" stage, which is in
fact a waste of time if the query consists only of this item */
fd = 2*ctx->radius;
if (fd > FD_MEDIAN_MAX) {
fprintf(stderr, "%s: PANIC: current filter diameter = %d "
"> FD_MEDIAN_MAX = %d\n", me, fd, FD_MEDIAN_MAX);
exit(1);
}
fw = ctx->fw + fd*3*gageKernel00;
/* HEY: this needs some optimization help */
wghtSum = 0;
nidx = 0;
for (xi=0; xi<fd; xi++) {
for (yi=0; yi<fd; yi++) {
for (zi=0; zi<fd; zi++) {
iv3wght[0 + 2*nidx] = pvl->iv3[nidx];
iv3wght[1 + 2*nidx] = fw[xi + 0*fd]*fw[yi + 1*fd]*fw[zi + 2*fd];
wghtSum += iv3wght[1 + 2*nidx];
nidx++;
}
}
}
qsort(iv3wght, fd*fd*fd, 2*sizeof(double), nrrdValCompare[nrrdTypeDouble]);
wght = 0;
for (nidx=0; nidx<fd*fd*fd; nidx++) {
wght += iv3wght[1 + 2*nidx];
if (wght > wghtSum/2) {
break;
}
}
pvl->directAnswer[gageSclMedian][0] = iv3wght[0 + 2*nidx];
}
return;
}
void
gageScl3PFilter2(gageShape *shape,
double *ivX, double *ivY, double *ivZ,
double *fw0, double *fw1, double *fw2,
double *val, double *gvec, double *hess,
const int *needD) {
int doV, doD1, doD2;
doV = needD[0];
doD1 = needD[1];
doD2 = needD[2];
/* fw? + 2*?
| |
| +- along which axis (0:x, 1:y, 2:z)
|
+ what information (0:value, 1:1st deriv, 2:2nd deriv)
ivX: 3D cube cache of original volume values
(its scanlines are along the X axis)
ivY: 2D square cache of intermediate filter results
(its scanlines are along the Y axis)
ivZ: 1D linear cache of intermediate filter results
(it is a scanline along the Z axis)
*/
#define DOT_2(a, b) ((a)[0]*(b)[0] + (a)[1]*(b)[1])
#define VL_2(i, axis) DOT_2(fw0 + (axis)*2, iv##axis + i*2)
#define D1_2(i, axis) DOT_2(fw1 + (axis)*2, iv##axis + i*2)
#define D2_2(i, axis) DOT_2(fw2 + (axis)*2, iv##axis + i*2)
/* x0 */
ivY[0] = VL_2(0,X); /* interpolate values of 0th scanline along X axis */
ivY[1] = VL_2(1,X);
ivY[2] = VL_2(2,X);
ivY[3] = VL_2(3,X);
/* x0y0 */
ivZ[0] = VL_2(0,Y);
ivZ[1] = VL_2(1,Y);
/* x0y0z0 */
if (doV) {
*val = VL_2(0,Z); /* f */
}
if (!( doD1 || doD2 ))
return;
/* x0y0z1 */
if (doD1) {
gvec[2] = D1_2(0,Z); /* g_z */
}
if (doD2) {
/* actually, there is no possible way in which it makes sense to
try to measure a second derivative with only two samples, so
all this "if (doD2)" code is basically bogus, but we'll keep it
around for generality . . . */
/* x0y0z2 */
hess[8] = D2_2(0,Z); /* h_zz */
}
/* x0y1 */
ivZ[0] = D1_2(0,Y);
ivZ[1] = D1_2(1,Y);
/* x0y1z0 */
if (doD1) {
gvec[1] = VL_2(0,Z); /* g_y */
}
if (doD2) {
/* x0y1z1 */
hess[5] = hess[7] = D1_2(0,Z); /* h_yz */
/* x0y2 */
ivZ[0] = D2_2(0,Y);
ivZ[1] = D2_2(1,Y);
/* x0y2z0 */
hess[4] = VL_2(0,Z); /* h_yy */
}
/* x1 */
ivY[0] = D1_2(0,X);
ivY[1] = D1_2(1,X);
ivY[2] = D1_2(2,X);
ivY[3] = D1_2(3,X);
/* x1y0 */
ivZ[0] = VL_2(0,Y);
ivZ[1] = VL_2(1,Y);
/* x1y0z0 */
if (doD1) {
gvec[0] = VL_2(0,Z); /* g_x */
}
ell_3mv_mul_d(gvec, shape->ItoWSubInvTransp, gvec);
if (!doD2)
return;
/* x1y0z1 */
hess[2] = hess[6] = D1_2(0,Z); /* h_xz */
/* x1y1 */
ivZ[0] = D1_2(0,Y);
ivZ[1] = D1_2(1,Y);
/* x1y1z0 */
hess[1] = hess[3] = VL_2(0,Z); /* h_xy */
/* x2 */
ivY[0] = D2_2(0,X);
ivY[1] = D2_2(1,X);
ivY[2] = D2_2(2,X);
ivY[3] = D2_2(3,X);
/* x2y0 */
ivZ[0] = VL_2(0,Y);
ivZ[1] = VL_2(1,Y);
/* x2y0z0 */
hess[0] = VL_2(0,Z); /* h_xx */
if (1) {
double matA[9];
ELL_3M_MUL(matA, shape->ItoWSubInvTransp, hess);
ELL_3M_MUL(hess, matA, shape->ItoWSubInv);
}
return;
}
void
gageScl3PFilter4(gageShape *shape,
double *ivX, double *ivY, double *ivZ,
double *fw0, double *fw1, double *fw2,
double *val, double *gvec, double *hess,
const int *needD) {
int doV, doD1, doD2;
doV = needD[0];
doD1 = needD[1];
doD2 = needD[2];
/* fw? + 4*?
| |
| +- along which axis (0:x, 1:y, 2:z)
|
+ what information (0:value, 1:1st deriv, 2:2nd deriv)
ivX: 3D cube cache of original volume values
(its scanlines are along the X axis)
ivY: 2D square cache of intermediate filter results
(its scanlines are along the Y axis)
ivZ: 1D linear cache of intermediate filter results
(it is a scanline along the Z axis)
*/
#define DOT_4(a,b) ((a)[0]*(b)[0]+(a)[1]*(b)[1]+(a)[2]*(b)[2]+(a)[3]*(b)[3])
#define VL_4(i, axis) DOT_4(fw0 + (axis)*4, iv##axis + i*4)
#define D1_4(i, axis) DOT_4(fw1 + (axis)*4, iv##axis + i*4)
#define D2_4(i, axis) DOT_4(fw2 + (axis)*4, iv##axis + i*4)
/* x0 */
ivY[ 0] = VL_4( 0,X);
ivY[ 1] = VL_4( 1,X);
ivY[ 2] = VL_4( 2,X);
ivY[ 3] = VL_4( 3,X);
ivY[ 4] = VL_4( 4,X);
ivY[ 5] = VL_4( 5,X);
ivY[ 6] = VL_4( 6,X);
ivY[ 7] = VL_4( 7,X);
ivY[ 8] = VL_4( 8,X);
ivY[ 9] = VL_4( 9,X);
ivY[10] = VL_4(10,X);
ivY[11] = VL_4(11,X);
ivY[12] = VL_4(12,X);
ivY[13] = VL_4(13,X);
ivY[14] = VL_4(14,X);
ivY[15] = VL_4(15,X);
/*
*/
/* x0y0 */
ivZ[ 0] = VL_4( 0,Y);
ivZ[ 1] = VL_4( 1,Y);
ivZ[ 2] = VL_4( 2,Y);
ivZ[ 3] = VL_4( 3,Y);
/* x0y0z0 */
if (doV) {
*val = VL_4( 0,Z); /* f */
}
if (!( doD1 || doD2 ))
return;
/* x0y0z1 */
if (doD1) {
gvec[2] = D1_4( 0,Z); /* g_z */
}
if (doD2) {
/* x0y0z2 */
hess[8] = D2_4( 0,Z); /* h_zz */
}
/* x0y1 */
ivZ[ 0] = D1_4( 0,Y);
ivZ[ 1] = D1_4( 1,Y);
ivZ[ 2] = D1_4( 2,Y);
ivZ[ 3] = D1_4( 3,Y);
/* x0y1z0 */
if (doD1) {
gvec[1] = VL_4( 0,Z); /* g_y */
}
if (doD2) {
/* x0y1z1 */
hess[5] = hess[7] = D1_4( 0,Z); /* h_yz */
/* x0y2 */
ivZ[ 0] = D2_4( 0,Y);
ivZ[ 1] = D2_4( 1,Y);
ivZ[ 2] = D2_4( 2,Y);
ivZ[ 3] = D2_4( 3,Y);
/* x0y2z0 */
hess[4] = VL_4( 0,Z); /* h_yy */
}
/* x1 */
ivY[ 0] = D1_4( 0,X);
ivY[ 1] = D1_4( 1,X);
ivY[ 2] = D1_4( 2,X);
ivY[ 3] = D1_4( 3,X);
ivY[ 4] = D1_4( 4,X);
ivY[ 5] = D1_4( 5,X);
ivY[ 6] = D1_4( 6,X);
ivY[ 7] = D1_4( 7,X);
ivY[ 8] = D1_4( 8,X);
ivY[ 9] = D1_4( 9,X);
ivY[10] = D1_4(10,X);
ivY[11] = D1_4(11,X);
ivY[12] = D1_4(12,X);
ivY[13] = D1_4(13,X);
ivY[14] = D1_4(14,X);
ivY[15] = D1_4(15,X);
/* x1y0 */
ivZ[ 0] = VL_4( 0,Y);
ivZ[ 1] = VL_4( 1,Y);
ivZ[ 2] = VL_4( 2,Y);
ivZ[ 3] = VL_4( 3,Y);
/* x1y0z0 */
if (doD1) {
gvec[0] = VL_4( 0,Z); /* g_x */
}
ell_3mv_mul_d(gvec, shape->ItoWSubInvTransp, gvec);
if (!doD2)
return;
/* x1y0z1 */
hess[2] = hess[6] = D1_4( 0,Z); /* h_xz */
/* x1y1 */
ivZ[ 0] = D1_4( 0,Y);
ivZ[ 1] = D1_4( 1,Y);
ivZ[ 2] = D1_4( 2,Y);
ivZ[ 3] = D1_4( 3,Y);
/* x1y1z0 */
hess[1] = hess[3] = VL_4( 0,Z); /* h_xy */
/* x2 */
ivY[ 0] = D2_4( 0,X);
ivY[ 1] = D2_4( 1,X);
ivY[ 2] = D2_4( 2,X);
ivY[ 3] = D2_4( 3,X);
ivY[ 4] = D2_4( 4,X);
ivY[ 5] = D2_4( 5,X);
ivY[ 6] = D2_4( 6,X);
ivY[ 7] = D2_4( 7,X);
ivY[ 8] = D2_4( 8,X);
ivY[ 9] = D2_4( 9,X);
ivY[10] = D2_4(10,X);
ivY[11] = D2_4(11,X);
ivY[12] = D2_4(12,X);
ivY[13] = D2_4(13,X);
ivY[14] = D2_4(14,X);
ivY[15] = D2_4(15,X);
/* x2y0 */
ivZ[ 0] = VL_4( 0,Y);
ivZ[ 1] = VL_4( 1,Y);
ivZ[ 2] = VL_4( 2,Y);
ivZ[ 3] = VL_4( 3,Y);
/* x2y0z0 */
hess[0] = VL_4( 0,Z); /* h_xx */
if (1) {
double matA[9];
ELL_3M_MUL(matA, shape->ItoWSubInvTransp, hess);
ELL_3M_MUL(hess, matA, shape->ItoWSubInv);
}
return;
}
void
_tenDwiGageAnswer(gageContext *ctx, gagePerVolume *pvl) {
char me[]="_tenDwiGageAnswer";
unsigned int dwiIdx;
tenDwiGageKindData *kindData;
tenDwiGagePvlData *pvlData;
double *dwiAll, dwiMean=0, tentmp[7];
kindData = AIR_CAST(tenDwiGageKindData *, pvl->kind->data);
pvlData = AIR_CAST(tenDwiGagePvlData *, pvl->data);
dwiAll = pvl->directAnswer[tenDwiGageAll];
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageAll)) {
/* done if doV */
if (ctx->verbose) {
for (dwiIdx=0; dwiIdx<pvl->kind->valLen; dwiIdx++) {
fprintf(stderr, "%s(%d+%g,%d+%g,%d+%g): dwi[%u] = %g\n", me,
ctx->point.xi, ctx->point.xf,
ctx->point.yi, ctx->point.yf,
ctx->point.zi, ctx->point.zf,
dwiIdx, dwiAll[dwiIdx]);
}
fprintf(stderr, "%s: type(ngrad) = %d = %s\n", me,
kindData->ngrad->type,
airEnumStr(nrrdType, kindData->ngrad->type));
}
}
/*
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageB0)) {
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageJustDWI)) {
done if doV
}
*/
/* HEY this isn't valid for multiple b-values */
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageADC)) {
double logdwi, logb0;
logb0 = log(AIR_MAX(kindData->valueMin,
pvl->directAnswer[tenDwiGageB0][0]));
for (dwiIdx=1; dwiIdx<pvl->kind->valLen; dwiIdx++) {
logdwi = log(AIR_MAX(kindData->valueMin,
pvl->directAnswer[tenDwiGageJustDWI][dwiIdx-1]));
pvl->directAnswer[tenDwiGageADC][dwiIdx-1]
= (logb0 - logdwi)/kindData->bval;
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageMeanDWIValue)) {
dwiMean = 0;
for (dwiIdx=1; dwiIdx<pvl->kind->valLen; dwiIdx++) {
dwiMean += dwiAll[dwiIdx];
}
dwiMean /= pvl->kind->valLen;
pvl->directAnswer[tenDwiGageMeanDWIValue][0] = dwiMean;
}
/* note: the gage interface to tenEstimate functionality
allows you exactly one kind of tensor estimation (per kind),
so the function call to do the estimation is actually
repeated over and over again; the copy into the answer
buffer is what changes... */
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorLLS)) {
tenEstimate1TensorSingle_d(pvlData->tec1, tentmp, dwiAll);
TEN_T_COPY(pvl->directAnswer[tenDwiGageTensorLLS], tentmp);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorLLSError)) {
pvl->directAnswer[tenDwiGageTensorLLSError][0] = pvlData->tec1->errorDwi;
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorLLSErrorLog)) {
pvl->directAnswer[tenDwiGageTensorLLSErrorLog][0]
= pvlData->tec1->errorLogDwi;
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorWLS)) {
tenEstimate1TensorSingle_d(pvlData->tec1, tentmp, dwiAll);
TEN_T_COPY(pvl->directAnswer[tenDwiGageTensorWLS], tentmp);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorNLS)) {
tenEstimate1TensorSingle_d(pvlData->tec1, tentmp, dwiAll);
TEN_T_COPY(pvl->directAnswer[tenDwiGageTensorNLS], tentmp);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorMLE)) {
tenEstimate1TensorSingle_d(pvlData->tec1, tentmp, dwiAll);
TEN_T_COPY(pvl->directAnswer[tenDwiGageTensorMLE], tentmp);
}
/* HEY: have to implement all the different kinds of errors */
/* BEGIN sneakiness ........ */
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensor)) {
gageItemEntry *item;
item = pvl->kind->table + tenDwiGageTensor;
TEN_T_COPY(pvl->directAnswer[tenDwiGageTensor],
pvl->directAnswer[item->prereq[0]]);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorError)) {
gageItemEntry *item;
item = pvl->kind->table + tenDwiGageTensorError;
pvl->directAnswer[tenDwiGageTensorError][0]
= pvl->directAnswer[item->prereq[0]][0];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorErrorLog)) {
gageItemEntry *item;
item = pvl->kind->table + tenDwiGageTensorErrorLog;
pvl->directAnswer[tenDwiGageTensorErrorLog][0]
= pvl->directAnswer[item->prereq[0]][0];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorLikelihood)) {
gageItemEntry *item;
item = pvl->kind->table + tenDwiGageTensorLikelihood;
pvl->directAnswer[tenDwiGageTensorLikelihood][0]
= pvl->directAnswer[item->prereq[0]][0];
}
/* END sneakiness ........ */
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageFA)) {
pvl->directAnswer[tenDwiGageFA][0]
= pvl->directAnswer[tenDwiGageTensor][0]
* tenAnisoTen_d(pvl->directAnswer[tenDwiGageTensor],
tenAniso_FA);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGageTensorAllDWIError)) {
const double *grads;
int gradcount;
double *ten, d;
int i;
/* HEY: should switch to tenEstimate-based DWI simulation */
ten = pvl->directAnswer[tenDwiGageTensor];
gradcount = pvl->kind->valLen -1; /* Dont count b0 */
grads = ((const double*) kindData->ngrad->data) +3; /* Ignore b0 grad */
for( i=0; i < gradcount; i++ ) {
d = dwiAll[0]*exp(- pvlData->tec1->bValue
* TEN_T3V_CONTR(ten, grads + 3*i));
pvl->directAnswer[tenDwiGageTensorAllDWIError][i] = dwiAll[i+1] - d;
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGage2TensorQSeg)) {
const double *grads;
int gradcount;
double *twoten;
unsigned int valIdx, E;
twoten = pvl->directAnswer[tenDwiGage2TensorQSeg];
gradcount = pvl->kind->valLen -1; /* Dont count b0 */
grads = ((const double*) kindData->ngrad->data) +3; /* Ignore b0 grad */
if (dwiAll[0] != 0) { /* S0 = 0 */
_tenQball(pvlData->tec2->bValue, gradcount, dwiAll, grads,
pvlData->qvals);
_tenQvals2points(gradcount, pvlData->qvals, grads, pvlData->qpoints);
_tenSegsamp2(gradcount, pvlData->qvals, grads, pvlData->qpoints,
pvlData->wght + 1, pvlData->dists );
} else {
/* stupid; should really return right here since data is garbage */
for (valIdx=1; valIdx < AIR_CAST(unsigned int, gradcount+1); valIdx++) {
pvlData->wght[valIdx] = valIdx % 2;
}
}
E = 0;
for (valIdx=1; valIdx<pvl->kind->valLen; valIdx++) {
if (!E) E |= tenEstimateSkipSet(pvlData->tec2, valIdx,
pvlData->wght[valIdx]);
}
if (!E) E |= tenEstimateUpdate(pvlData->tec2);
if (!E) E |= tenEstimate1TensorSingle_d(pvlData->tec2,
twoten + 0, dwiAll);
for (valIdx=1; valIdx<pvl->kind->valLen; valIdx++) {
if (!E) E |= tenEstimateSkipSet(pvlData->tec2, valIdx,
1 - pvlData->wght[valIdx]);
}
if (!E) E |= tenEstimateUpdate(pvlData->tec2);
if (!E) E |= tenEstimate1TensorSingle_d(pvlData->tec2,
twoten + 7, dwiAll);
if (E) {
fprintf(stderr, "!%s: (trouble) %s\n", me, biffGetDone(TEN));
}
/* hack: confidence for two-tensor fit */
twoten[0] = (twoten[0] + twoten[7])/2;
twoten[7] = 0.5; /* fraction that is the first tensor (initial value) */
/* twoten[1 .. 6] = first tensor */
/* twoten[8 .. 13] = second tensor */
/* Compute fraction between tensors if not garbage in this voxel */
if (twoten[0] > 0.5) {
double exp0,exp1,d,e=0,g=0, a=0,b=0;
int i;
for( i=0; i < gradcount; i++ ) {
exp0 = exp(-pvlData->tec2->bValue * TEN_T3V_CONTR(twoten + 0,
grads + 3*i));
exp1 = exp(-pvlData->tec2->bValue * TEN_T3V_CONTR(twoten + 7,
grads + 3*i));
d = dwiAll[i+1] / dwiAll[0];
e = exp0 - exp1;
g = d - exp1;
a += .5*e*e;
b += e*g;
}
twoten[7] = AIR_CLAMP(0, 0.5*(b/a), 1);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGage2TensorQSegError)) {
const double *grads;
int gradcount;
double *twoten, d;
int i;
/* HEY: should switch to tenEstimate-based DWI simulation */
if (dwiAll[0] != 0) { /* S0 = 0 */
twoten = pvl->directAnswer[tenDwiGage2TensorQSeg];
gradcount = pvl->kind->valLen -1; /* Dont count b0 */
grads = ((const double*) kindData->ngrad->data) +3; /* Ignore b0 grad */
pvl->directAnswer[tenDwiGage2TensorQSegError][0] = 0;
for( i=0; i < gradcount; i++ ) {
d = twoten[7]*exp(-pvlData->tec2->bValue * TEN_T3V_CONTR(twoten + 0,
grads + 3*i));
d += (1 - twoten[7])*exp(-pvlData->tec2->bValue
*TEN_T3V_CONTR(twoten + 7, grads + 3*i));
d = dwiAll[i+1]/dwiAll[0] - d;
pvl->directAnswer[tenDwiGage2TensorQSegError][0] += d*d;
}
pvl->directAnswer[tenDwiGage2TensorQSegError][0] =
sqrt( pvl->directAnswer[tenDwiGage2TensorQSegError][0] );
} else {
/* HEY: COMPLETELY WRONG!! An error is not defined! */
pvl->directAnswer[tenDwiGage2TensorQSegError][0] = 0;
}
/* printf("%f\n",pvl->directAnswer[tenDwiGage2TensorQSegError][0]); */
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGage2TensorQSegAndError)) {
double *twoten, *err, *twotenerr;
twoten = pvl->directAnswer[tenDwiGage2TensorQSeg];
err = pvl->directAnswer[tenDwiGage2TensorQSegError];
twotenerr = pvl->directAnswer[tenDwiGage2TensorQSegAndError];
TEN_T_COPY(twotenerr + 0, twoten + 0);
TEN_T_COPY(twotenerr + 7, twoten + 7);
twotenerr[14] = err[0];
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGage2TensorPeled)) {
#if TEEM_LEVMAR
#define PARAMS 4
double *twoTen, Cp /* , residual, AICSingFit, AICTwoFit */;
/* Vars for the NLLS */
double guess[PARAMS], loBnd[PARAMS], upBnd[PARAMS],
opts[LM_OPTS_SZ], *grad, *egrad, tenA[7], tenB[7],
matA[9], matB[9], matTmp[9], rott[9];
unsigned int gi;
int lmret;
/* Pointer to the location where the two tensor will be written */
twoTen = pvl->directAnswer[tenDwiGage2TensorPeled];
/* Estimate the DWI error, error is given as standard deviation */
pvlData->tec2->recordErrorDwi = AIR_FALSE;
/* Estimate the single tensor */
tenEstimate1TensorSingle_d(pvlData->tec2, pvlData->ten1, dwiAll);
/* Get the eigenValues and eigen vectors for this tensor */
tenEigensolve_d(pvlData->ten1Eval, pvlData->ten1Evec, pvlData->ten1);
/* Get westins Cp */
Cp = tenAnisoEval_d(pvlData->ten1Eval, tenAniso_Cp1);
/* Calculate the residual, need the variance to sqr it */
/* residual = pvlData->tec2->errorDwi*pvlData->tec2->errorDwi; */
/* Calculate the AIC for single tensor fit */
/* AICSingFit = _tenComputeAIC(residual, pvlData->tec2->dwiNum, 6); */
/* the CP-based test is gone; caller's responsibility */
/* rotate DW gradients by inverse of eigenvector column matrix
and place into pvlData->nten1EigenGrads (which has been
allocated by _tenDwiGagePvlDataNew()) */
grad = AIR_CAST(double *, kindData->ngrad->data);
egrad = AIR_CAST(double *, pvlData->nten1EigenGrads->data);
for (gi=0; gi<kindData->ngrad->axis[1].size; gi++) {
/* yes, this is also transforming some zero-length (B0) gradients;
that's harmless */
ELL_3MV_MUL(egrad, pvlData->ten1Evec, grad);
grad += 3;
egrad += 3;
}
/* Lower and upper bounds for the NLLS routine */
loBnd[0] = 0.0;
loBnd[1] = 0.0;
loBnd[2] = -AIR_PI/2;
loBnd[3] = -AIR_PI/2;
upBnd[0] = pvlData->ten1Eval[0]*5;
upBnd[1] = 1.0;
upBnd[2] = AIR_PI/2;
upBnd[3] = AIR_PI/2;
/* Starting point for the NLLS */
guess[0] = pvlData->ten1Eval[0];
guess[1] = 0.5;
guess[2] = AIR_PI/4;
guess[3] = -AIR_PI/4;
/*
guess[2] = AIR_AFFINE(0, airDrandMT_r(pvlData->randState), 1,
AIR_PI/6, AIR_PI/3);
guess[3] = AIR_AFFINE(0, airDrandMT_r(pvlData->randState), 1,
-AIR_PI/6, -AIR_PI/3);
*/
/* Fill in the constraints for the LM optimization,
the threshold of error difference */
opts[0] = pvlData->levmarTau;
opts[1] = pvlData->levmarEps1;
opts[2] = pvlData->levmarEps2;
opts[3] = pvlData->levmarEps3;
/* Very imp to set this opt, note that only forward
differences are used to approx Jacobian */
opts[4] = pvlData->levmarDelta;
/* run NLLS, results are stored back into guess[] */
pvlData->levmarUseFastExp = AIR_FALSE;
lmret = dlevmar_bc_dif(_tenLevmarPeledCB, guess, pvlData->tec2->dwi,
PARAMS, pvlData->tec2->dwiNum, loBnd, upBnd,
pvlData->levmarMaxIter, opts,
pvlData->levmarInfo,
NULL, NULL, pvlData);
if (-1 == lmret) {
ctx->errNum = 1;
sprintf(ctx->errStr, "%s: dlevmar_bc_dif() failed!", me);
} else {
/* Get the AIC for the two tensor fit, use the levmarinfo
to get the residual */
/*
residual = pvlData->levmarInfo[1]/pvlData->tec2->dwiNum;
AICTwoFit = _tenComputeAIC(residual, pvlData->tec2->dwiNum, 12);
*/
/* Form the tensors using the estimated pp, returned in guess */
_tenPeledRotate2D(tenA, guess[0], pvlData->ten1Eval[2], guess[2]);
_tenPeledRotate2D(tenB, guess[0], pvlData->ten1Eval[2], guess[3]);
TEN_T2M(matA, tenA);
TEN_T2M(matB, tenB);
ELL_3M_TRANSPOSE(rott, pvlData->ten1Evec);
ELL_3M_MUL(matTmp, matA, pvlData->ten1Evec);
ELL_3M_MUL(matA, rott, matTmp);
ELL_3M_MUL(matTmp, matB, pvlData->ten1Evec);
ELL_3M_MUL(matB, rott, matTmp);
/* Copy two two tensors */
/* guess[1] is population fraction of first tensor */
if (guess[1] > 0.5) {
twoTen[7] = guess[1];
TEN_M2T(twoTen + 0, matA);
TEN_M2T(twoTen + 7, matB);
} else {
twoTen[7] = 1 - guess[1];
TEN_M2T(twoTen + 0, matB);
TEN_M2T(twoTen + 7, matA);
}
twoTen[0] = 1;
}
#undef PARAMS
#else
double *twoTen;
twoTen = pvl->directAnswer[tenDwiGage2TensorPeled];
TEN_T_SET(twoTen + 0, AIR_NAN, AIR_NAN, AIR_NAN, AIR_NAN,
AIR_NAN, AIR_NAN, AIR_NAN);
TEN_T_SET(twoTen + 7, AIR_NAN, AIR_NAN, AIR_NAN, AIR_NAN,
AIR_NAN, AIR_NAN, AIR_NAN);
fprintf(stderr, "%s: sorry, not compiled with TEEM_LEVMAR\n", me);
#endif
}
static int
csimDo(double tm[7], double tcov[21], double rm[3], double rv[3],
Nrrd *ntbuff, tenEstimateContext *tec, double *dwibuff, double sigma,
double bvalue, double B0, unsigned int NN, int randrot,
double _tenOrig[7]) {
char me[]="csimDo", err[BIFF_STRLEN];
double *tbuff;
unsigned int II, taa, tbb, cc;
if (!(ntbuff
&& ntbuff->data
&& 2 == ntbuff->dim
&& 7 == ntbuff->axis[0].size
&& NN == ntbuff->axis[1].size)) {
sprintf(err, "%s: ntbuff not allocated for 2-by-%u array of %s", me,
NN, airEnumStr(nrrdType, nrrdTypeDouble));
biffAdd(TEN, err); return 1;
}
/* find all tensors from simulated DWIs */
tbuff = AIR_CAST(double *, ntbuff->data);
for (II=0; II<NN; II++) {
double tenOrig[7], rotf[9], rotb[9], matA[9], matB[9], qq[4], tmp;
ELL_3M_IDENTITY_SET(rotf); /* sssh warnings */
ELL_3M_IDENTITY_SET(rotb); /* sssh warnings */
if (randrot) {
if (1) {
double eval[3], evec[9], eps, ma[9], mb[9], rf[9], rb[9];
tenEigensolve_d(eval, evec, _tenOrig);
airNormalRand(&eps, NULL);
ell_aa_to_3m_d(rf, 0*eps/20, evec + 0);
TEN_T_SCALE_INCR(_tenOrig, 0*eps/30, _tenOrig);
TEN_T2M(ma, _tenOrig);
ELL_3M_TRANSPOSE(rb, rf);
ELL_3M_MUL(mb, ma, rf);
ELL_3M_MUL(ma, rb, mb);
TEN_M2T(_tenOrig, ma);
}
TEN_T2M(matA, _tenOrig);
airNormalRand(qq+0, qq+1);
airNormalRand(qq+2, qq+3);
ELL_4V_NORM(qq, qq, tmp);
ell_q_to_3m_d(rotf, qq);
ELL_3M_TRANSPOSE(rotb, rotf);
ELL_3M_MUL(matB, matA, rotf);
ELL_3M_MUL(matA, rotb, matB);
TEN_M2T(tenOrig, matA);
} else {
TEN_T_COPY(tenOrig, _tenOrig);
}
if (tenEstimate1TensorSimulateSingle_d(tec, dwibuff, sigma,
bvalue, B0, tenOrig)
|| tenEstimate1TensorSingle_d(tec, tbuff, dwibuff)) {
sprintf(err, "%s: trouble on exp %u/%u", me, II, NN);
biffAdd(TEN, err); return 1;
}
if (randrot) {
TEN_T2M(matA, tbuff);
ELL_3M_MUL(matB, matA, rotb);
ELL_3M_MUL(matA, rotf, matB);
TEN_M2T(tbuff, matA);
} /* else we leave tbuff as it is */
/*
if (_tenOrig[0] > 0.5) {
double tdiff[7];
TEN_T_SUB(tdiff, _tenOrig, tbuff);
fprintf(stderr, "!%s: %g\n"
" (%g) %g,%g,%g %g,%g %g\n"
" (%g) %g,%g,%g %g,%g %g\n",
me, TEN_T_NORM(tdiff),
_tenOrig[0], _tenOrig[1], _tenOrig[2], _tenOrig[3], _tenOrig[4],
_tenOrig[5], _tenOrig[6],
tbuff[0], tbuff[1], tbuff[2], tbuff[3], tbuff[4],
tbuff[5], tbuff[6]);
}
*/
tbuff += 7;
}
/* find mean tensor, and mean R_i */
tbuff = AIR_CAST(double *, ntbuff->data);
TEN_T_SET(tm, 0, 0, 0, 0, 0, 0, 0);
ELL_3V_SET(rm, 0, 0, 0);
for (II=0; II<NN; II++) {
TEN_T_INCR(tm, tbuff);
rm[0] += sqrt(_tenAnisoTen_d[tenAniso_S](tbuff));
rm[1] += _tenAnisoTen_d[tenAniso_FA](tbuff);
rm[2] += _tenAnisoTen_d[tenAniso_Mode](tbuff);
tbuff += 7;
}
rm[0] /= NN;
rm[1] /= NN;
rm[2] /= NN;
TEN_T_SCALE(tm, 1.0/NN, tm);
/* accumulate covariance tensor, and R_i variances */
for (cc=0; cc<21; cc++) {
tcov[cc] = 0;
}
ELL_3V_SET(rv, 0, 0, 0);
tbuff = AIR_CAST(double *, ntbuff->data);
for (II=0; II<NN; II++) {
double r[3];
r[0] = sqrt(_tenAnisoTen_d[tenAniso_S](tbuff));
r[1] = _tenAnisoTen_d[tenAniso_FA](tbuff);
r[2] = _tenAnisoTen_d[tenAniso_Mode](tbuff);
cc = 0;
rv[0] += (r[0] - rm[0])*(r[0] - rm[0])/(NN-1);
rv[1] += (r[1] - rm[1])*(r[1] - rm[1])/(NN-1);
rv[2] += (r[2] - rm[2])*(r[2] - rm[2])/(NN-1);
for (taa=0; taa<6; taa++) {
for (tbb=taa; tbb<6; tbb++) {
tcov[cc] += (10000*(tbuff[taa+1]-tm[taa+1])
*10000*(tbuff[tbb+1]-tm[tbb+1])/(NN-1));
cc++;
}
}
tbuff += 7;
}
return 0;
}