int
mossImageAlloc (Nrrd *image, int type, int sx, int sy, int ncol) {
static const char me[]="mossImageAlloc";
int ret;
if (!(image && AIR_IN_OP(nrrdTypeUnknown, type, nrrdTypeBlock)
&& sx > 0 && sy > 0 && ncol > 0)) {
biffAddf(MOSS, "%s: got NULL pointer or bad args", me);
return 1;
}
if (1 == ncol) {
ret = nrrdMaybeAlloc_va(image, type, 2,
AIR_CAST(size_t, sx),
AIR_CAST(size_t, sy));
} else {
ret = nrrdMaybeAlloc_va(image, type, 3,
AIR_CAST(size_t, ncol),
AIR_CAST(size_t, sx),
AIR_CAST(size_t, sy));
}
if (ret) {
biffMovef(MOSS, NRRD, "%s: couldn't allocate image", me);
return 1;
}
return 0;
}
int
mossImageAlloc (Nrrd *image, int type, int sx, int sy, int ncol) {
char me[]="mossImageAlloc", err[BIFF_STRLEN];
int ret;
if (!(image && AIR_IN_OP(nrrdTypeUnknown, type, nrrdTypeBlock)
&& sx > 0 && sy > 0 && ncol > 0)) {
sprintf(err, "%s: got NULL pointer or bad args", me);
biffAdd(MOSS, err);
return 1;
}
if (1 == ncol) {
ret = nrrdMaybeAlloc_va(image, type, 2,
AIR_CAST(size_t, sx),
AIR_CAST(size_t, sy));
} else {
ret = nrrdMaybeAlloc_va(image, type, 3,
AIR_CAST(size_t, ncol),
AIR_CAST(size_t, sx),
AIR_CAST(size_t, sy));
}
if (ret) {
sprintf(err, "%s: couldn't allocate image", me);
biffMove(MOSS, err, NRRD);
return 1;
}
return 0;
}
/*
******** tenGradientRandom
**
** generates num random unit vectors of type double
*/
int
tenGradientRandom(Nrrd *ngrad, unsigned int num, unsigned int seed) {
static const char me[]="tenGradientRandom";
double *grad, len;
unsigned int gi;
if (nrrdMaybeAlloc_va(ngrad, nrrdTypeDouble, 2,
AIR_CAST(size_t, 3), AIR_CAST(size_t, num))) {
biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
airSrandMT(seed);
grad = AIR_CAST(double*, ngrad->data);
for (gi=0; gi<num; gi++) {
do {
grad[0] = AIR_AFFINE(0, airDrandMT(), 1, -1, 1);
grad[1] = AIR_AFFINE(0, airDrandMT(), 1, -1, 1);
grad[2] = AIR_AFFINE(0, airDrandMT(), 1, -1, 1);
len = ELL_3V_LEN(grad);
} while (len > 1 || !len);
ELL_3V_SCALE(grad, 1.0/len, grad);
grad += 3;
}
return 0;
}
Nrrd *
_baneGkmsDonNew(int invert) {
char me[]="_baneGkmsDonNew", err[BIFF_STRLEN];
Nrrd *ret;
float *data;
if (nrrdMaybeAlloc_va(ret=nrrdNew(), nrrdTypeFloat, 2,
AIR_CAST(size_t, 4), AIR_CAST(size_t, 23))) {
sprintf(err, "%s: can't create output", me);
biffAdd(BANE, err); return NULL;
}
data = (float *)ret->data;
memcpy(data, _baneGkmsDonData, 4*23*sizeof(float));
data[0 + 4*0] = AIR_NEG_INF;
data[0 + 4*1] = AIR_NAN;
data[0 + 4*2] = AIR_POS_INF;
if (invert) {
INVERT(data, 0);
INVERT(data, 1);
INVERT(data, 2);
INVERT(data, 12);
INVERT(data, 13);
}
return ret;
}
int
limnSplineSample(Nrrd *nout, limnSpline *spline,
double minT, size_t M, double maxT) {
char me[]="limnSplineSample", err[BIFF_STRLEN];
airArray *mop;
Nrrd *ntt;
double *tt;
size_t I;
if (!(nout && spline)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(LIMN, err); return 1;
}
mop = airMopNew();
airMopAdd(mop, ntt=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(ntt, nrrdTypeDouble, 1,
M)) {
sprintf(err, "%s: trouble allocating tmp nrrd", me);
biffMove(LIMN, err, NRRD); airMopError(mop); return 1;
}
tt = (double*)(ntt->data);
for (I=0; I<M; I++) {
tt[I] = AIR_AFFINE(0, I, M-1, minT, maxT);
}
if (limnSplineNrrdEvaluate(nout, spline, ntt)) {
sprintf(err, "%s: trouble", me);
biffAdd(LIMN, err); airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
/*
******** ell_Nm_inv
**
** computes the inverse of given matrix in nmat, and puts the
** inverse in the (maybe allocated) ninv. Does not touch the
** values in nmat.
*/
int
ell_Nm_inv(Nrrd *ninv, Nrrd *nmat) {
static const char me[]="ell_Nm_inv";
double *mat, *inv;
size_t NN;
if (!( ninv && !ell_Nm_check(nmat, AIR_FALSE) )) {
biffAddf(ELL, "%s: NULL or invalid args", me);
return 1;
}
NN = nmat->axis[0].size;
if (!( NN == nmat->axis[1].size )) {
char stmp[2][AIR_STRLEN_SMALL];
biffAddf(ELL, "%s: need a square matrix, not %s-by-%s", me,
airSprintSize_t(stmp[0], nmat->axis[1].size),
airSprintSize_t(stmp[1], NN));
return 1;
}
if (nrrdMaybeAlloc_va(ninv, nrrdTypeDouble, 2,
NN, NN)) {
biffMovef(ELL, NRRD, "%s: trouble", me);
return 1;
}
inv = (double*)(ninv->data);
mat = (double*)(nmat->data);
if (_ell_inv(inv, mat, NN)) {
biffAddf(ELL, "%s: trouble", me);
return 1;
}
return 0;
}
int
alanUpdate(alanContext *actx) {
char me[]="alanUpdate", err[BIFF_STRLEN];
int ret;
if (_alanCheck(actx)) {
sprintf(err, "%s: ", me);
biffAdd(ALAN, err); return 1;
}
if (actx->_nlev[0] || actx->_nlev[0]) {
sprintf(err, "%s: confusion: _nlev[0,1] already allocated?", me);
biffAdd(ALAN, err); return 1;
}
actx->_nlev[0] = nrrdNew();
actx->_nlev[1] = nrrdNew();
actx->nparm = nrrdNew();
if (2 == actx->dim) {
ret = (nrrdMaybeAlloc_va(actx->_nlev[0], alan_nt, 3,
AIR_CAST(size_t, 2),
AIR_CAST(size_t, actx->size[0]),
AIR_CAST(size_t, actx->size[1]))
|| nrrdCopy(actx->_nlev[1], actx->_nlev[0])
|| nrrdMaybeAlloc_va(actx->nparm, alan_nt, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, actx->size[0]),
AIR_CAST(size_t, actx->size[1])));
} else {
ret = (nrrdMaybeAlloc_va(actx->_nlev[0], alan_nt, 4,
AIR_CAST(size_t, 2),
AIR_CAST(size_t, actx->size[0]),
AIR_CAST(size_t, actx->size[1]),
AIR_CAST(size_t, actx->size[2]))
|| nrrdCopy(actx->_nlev[1], actx->_nlev[0])
|| nrrdMaybeAlloc_va(actx->nparm, alan_nt, 4,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, actx->size[0]),
AIR_CAST(size_t, actx->size[1]),
AIR_CAST(size_t, actx->size[2])));
}
if (ret) {
sprintf(err, "%s: trouble allocating buffers", me);
biffMove(ALAN, err, NRRD); return 1;
}
return 0;
}
/*
******** nrrdPPM()
**
** for making a nrrd suitable for holding PPM data
**
** "don't mess with peripheral information"
*/
int
nrrdPPM(Nrrd *ppm, size_t sx, size_t sy) {
char me[]="nrrdPPM", err[BIFF_STRLEN];
if (nrrdMaybeAlloc_va(ppm, nrrdTypeUChar, 3,
AIR_CAST(size_t, 3), sx, sy)) {
sprintf(err, "%s: couldn't allocate " _AIR_SIZE_T_CNV
" x " _AIR_SIZE_T_CNV " 24-bit image", me, sx, sy);
biffAdd(NRRD, err); return 1;
}
return 0;
}
/*
******** ell_Nm_mul
**
** Currently, only useful for matrix-matrix multiplication
**
** matrix-matrix: M N
** L [A] . M [B]
*/
int
ell_Nm_mul(Nrrd *nAB, Nrrd *nA, Nrrd *nB) {
static const char me[]="ell_Nm_mul";
double *A, *B, *AB, tmp;
size_t LL, MM, NN, ll, mm, nn;
char stmp[4][AIR_STRLEN_SMALL];
if (!( nAB && !ell_Nm_check(nA, AIR_FALSE)
&& !ell_Nm_check(nB, AIR_FALSE) )) {
biffAddf(ELL, "%s: NULL or invalid args", me);
return 1;
}
if (nAB == nA || nAB == nB) {
biffAddf(ELL, "%s: can't do in-place multiplication", me);
return 1;
}
LL = nA->axis[1].size;
MM = nA->axis[0].size;
NN = nB->axis[0].size;
if (MM != nB->axis[1].size) {
biffAddf(ELL, "%s: size mismatch: %s-by-%s times %s-by-%s", me,
airSprintSize_t(stmp[0], LL),
airSprintSize_t(stmp[1], MM),
airSprintSize_t(stmp[2], nB->axis[1].size),
airSprintSize_t(stmp[3], NN));
return 1;
}
if (nrrdMaybeAlloc_va(nAB, nrrdTypeDouble, 2,
NN, LL)) {
biffMovef(ELL, NRRD, "%s: trouble", me);
return 1;
}
A = (double*)(nA->data);
B = (double*)(nB->data);
AB = (double*)(nAB->data);
for (ll=0; ll<LL; ll++) {
for (nn=0; nn<NN; nn++) {
tmp = 0;
for (mm=0; mm<MM; mm++) {
tmp += A[mm + MM*ll]*B[nn + NN*mm];
}
AB[ll*NN + nn] = tmp;
}
}
return 0;
}
int
baneGkmsParseBEF(void *ptr, char *str, char err[AIR_STRLEN_HUGE]) {
char me[]="baneGkmsParseBEF", mesg[AIR_STRLEN_MED], *nerr;
float cent, width, shape, alpha, off, *bef;
Nrrd **nrrdP;
airArray *mop;
if (!(ptr && str)) {
sprintf(err, "%s: got NULL pointer", me);
return 1;
}
mop = airMopNew();
nrrdP = (Nrrd **)ptr;
airMopAdd(mop, *nrrdP=nrrdNew(), (airMopper)nrrdNuke, airMopOnError);
if (4 == sscanf(str, "%g,%g,%g,%g", &shape, &width, ¢, &alpha)) {
/* its a valid BEF specification, we make the nrrd ourselves */
if (nrrdMaybeAlloc_va(*nrrdP, nrrdTypeFloat, 2,
AIR_CAST(size_t, 2), AIR_CAST(size_t, 6))) {
airMopAdd(mop, nerr = biffGetDone(NRRD), airFree, airMopOnError);
strncpy(err, nerr, AIR_STRLEN_HUGE-1);
airMopError(mop);
return 1;
}
bef = (float *)((*nrrdP)->data);
off = AIR_CAST(float, AIR_AFFINE(0.0, shape, 1.0, 0.0, width/2));
/* positions */
bef[0 + 2*0] = cent - 2*width;
bef[0 + 2*1] = cent - width/2 - off;
bef[0 + 2*2] = cent - width/2 + off;
bef[0 + 2*3] = cent + width/2 - off;
bef[0 + 2*4] = cent + width/2 + off;
bef[0 + 2*5] = cent + 2*width;
if (bef[0 + 2*1] == bef[0 + 2*2]) bef[0 + 2*1] -= 0.001f;
if (bef[0 + 2*2] == bef[0 + 2*3]) bef[0 + 2*2] -= 0.001f;
if (bef[0 + 2*3] == bef[0 + 2*4]) bef[0 + 2*4] += 0.001f;
/* opacities */
bef[1 + 2*0] = 0.0;
bef[1 + 2*1] = 0.0;
bef[1 + 2*2] = alpha;
bef[1 + 2*3] = alpha;
bef[1 + 2*4] = 0.0;
bef[1 + 2*5] = 0.0;
/* to tell gkms opac that this came from four floats */
(*nrrdP)->ptr = *nrrdP;
} else {
if (nrrdLoad(*nrrdP, str, NULL)) {
int
limnPolyDataSpiralTubeWrap(limnPolyData *pldOut, const limnPolyData *pldIn,
unsigned int infoBitFlag, Nrrd *nvertmap,
unsigned int tubeFacet, unsigned int endFacet,
double radius) {
char me[]="limnPolyDataSpiralTubeWrap", err[BIFF_STRLEN];
double *cost, *sint;
unsigned int tubeVertNum = 0, tubeIndxNum = 0, primIdx, pi, *vertmap;
unsigned int inVertTotalIdx = 0, outVertTotalIdx = 0, outIndxIdx = 0;
int color;
airArray *mop;
if (!( pldOut && pldIn )) {
sprintf(err, "%s: got NULL pointer", me);
return 1;
}
if ((1 << limnPrimitiveLineStrip) != limnPolyDataPrimitiveTypes(pldIn)) {
sprintf(err, "%s: sorry, can only handle %s primitives", me,
airEnumStr(limnPrimitive, limnPrimitiveLineStrip));
biffAdd(LIMN, err); return 1;
}
for (primIdx=0; primIdx<pldIn->primNum; primIdx++) {
tubeVertNum += tubeFacet*(2*endFacet
+ pldIn->icnt[primIdx]) + 1;
tubeIndxNum += 2*tubeFacet*(2*endFacet
+ pldIn->icnt[primIdx] + 1)-2;
}
if (limnPolyDataAlloc(pldOut,
/* sorry have to have normals, even if they weren't
asked for, because currently they're used as part
of vertex position calc */
(infoBitFlag | (1 << limnPolyDataInfoNorm)),
tubeVertNum, tubeIndxNum, pldIn->primNum)) {
sprintf(err, "%s: trouble allocating output", me);
biffAdd(LIMN, err); return 1;
}
if (nvertmap) {
if (nrrdMaybeAlloc_va(nvertmap, nrrdTypeUInt, 1,
AIR_CAST(size_t, tubeVertNum))) {
sprintf(err, "%s: trouble allocating vert map", me);
biffMove(LIMN, err, NRRD); return 1;
}
vertmap = AIR_CAST(unsigned int *, nvertmap->data);
} else {
/*
******** nrrd1DIrregAclGenerate()
**
** Generates the "acl" that is used to speed up the action of
** nrrdApply1DIrregMap(). Basically, the domain of the map
** is quantized into "acllen" bins, and for each bin, the
** lowest and highest possible map interval is stored. This
** either obviates or speeds up the task of finding which
** interval contains a given value.
**
** Assumes that nrrd1DIrregMapCheck has been called on "nmap".
*/
int
nrrd1DIrregAclGenerate(Nrrd *nacl, const Nrrd *nmap, size_t aclLen) {
char me[]="nrrd1DIrregAclGenerate", err[BIFF_STRLEN];
int posLen;
unsigned int ii;
unsigned short *acl;
double lo, hi, min, max, *pos;
if (!(nacl && nmap)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(NRRD, err); return 1;
}
if (!(aclLen >= 2)) {
sprintf(err, "%s: given acl length (" _AIR_SIZE_T_CNV
") is too small", me, aclLen);
biffAdd(NRRD, err); return 1;
}
if (nrrdMaybeAlloc_va(nacl, nrrdTypeUShort, 2,
AIR_CAST(size_t, 2), AIR_CAST(size_t, aclLen))) {
sprintf(err, "%s: ", me);
biffAdd(NRRD, err); return 1;
}
acl = (unsigned short *)nacl->data;
pos = _nrrd1DIrregMapDomain(&posLen, NULL, nmap);
if (!pos) {
sprintf(err, "%s: couldn't determine domain", me);
biffAdd(NRRD, err); return 1;
}
nacl->axis[1].min = min = pos[0];
nacl->axis[1].max = max = pos[posLen-1];
for (ii=0; ii<=aclLen-1; ii++) {
lo = AIR_AFFINE(0, ii, aclLen, min, max);
hi = AIR_AFFINE(0, ii+1, aclLen, min, max);
acl[0 + 2*ii] = _nrrd1DIrregFindInterval(pos, lo, 0, posLen-2);
acl[1 + 2*ii] = _nrrd1DIrregFindInterval(pos, hi, 0, posLen-2);
}
free(pos);
return 0;
}
/*
******** ell_Nm_tran
**
** M N
** N [trn] <-- M [mat]
*/
int
ell_Nm_tran(Nrrd *ntrn, Nrrd *nmat) {
static const char me[]="ell_Nm_tran";
double *mat, *trn;
size_t MM, NN, mm, nn;
if (!( ntrn && !ell_Nm_check(nmat, AIR_FALSE) )) {
biffAddf(ELL, "%s: NULL or invalid args", me);
return 1;
}
if (ntrn == nmat) {
biffAddf(ELL, "%s: sorry, can't work in-place yet", me);
return 1;
}
/*
if (nrrdAxesSwap(ntrn, nmat, 0, 1)) {
biffMovef(ELL, NRRD, "%s: trouble", me);
return 1;
}
*/
NN = nmat->axis[0].size;
MM = nmat->axis[1].size;
if (nrrdMaybeAlloc_va(ntrn, nrrdTypeDouble, 2,
MM, NN)) {
biffMovef(ELL, NRRD, "%s: trouble", me);
return 1;
}
mat = AIR_CAST(double *, nmat->data);
trn = AIR_CAST(double *, ntrn->data);
for (nn=0; nn<NN; nn++) {
for (mm=0; mm<MM; mm++) {
trn[mm + MM*nn] = mat[nn + NN*mm];
}
}
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *err, *outS;
hestOpt *hopt=NULL;
airArray *mop;
int sx, sy, xi, yi, samp, version, whole, right;
float *tdata;
double p[3], xyz[3], q[4], len, hackcp=0, maxca;
double ca, cp, mD[9], mRF[9], mRI[9], mT[9], hack;
Nrrd *nten;
mop = airMopNew();
me = argv[0];
hestOptAdd(&hopt, "n", "# samples", airTypeInt, 1, 1, &samp, "4",
"number of glyphs along each edge of triangle");
hestOptAdd(&hopt, "p", "x y z", airTypeDouble, 3, 3, p, NULL,
"location in quaternion quotient space");
hestOptAdd(&hopt, "ca", "max ca", airTypeDouble, 1, 1, &maxca, "0.8",
"maximum ca to use at bottom edge of triangle");
hestOptAdd(&hopt, "r", NULL, airTypeInt, 0, 0, &right, NULL,
"sample a right-triangle-shaped region, instead of "
"a roughly equilateral triangle. ");
hestOptAdd(&hopt, "w", NULL, airTypeInt, 0, 0, &whole, NULL,
"sample the whole triangle of constant trace, "
"instead of just the "
"sixth of it in which the eigenvalues have the "
"traditional sorted order. ");
hestOptAdd(&hopt, "hack", "hack", airTypeDouble, 1, 1, &hack, "0.04",
"this is a hack");
hestOptAdd(&hopt, "v", "version", airTypeInt, 1, 1, &version, "1",
"which version of the Westin metrics to use to parameterize "
"triangle; \"1\" for ISMRM 97, \"2\" for MICCAI 99");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output file to save tensors into");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nten = nrrdNew();
airMopAdd(mop, nten, (airMopper)nrrdNuke, airMopAlways);
if (!( 1 == version || 2 == version )) {
fprintf(stderr, "%s: version must be 1 or 2 (not %d)\n", me, version);
airMopError(mop);
return 1;
}
if (right) {
sx = samp;
sy = (int)(1.0*samp/sqrt(3.0));
} else {
sx = 2*samp-1;
sy = samp;
}
if (nrrdMaybeAlloc_va(nten, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7),
AIR_CAST(size_t, sx),
AIR_CAST(size_t, sy),
AIR_CAST(size_t, 3))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
q[0] = 1.0;
q[1] = p[0];
q[2] = p[1];
q[3] = p[2];
len = ELL_4V_LEN(q);
ELL_4V_SCALE(q, 1.0/len, q);
washQtoM3(mRF, q);
ELL_3M_TRANSPOSE(mRI, mRF);
if (right) {
_ra2t(nten, 0.00, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.10, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.10, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.20, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.20, 30.0, mRI, mRF, hack);
_ra2t(nten, 0.20, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.30, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.30, 20.0, mRI, mRF, hack);
_ra2t(nten, 0.30, 40.0, mRI, mRF, hack);
_ra2t(nten, 0.30, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.40, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.40, 15.0, mRI, mRF, hack);
_ra2t(nten, 0.40, 30.0, mRI, mRF, hack);
_ra2t(nten, 0.40, 45.0, mRI, mRF, hack);
_ra2t(nten, 0.40, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.50, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.50, 12.0, mRI, mRF, hack);
_ra2t(nten, 0.50, 24.0, mRI, mRF, hack);
_ra2t(nten, 0.50, 36.0, mRI, mRF, hack);
_ra2t(nten, 0.50, 48.0, mRI, mRF, hack);
_ra2t(nten, 0.50, 60.0, mRI, mRF, hack);
/* _ra2t(nten, 0.60, 30.0, mRI, mRF, hack); */
_ra2t(nten, 0.60, 40.0, mRI, mRF, hack);
_ra2t(nten, 0.60, 50.0, mRI, mRF, hack);
_ra2t(nten, 0.60, 60.0, mRI, mRF, hack);
/* _ra2t(nten, 0.70, 34.3, mRI, mRF, hack); */
/* _ra2t(nten, 0.70, 42.8, mRI, mRF, hack); */
_ra2t(nten, 0.70, 51.4, mRI, mRF, hack);
_ra2t(nten, 0.70, 60.0, mRI, mRF, hack);
/* _ra2t(nten, 0.80, 45.0, mRI, mRF, hack); */
_ra2t(nten, 0.80, 52.5, mRI, mRF, hack);
_ra2t(nten, 0.80, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.90, 60.0, mRI, mRF, hack);
_ra2t(nten, 1.00, 60.0, mRI, mRF, hack);
/*
_ra2t(nten, 0.000, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.125, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.125, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.250, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.250, 30.0, mRI, mRF, hack);
_ra2t(nten, 0.250, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.375, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.375, 20.0, mRI, mRF, hack);
_ra2t(nten, 0.375, 40.0, mRI, mRF, hack);
_ra2t(nten, 0.375, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.500, 0.0, mRI, mRF, hack);
_ra2t(nten, 0.500, 15.0, mRI, mRF, hack);
_ra2t(nten, 0.500, 30.0, mRI, mRF, hack);
_ra2t(nten, 0.500, 45.0, mRI, mRF, hack);
_ra2t(nten, 0.500, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.625, 37.0, mRI, mRF, hack);
_ra2t(nten, 0.625, 47.5, mRI, mRF, hack);
_ra2t(nten, 0.625, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.750, 49.2, mRI, mRF, hack);
_ra2t(nten, 0.750, 60.0, mRI, mRF, hack);
_ra2t(nten, 0.875, 60.0, mRI, mRF, hack);
_ra2t(nten, 1.000, 60.0, mRI, mRF, hack);
*/
nten->axis[1].spacing = 1;
nten->axis[2].spacing = (sx-1)/(sqrt(3.0)*(sy-1));
nten->axis[3].spacing = 1;
} else {
for (yi=0; yi<samp; yi++) {
if (whole) {
ca = AIR_AFFINE(0, yi, samp-1, 0.0, 1.0);
} else {
ca = AIR_AFFINE(0, yi, samp-1, hack, maxca);
hackcp = AIR_AFFINE(0, yi, samp-1, hack, 0);
}
for (xi=0; xi<=yi; xi++) {
if (whole) {
cp = AIR_AFFINE(0, xi, samp-1, 0.0, 1.0);
} else {
cp = AIR_AFFINE(0, xi, samp-1, hackcp, maxca-hack/2.0);
}
_cap2xyz(xyz, ca, cp, version, whole);
/*
fprintf(stderr, "%s: (%d,%d) -> (%g,%g) -> %g %g %g\n", me,
yi, xi, ca, cp, xyz[0], xyz[1], xyz[2]);
*/
ELL_3M_IDENTITY_SET(mD);
ELL_3M_DIAG_SET(mD, xyz[0], xyz[1], xyz[2]);
ELL_3M_IDENTITY_SET(mT);
ell_3m_post_mul_d(mT, mRI);
ell_3m_post_mul_d(mT, mD);
ell_3m_post_mul_d(mT, mRF);
tdata = (float*)nten->data +
7*(2*(samp-1-xi) - (samp-1-yi) + (2*samp-1)*((samp-1-yi) + samp));
tdata[0] = 1.0;
TEN_M2T(tdata, mT);
}
}
nten->axis[1].spacing = 1;
nten->axis[2].spacing = 1.5;
nten->axis[3].spacing = 1;
}
if (nrrdSave(outS, nten, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
limnEnvMapFill(Nrrd *map, limnEnvMapCB cb, int qnMethod, void *data) {
char me[]="limnEnvMapFill", err[128];
int sx, sy;
int qn;
float vec[3], *mapData;
if (!(map && cb)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(LIMN, err); return 1;
}
if (!AIR_IN_OP(limnQNUnknown, qnMethod, limnQNLast)) {
sprintf(err, "%s: QN method %d invalid", me, qnMethod);
biffAdd(LIMN, err); return 1;
}
switch(qnMethod) {
case limnQN16checker:
case limnQN16octa:
sx = sy = 256;
break;
case limnQN14checker:
case limnQN14octa:
sx = sy = 128;
break;
case limnQN12checker:
case limnQN12octa:
sx = sy = 64;
break;
case limnQN10checker:
case limnQN10octa:
sx = sy = 32;
break;
case limnQN8checker:
case limnQN8octa:
sx = sy = 16;
break;
case limnQN15octa:
sx = 128;
sy = 256;
break;
case limnQN13octa:
sx = 64;
sy = 128;
break;
case limnQN11octa:
sx = 32;
sy = 64;
break;
case limnQN9octa:
sx = 16;
sy = 32;
break;
default:
sprintf(err, "%s: sorry, QN method %d not implemented", me, qnMethod);
biffAdd(LIMN, err); return 1;
}
if (nrrdMaybeAlloc_va(map, nrrdTypeFloat, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, sx),
AIR_CAST(size_t, sy))) {
sprintf(err, "%s: couldn't alloc output", me);
biffMove(LIMN, err, NRRD); return 1;
}
mapData = (float *)map->data;
for (qn=0; qn<sx*sy; qn++) {
limnQNtoV_f[qnMethod](vec, qn);
cb(mapData + 3*qn, vec, data);
}
return 0;
}
int
main(int argc, const char *argv[]) {
const char *me;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, *outS;
double sigmaMax, convEps, cutoff;
int measr[2], tentRecon;
unsigned int sampleNumMax, dim, measrSampleNum, maxIter, num, ii;
gageOptimSigParm *osparm;
double *scalePos, *out, info[512];
Nrrd *nout;
double *plotPos; unsigned int plotPosNum;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "num", "# samp", airTypeUInt, 1, 1, &sampleNumMax, NULL,
"maximum number of samples to optimize");
hestOptAdd(&hopt, "dim", "dimension", airTypeUInt, 1, 1, &dim, "3",
"dimension of image to work with");
hestOptAdd(&hopt, "max", "sigma", airTypeDouble, 1, 1, &sigmaMax, NULL,
"sigma to use for top sample (using 0 for bottom sample)");
hestOptAdd(&hopt, "cut", "cut", airTypeDouble, 1, 1, &cutoff, "4",
"at how many sigmas to cut-off discrete gaussian");
hestOptAdd(&hopt, "mi", "max", airTypeUInt, 1, 1, &maxIter, "1000",
"maximum # iterations");
hestOptAdd(&hopt, "N", "# samp", airTypeUInt, 1, 1, &measrSampleNum, "300",
"number of samples in the measurement of error across scales");
hestOptAdd(&hopt, "eps", "eps", airTypeDouble, 1, 1, &convEps, "0.0001",
"convergence threshold for optimization");
hestOptAdd(&hopt, "m", "m1 m2", airTypeEnum, 2, 2, measr, "l2 l2",
"how to measure error across image, and across scales",
NULL, nrrdMeasure);
hestOptAdd(&hopt, "p", "s0 s1", airTypeDouble, 2, -1, &plotPos, "nan nan",
"hack: dont do optimization; just plot the recon error given "
"these samples along scale", &plotPosNum);
hestOptAdd(&hopt, "tent", NULL, airTypeInt, 0, 0, &tentRecon, NULL,
"same hack: plot error with tent recon, not hermite");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL,
"output array");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, optsigInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, AIR_CAST(airMopper, nrrdNuke), airMopAlways);
osparm = gageOptimSigParmNew(sampleNumMax);
airMopAdd(mop, osparm, AIR_CAST(airMopper, gageOptimSigParmNix),
airMopAlways);
scalePos = AIR_CAST(double *, calloc(sampleNumMax, sizeof(double)));
airMopAdd(mop, scalePos, airFree, airMopAlways);
osparm->plotting = (AIR_EXISTS(plotPos[0]) && AIR_EXISTS(plotPos[1]));
if (gageOptimSigTruthSet(osparm, dim, sigmaMax, cutoff, measrSampleNum)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
if (osparm->plotting) {
if (gageOptimSigPlot(osparm, nout, plotPos, plotPosNum,
measr[0], tentRecon)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
} else {
/* do sample position optimization */
if (nrrdMaybeAlloc_va(nout, nrrdTypeDouble, 2,
AIR_CAST(size_t, sampleNumMax+1),
AIR_CAST(size_t, sampleNumMax+1))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating output:\n%s", me, err);
airMopError(mop); return 1;
}
out = AIR_CAST(double *, nout->data);
/* hacky way of saving some of the computation information */
info[0] = cutoff;
info[1] = measrSampleNum;
info[2] = measr[0];
info[3] = measr[1];
info[4] = convEps;
info[5] = maxIter;
for (ii=0; ii<sampleNumMax+1; ii++) {
out[ii] = info[ii];
}
for (num=2; num<=sampleNumMax; num++) {
printf("\n%s: ======= optimizing %u/%u samples (sigmaMax %g) \n\n",
me, num, sampleNumMax, sigmaMax);
if (gageOptimSigCalculate(osparm, scalePos, num,
measr[0], measr[1],
convEps, maxIter)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
out[sampleNumMax + (sampleNumMax+1)*num] = osparm->finalErr;
for (ii=0; ii<num; ii++) {
out[ii + (sampleNumMax+1)*num] = scalePos[ii];
}
}
}
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble saving output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
exit(0);
}
/*
******** tenFiberTraceSet
**
** slightly more flexible API for fiber tracking than tenFiberTrace
**
** EITHER: pass a non-NULL nfiber, and NULL, 0, NULL, NULL for
** the following arguments, and things are the same as with tenFiberTrace:
** data inside the nfiber is allocated, and the tract vertices are copied
** into it, having been stored in dynamically allocated airArrays
**
** OR: pass a NULL nfiber, and a buff allocated for 3*(2*halfBuffLen + 1)
** (note the "+ 1" !!!) doubles. The fiber tracking on each half will stop
** at halfBuffLen points. The given seedpoint will be stored in
** buff[0,1,2 + 3*halfBuffLen]. The indices for the end of the first
** tract half, and the end of the second tract half, will be set in
** *startIdxP and *endIdxP respectively.
*/
int
tenFiberTraceSet(tenFiberContext *tfx, Nrrd *nfiber,
double *buff, unsigned int halfBuffLen,
unsigned int *startIdxP, unsigned int *endIdxP,
double seed[3]) {
char me[]="tenFiberTraceSet", err[BIFF_STRLEN];
airArray *fptsArr[2]; /* airArrays of backward (0) and forward (1)
fiber points */
double *fpts[2]; /* arrays storing forward and backward
fiber points */
double
tmp[3],
iPos[3],
currPoint[3],
forwDir[3],
*fiber; /* array of both forward and backward points,
when finished */
int ret, whyStop, buffIdx, fptsIdx, outIdx, oldStop;
unsigned int i;
airArray *mop;
if (!(tfx)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(TEN, err); return 1;
}
/* HEY: a hack to preserve the state inside tenFiberContext so that
we have fewer side effects (tfx->maxNumSteps may still be set) */
oldStop = tfx->stop;
if (!nfiber) {
if (!( buff && halfBuffLen > 0 && startIdxP && startIdxP )) {
sprintf(err, "%s: need either non-NULL nfiber or fpts buffer info", me);
biffAdd(TEN, err); return 1;
}
if (tenFiberStopSet(tfx, tenFiberStopNumSteps, halfBuffLen)) {
sprintf(err, "%s: error setting new fiber stop", me);
biffAdd(TEN, err); return 1;
}
}
/* initialize the quantities which describe the fiber halves */
tfx->halfLen[0] = tfx->halfLen[1] = 0.0;
tfx->numSteps[0] = tfx->numSteps[1] = 0;
tfx->whyStop[0] = tfx->whyStop[1] = tenFiberStopUnknown;
/* try probing once */
if (tfx->useIndexSpace) {
ret = gageProbe(tfx->gtx,
AIR_CAST(gage_t, seed[0]),
AIR_CAST(gage_t, seed[1]),
AIR_CAST(gage_t, seed[2]));
} else {
gageShapeWtoI(tfx->gtx->shape, tmp, seed);
ret = gageProbe(tfx->gtx,
AIR_CAST(gage_t, tmp[0]),
AIR_CAST(gage_t, tmp[1]),
AIR_CAST(gage_t, tmp[2]));
}
if (ret) {
sprintf(err, "%s: first gageProbe failed: %s (%d)",
me, tfx->gtx->errStr, tfx->gtx->errNum);
biffAdd(TEN, err); return 1;
}
/* see if we're doomed */
if ((whyStop = _tenFiberStopCheck(tfx))) {
/* stopped immediately at seed point, but that's not an error */
tfx->whyNowhere = whyStop;
if (nfiber) {
nrrdEmpty(nfiber);
} else {
*startIdxP = *endIdxP = 0;
}
return 0;
} else {
/* did not immediately halt */
tfx->whyNowhere = tenFiberStopUnknown;
}
/* record the principal eigenvector at the seed point, which
is needed to align the 4 intermediate steps of RK4 for the
FIRST step of each half of the tract */
ELL_3V_COPY(tfx->firstEvec, tfx->evec + 3*0);
/* airMop{Error,Okay}() can safely be called on NULL */
mop = nfiber ? airMopNew() : NULL;
for (tfx->dir=0; tfx->dir<=1; tfx->dir++) {
if (nfiber) {
fptsArr[tfx->dir] = airArrayNew((void**)&(fpts[tfx->dir]), NULL,
3*sizeof(double), TEN_FIBER_INCR);
airMopAdd(mop, fptsArr[tfx->dir], (airMopper)airArrayNuke, airMopAlways);
buffIdx = -1;
} else {
fptsArr[tfx->dir] = NULL;
fpts[tfx->dir] = NULL;
buffIdx = halfBuffLen;
fptsIdx = -1;
}
tfx->halfLen[tfx->dir] = 0;
if (tfx->useIndexSpace) {
ELL_3V_COPY(iPos, seed);
gageShapeItoW(tfx->gtx->shape, tfx->wPos, iPos);
} else {
gageShapeWtoI(tfx->gtx->shape, iPos, seed);
ELL_3V_COPY(tfx->wPos, seed);
}
ELL_3V_SET(tfx->lastDir, 0, 0, 0);
tfx->lastDirSet = AIR_FALSE;
for (tfx->numSteps[tfx->dir] = 0; AIR_TRUE; tfx->numSteps[tfx->dir]++) {
if (_tenFiberProbe(tfx, tfx->wPos)) {
/* even if gageProbe had an error OTHER than going out of bounds,
we're not going to report it any differently here, alas */
tfx->whyStop[tfx->dir] = tenFiberStopBounds;
break;
}
if ((whyStop = _tenFiberStopCheck(tfx))) {
if (tenFiberStopNumSteps == whyStop) {
/* we stopped along this direction because tfx->numSteps[tfx->dir]
exceeded tfx->maxNumSteps. Okay. But tfx->numSteps[tfx->dir]
is supposed to be a record of how steps were (successfully)
taken. So we need to decrementing before moving on ... */
tfx->numSteps[tfx->dir]--;
}
tfx->whyStop[tfx->dir] = whyStop;
break;
}
if (tfx->useIndexSpace) {
gageShapeWtoI(tfx->gtx->shape, iPos, tfx->wPos);
ELL_3V_COPY(currPoint, iPos);
} else {
ELL_3V_COPY(currPoint, tfx->wPos);
}
if (nfiber) {
fptsIdx = airArrayLenIncr(fptsArr[tfx->dir], 1);
ELL_3V_COPY(fpts[tfx->dir] + 3*fptsIdx, currPoint);
} else {
ELL_3V_COPY(buff + 3*buffIdx, currPoint);
/*
fprintf(stderr, "!%s: (dir %d) saving to %d pnt %g %g %g\n", me,
tfx->dir, buffIdx,
currPoint[0], currPoint[1], currPoint[2]);
*/
buffIdx += !tfx->dir ? -1 : 1;
}
/* forwDir is set by this to point to the next fiber point */
if (_tenFiberIntegrate[tfx->intg](tfx, forwDir)) {
tfx->whyStop[tfx->dir] = tenFiberStopBounds;
break;
}
ELL_3V_COPY(tfx->lastDir, forwDir);
tfx->lastDirSet = AIR_TRUE;
ELL_3V_ADD2(tfx->wPos, tfx->wPos, forwDir);
tfx->halfLen[tfx->dir] += ELL_3V_LEN(forwDir);
}
}
if (nfiber) {
if (nrrdMaybeAlloc_va(nfiber, nrrdTypeDouble, 2,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, (fptsArr[0]->len
+ fptsArr[1]->len - 1)))) {
sprintf(err, "%s: couldn't allocate fiber nrrd", me);
biffMove(TEN, err, NRRD); airMopError(mop); return 1;
}
fiber = (double*)(nfiber->data);
outIdx = 0;
for (i=fptsArr[0]->len-1; i>=1; i--) {
ELL_3V_COPY(fiber + 3*outIdx, fpts[0] + 3*i);
outIdx++;
}
for (i=0; i<=fptsArr[1]->len-1; i++) {
ELL_3V_COPY(fiber + 3*outIdx, fpts[1] + 3*i);
outIdx++;
}
} else {
*startIdxP = halfBuffLen - tfx->numSteps[0];
*endIdxP = halfBuffLen + tfx->numSteps[1];
}
tfx->stop = oldStop;
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err;
Nrrd *nin, *nhist;
double vmin, vmax, rmax, val, cent[2], rad;
int bins[2], sx, sy, xi, yi, ridx, hidx, rbins, hbins;
NrrdRange *range;
double (*lup)(const void *v, size_t I), *hist;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input image", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "rbins hbins", airTypeInt, 2, 2, bins, NULL,
"# of histogram bins: radial and value");
hestOptAdd(&hopt, "min", "value", airTypeDouble, 1, 1, &vmin, "nan",
"Value at low end of histogram. Defaults to lowest value "
"found in input nrrd.");
hestOptAdd(&hopt, "max", "value", airTypeDouble, 1, 1, &vmax, "nan",
"Value at high end of histogram. Defaults to highest value "
"found in input nrrd.");
hestOptAdd(&hopt, "rmax", "max radius", airTypeDouble, 1, 1, &rmax, "nan",
"largest radius to include in histogram");
hestOptAdd(&hopt, "c", "center x, y", airTypeDouble, 2, 2, cent, NULL,
"The center point around which to build radial histogram");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write histogram to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, histradInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (2 != nin->dim) {
fprintf(stderr, "%s: need 2-D input (not %d-D)\n", me, nin->dim);
airMopError(mop); return 1;
}
rbins = bins[0];
hbins = bins[1];
nhist = nrrdNew();
airMopAdd(mop, nhist, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nhist, nrrdTypeDouble, 2,
AIR_CAST(size_t, rbins),
AIR_CAST(size_t, hbins))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate histogram:\n%s", me, err);
airMopError(mop); return 1;
}
if (!( AIR_EXISTS(vmin) && AIR_EXISTS(vmax) )) {
range = nrrdRangeNewSet(nin, nrrdStateBlind8BitRange);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
vmin = AIR_EXISTS(vmin) ? vmin : range->min;
vmax = AIR_EXISTS(vmax) ? vmax : range->max;
}
#define DIST(x0, y0, x1, y1) (sqrt((x0-x1)*(x0-x1) + (y0-y1)*(y0-y1)))
sx = nin->axis[0].size;
sy = nin->axis[1].size;
if (!AIR_EXISTS(rmax)) {
rmax = 0;
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], 0, 0));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], sx-1, 0));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], 0, sy-1));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], sx-1, sy-1));
}
lup = nrrdDLookup[nin->type];
hist = (double*)(nhist->data);
for (xi=0; xi<sx; xi++) {
for (yi=0; yi<sy; yi++) {
rad = DIST(cent[0], cent[1], xi, yi);
if (!AIR_IN_OP(0, rad, rmax)) {
continue;
}
val = lup(nin->data, xi + sx*yi);
if (!AIR_IN_OP(vmin, val, vmax)) {
continue;
}
ridx = airIndex(0, rad, rmax, rbins);
hidx = airIndex(vmin, val, vmax, hbins);
hist[ridx + rbins*hidx] += 1;
}
}
nhist->axis[0].min = 0;
nhist->axis[0].max = rmax;
nhist->axis[1].min = vmin;
nhist->axis[1].max = vmax;
if (nrrdSave(outS, nhist, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
tend_evecMain(int argc, char **argv, char *me, hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
int ret, *comp, compLen, cc;
Nrrd *nin, *nout;
char *outS;
float thresh, *edata, *tdata, eval[3], evec[9], scl;
size_t N, I, sx, sy, sz;
hestOptAdd(&hopt, "c", "c0 ", airTypeInt, 1, 3, &comp, NULL,
"which eigenvalues should be saved out. \"0\" for the "
"largest, \"1\" for the middle, \"2\" for the smallest, "
"\"0 1\", \"1 2\", \"0 1 2\" or similar for more than one",
&compLen);
hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5",
"confidence threshold");
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
"input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_evecInfoL);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
for (cc=0; cc<compLen; cc++) {
if (!AIR_IN_CL(0, comp[cc], 2)) {
fprintf(stderr, "%s: requested component %d (%d of 3) not in [0..2]\n",
me, comp[cc], cc+1);
airMopError(mop); return 1;
}
}
if (tenTensorCheck(nin, nrrdTypeFloat, AIR_TRUE, AIR_TRUE)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: didn't get a valid DT volume:\n%s\n", me, err);
airMopError(mop); return 1;
}
sx = nin->axis[1].size;
sy = nin->axis[2].size;
sz = nin->axis[3].size;
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
ret = nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 4,
AIR_CAST(size_t, 3*compLen), sx, sy, sz);
if (ret) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating output:\n%s\n", me, err);
airMopError(mop); return 1;
}
N = sx*sy*sz;
edata = (float *)nout->data;
tdata = (float *)nin->data;
if (1 == compLen) {
for (I=0; I<N; I++) {
tenEigensolve_f(eval, evec, tdata);
scl = AIR_CAST(float, tdata[0] >= thresh);
ELL_3V_SCALE(edata, scl, evec+3*comp[0]);
edata += 3;
tdata += 7;
}
} else {
for (I=0; I<N; I++) {
/*
******** nrrdHisto()
**
** makes a 1D histogram of a given size and type
**
** pre-NrrdRange policy:
** this looks at nin->min and nin->max to see if they are both non-NaN.
** If so, it uses these as the range of the histogram, otherwise it
** finds the min and max present in the volume. If nin->min and nin->max
** are being used as the histogram range, then values which fall outside
** this are ignored (they don't contribute to the histogram).
**
** post-NrrdRange policy:
*/
int
nrrdHisto(Nrrd *nout, const Nrrd *nin, const NrrdRange *_range,
const Nrrd *nwght, size_t bins, int type) {
static const char me[]="nrrdHisto", func[]="histo";
size_t I, num, idx;
airArray *mop;
NrrdRange *range;
double min, max, eps, val, count, incr, (*lup)(const void *v, size_t I);
if (!(nin && nout)) {
/* _range and nwght can be NULL */
biffAddf(NRRD, "%s: got NULL pointer", me);
return 1;
}
if (nout == nin) {
biffAddf(NRRD, "%s: nout==nin disallowed", me);
return 1;
}
if (!(bins > 0)) {
biffAddf(NRRD, "%s: bins value (" _AIR_SIZE_T_CNV ") invalid", me, bins);
return 1;
}
if (airEnumValCheck(nrrdType, type) || nrrdTypeBlock == type) {
biffAddf(NRRD, "%s: invalid nrrd type %d", me, type);
return 1;
}
if (nwght) {
if (nout==nwght) {
biffAddf(NRRD, "%s: nout==nwght disallowed", me);
return 1;
}
if (nrrdTypeBlock == nwght->type) {
biffAddf(NRRD, "%s: nwght type %s invalid", me,
airEnumStr(nrrdType, nrrdTypeBlock));
return 1;
}
if (!nrrdSameSize(nin, nwght, AIR_TRUE)) {
biffAddf(NRRD, "%s: nwght size mismatch with nin", me);
return 1;
}
lup = nrrdDLookup[nwght->type];
} else {
lup = NULL;
}
if (nrrdMaybeAlloc_va(nout, type, 1, bins)) {
biffAddf(NRRD, "%s: failed to alloc histo array (len " _AIR_SIZE_T_CNV
")", me, bins);
return 1;
}
mop = airMopNew();
/* nout->axis[0].size set */
nout->axis[0].spacing = AIR_NAN;
nout->axis[0].thickness = AIR_NAN;
if (nout && AIR_EXISTS(nout->axis[0].min) && AIR_EXISTS(nout->axis[0].max)) {
/* HEY: total hack to externally nail down min and max of histogram:
use the min and max already set on axis[0] */
/* HEY: shouldn't this blatent hack be further restricted by also
checking the existence of range->min and range->max ? */
min = nout->axis[0].min;
max = nout->axis[0].max;
} else {
if (_range) {
range = nrrdRangeCopy(_range);
nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
} else {
range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
}
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
min = range->min;
max = range->max;
nout->axis[0].min = min;
nout->axis[0].max = max;
}
eps = (min == max ? 1.0 : 0.0);
nout->axis[0].center = nrrdCenterCell;
/* nout->axis[0].label set below */
/* make histogram */
num = nrrdElementNumber(nin);
for (I=0; I<num; I++) {
val = nrrdDLookup[nin->type](nin->data, I);
if (AIR_EXISTS(val)) {
if (val < min || val > max+eps) {
/* value is outside range; ignore it */
continue;
}
if (AIR_IN_CL(min, val, max)) {
idx = airIndex(min, val, max+eps, AIR_CAST(unsigned int, bins));
/*
printf("!%s: %d: index(%g, %g, %g, %d) = %d\n",
me, (int)I, min, val, max, bins, idx);
*/
/* count is a double in order to simplify clamping the
hit values to the representable range for nout->type */
count = nrrdDLookup[nout->type](nout->data, idx);
incr = nwght ? lup(nwght->data, I) : 1;
count = nrrdDClamp[nout->type](count + incr);
nrrdDInsert[nout->type](nout->data, idx, count);
}
}
}
if (nrrdContentSet_va(nout, func, nin, "%d", bins)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
nout->axis[0].label = (char *)airFree(nout->axis[0].label);
nout->axis[0].label = (char *)airStrdup(nout->content);
if (!nrrdStateKindNoop) {
nout->axis[0].kind = nrrdKindDomain;
}
airMopOkay(mop);
return 0;
}
int
main(int argc, const char **argv) {
const char *me;
Nrrd *nscl;
double *dscl;
airArray *mop;
char *fullname;
gageContext *igctx[INTERP_KERN_NUM], *bgctx[BLUR_KERN_NUM];
const NrrdKernel *ikern[INTERP_KERN_NUM] = {
nrrdKernelBox,
nrrdKernelTent,
nrrdKernelBCCubic,
nrrdKernelCatmullRom,
};
double ikparm[INTERP_KERN_NUM][NRRD_KERNEL_PARMS_NUM] = {
{1.0},
{1.0},
{1.0, 0.0, 0.5},
{AIR_NAN},
};
const NrrdKernel *bkern[BLUR_KERN_NUM] = {
nrrdKernelTent,
nrrdKernelBSpline3,
nrrdKernelBSpline5,
nrrdKernelBCCubic,
nrrdKernelGaussian,
};
const NrrdKernel *bkernD[BLUR_KERN_NUM] = {
nrrdKernelForwDiff,
nrrdKernelBSpline3D,
nrrdKernelBSpline5D,
nrrdKernelBCCubicD,
nrrdKernelGaussianD,
};
const NrrdKernel *bkernDD[BLUR_KERN_NUM] = {
nrrdKernelZero,
nrrdKernelBSpline3DD,
nrrdKernelBSpline5DD,
nrrdKernelBCCubicDD,
nrrdKernelGaussianDD,
};
double bkparm[BLUR_KERN_NUM][NRRD_KERNEL_PARMS_NUM] = {
{1.0},
{AIR_NAN},
{AIR_NAN},
{2.0, 1.0, 0.0},
{1.2, 5.0},
};
const double *ivalAns[INTERP_KERN_NUM], *bvalAns[BLUR_KERN_NUM],
*bgrdAns[BLUR_KERN_NUM], *bhesAns[BLUR_KERN_NUM];
int E;
unsigned int sx, sy, sz, ki;
AIR_UNUSED(argc);
me = argv[0];
mop = airMopNew();
nscl = nrrdNew();
airMopAdd(mop, nscl, (airMopper)nrrdNuke, airMopAlways);
fullname = testDataPathPrefix("fmob-c4h.nrrd");
airMopAdd(mop, fullname, airFree, airMopAlways);
if (nrrdLoad(nscl, fullname, NULL)) {
char *err;
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble reading data \"%s\":\n%s",
me, fullname, err);
airMopError(mop); return 1;
}
/* make sure its a double-type volume (assumed below) */
if (nrrdTypeDouble != nscl->type) {
fprintf(stderr, "%s: volume type %s != expected type %s\n", me,
airEnumStr(nrrdType, nscl->type),
airEnumStr(nrrdType, nrrdTypeDouble));
airMopError(mop); return 1;
}
dscl = AIR_CAST(double *, nscl->data);
sx = AIR_CAST(unsigned int, nscl->axis[0].size);
sy = AIR_CAST(unsigned int, nscl->axis[1].size);
sz = AIR_CAST(unsigned int, nscl->axis[2].size);
for (ki=0; ki<INTERP_KERN_NUM; ki++) {
gagePerVolume *gpvl;
igctx[ki] = gageContextNew();
airMopAdd(mop, igctx[ki], (airMopper)gageContextNix, airMopAlways);
gageParmSet(igctx[ki], gageParmRenormalize, AIR_FALSE);
gageParmSet(igctx[ki], gageParmCheckIntegrals, AIR_TRUE);
gageParmSet(igctx[ki], gageParmOrientationFromSpacing, AIR_FALSE);
E = 0;
if (!E) E |= !(gpvl = gagePerVolumeNew(igctx[ki], nscl, gageKindScl));
if (!E) E |= gageKernelSet(igctx[ki], gageKernel00,
ikern[ki], ikparm[ki]);
if (!E) E |= gagePerVolumeAttach(igctx[ki], gpvl);
if (!E) E |= gageQueryItemOn(igctx[ki], gpvl, gageSclValue);
if (!E) E |= gageUpdate(igctx[ki]);
if (E) {
char *err;
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble %s set-up:\n%s\n", me,
ikern[ki]->name, err);
airMopError(mop); return 1;
}
ivalAns[ki] = gageAnswerPointer(igctx[ki], gpvl, gageSclValue);
}
/* traverse all samples of volume, probing with the interpolating
kernels, make sure we recover the original values */
{
unsigned int xi, yi, zi;
double pval[INTERP_KERN_NUM], err, rval;
int pret;
for (zi=0; zi<sz; zi++) {
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
rval = dscl[xi + sx*(yi + sy*zi)];
for (ki=0; ki<INTERP_KERN_NUM; ki++) {
pret = gageProbeSpace(igctx[ki], xi, yi, zi,
AIR_TRUE /* indexSpace */,
AIR_FALSE /* clamp */);
if (pret) {
fprintf(stderr, "%s: %s probe error(%d): %s\n", me,
ikern[ki]->name, igctx[ki]->errNum, igctx[ki]->errStr);
airMopError(mop); return 1;
}
pval[ki] = *ivalAns[ki];
err = AIR_ABS(rval - pval[ki]);
if (err) {
fprintf(stderr, "%s: interp's [%u,%u,%u] %s probe %f "
"!= true %f (err %f)\n", me, xi, yi, zi,
ikern[ki]->name, pval[ki], rval, err);
airMopError(mop); return 1;
}
}
}
}
}
}
/* set up contexts for non-interpolating (blurring) kernels,
and their first and second derivatives */
for (ki=0; ki<BLUR_KERN_NUM; ki++) {
gagePerVolume *gpvl;
bgctx[ki] = gageContextNew();
airMopAdd(mop, bgctx[ki], (airMopper)gageContextNix, airMopAlways);
gageParmSet(bgctx[ki], gageParmRenormalize, AIR_TRUE);
gageParmSet(bgctx[ki], gageParmCheckIntegrals, AIR_TRUE);
gageParmSet(bgctx[ki], gageParmOrientationFromSpacing, AIR_FALSE);
E = 0;
if (!E) E |= !(gpvl = gagePerVolumeNew(bgctx[ki], nscl, gageKindScl));
if (!E) E |= gageKernelSet(bgctx[ki], gageKernel00,
bkern[ki], bkparm[ki]);
if (!E) E |= gageKernelSet(bgctx[ki], gageKernel11,
bkernD[ki], bkparm[ki]);
if (!E) E |= gageKernelSet(bgctx[ki], gageKernel22,
bkernDD[ki], bkparm[ki]);
if (!E) E |= gagePerVolumeAttach(bgctx[ki], gpvl);
if (!E) E |= gageQueryItemOn(bgctx[ki], gpvl, gageSclValue);
if (!E) E |= gageQueryItemOn(bgctx[ki], gpvl, gageSclGradVec);
if (!E) E |= gageQueryItemOn(bgctx[ki], gpvl, gageSclHessian);
if (!E) E |= gageUpdate(bgctx[ki]);
if (E) {
char *err;
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble %s set-up:\n%s\n", me,
bkern[ki]->name, err);
airMopError(mop); return 1;
}
fprintf(stderr, "%s radius = %u\n", bkern[ki]->name, bgctx[ki]->radius);
bvalAns[ki] = gageAnswerPointer(bgctx[ki], gpvl, gageSclValue);
bgrdAns[ki] = gageAnswerPointer(bgctx[ki], gpvl, gageSclGradVec);
bhesAns[ki] = gageAnswerPointer(bgctx[ki], gpvl, gageSclHessian);
}
{
#define POS_NUM 12
double xp[POS_NUM], yp[POS_NUM], zp[POS_NUM],
pos[POS_NUM*POS_NUM*POS_NUM][3], *prbd,
offs[POS_NUM/2] = {0, 1.22222, 2.444444, 3.777777, 5.88888, 7.55555};
Nrrd *nprbd, *ncorr;
unsigned int ii, jj, kk, qlen = 1 + 3 + 9;
char *corrfn, explain[AIR_STRLEN_LARGE];
int pret, differ;
corrfn = testDataPathPrefix("test/probeSclAns.nrrd");
airMopAdd(mop, corrfn, airFree, airMopAlways);
ncorr = nrrdNew();
airMopAdd(mop, ncorr, (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(ncorr, corrfn, NULL)) {
char *err;
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble reading data \"%s\":\n%s",
me, corrfn, err);
airMopError(mop); return 1;
}
for (ii=0; ii<POS_NUM/2; ii++) {
xp[ii] = yp[ii] = zp[ii] = offs[ii];
xp[POS_NUM-1-ii] = AIR_CAST(double, sx)-1.0-offs[ii];
yp[POS_NUM-1-ii] = AIR_CAST(double, sy)-1.0-offs[ii];
zp[POS_NUM-1-ii] = AIR_CAST(double, sz)-1.0-offs[ii];
}
for (kk=0; kk<POS_NUM; kk++) {
for (jj=0; jj<POS_NUM; jj++) {
for (ii=0; ii<POS_NUM; ii++) {
ELL_3V_SET(pos[ii + POS_NUM*(jj + POS_NUM*kk)],
xp[ii], yp[jj], zp[kk]);
}
}
}
nprbd = nrrdNew();
airMopAdd(mop, nprbd, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nprbd, nrrdTypeDouble, 3,
AIR_CAST(size_t, qlen),
AIR_CAST(size_t, BLUR_KERN_NUM),
AIR_CAST(size_t, POS_NUM*POS_NUM*POS_NUM))) {
char *err;
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble setting up prbd:\n%s", me, err);
airMopError(mop); return 1;
}
prbd = AIR_CAST(double *, nprbd->data);
for (ii=0; ii<POS_NUM*POS_NUM*POS_NUM; ii++) {
for (ki=0; ki<BLUR_KERN_NUM; ki++) {
pret = gageProbeSpace(bgctx[ki], pos[ii][0], pos[ii][1], pos[ii][2],
AIR_TRUE /* indexSpace */,
AIR_FALSE /* clamp */);
if (pret) {
fprintf(stderr, "%s: %s probe error(%d): %s\n", me,
bkern[ki]->name, bgctx[ki]->errNum, bgctx[ki]->errStr);
airMopError(mop); return 1;
}
prbd[0 + qlen*(ki + BLUR_KERN_NUM*(ii))] = bvalAns[ki][0];
ELL_3V_COPY(prbd + 1 + qlen*(ki + BLUR_KERN_NUM*(ii)), bgrdAns[ki]);
ELL_9V_COPY(prbd + 4 + qlen*(ki + BLUR_KERN_NUM*(ii)), bhesAns[ki]);
}
}
/* HEY: weirdly, so far its only on Windows (and more than 10 times worse
on Cygwin) this epsilon needs to be larger than zero, and only for the
radius 6 Gaussian? */
if (nrrdCompare(ncorr, nprbd, AIR_FALSE /* onlyData */,
8.0e-14 /* epsilon */, &differ, explain)) {
char *err;
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble comparing:\n%s", me, err);
airMopError(mop); return 1;
}
if (differ) {
fprintf(stderr, "%s: probed values not correct: %s\n", me, explain);
airMopError(mop); return 1;
} else {
fprintf(stderr, "all good\n");
}
}
airMopOkay(mop);
return 0;
}
int
baneGkms_txfMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *perr, err[BIFF_STRLEN];
Nrrd *nout;
airArray *mop;
int pret, E, res[2], vi, gi, step;
float min[2], max[2], top[2], v0, g0, *data, v, g,
gwidth, width, mwidth,
tvl, tvr, vl, vr, tmp, maxa;
hestOptAdd(&opt, "r", "Vres Gres", airTypeInt, 2, 2, res, "256 256",
"resolution of the transfer function in value and gradient "
"magnitude");
hestOptAdd(&opt, "min", "Vmin Gmin", airTypeFloat, 2, 2, min, "0.0 0.0",
"minimum value and grad mag in txf");
hestOptAdd(&opt, "max", "Vmax Gmax", airTypeFloat, 2, 2, max, NULL,
"maximum value and grad mag in txf");
hestOptAdd(&opt, "v", "base value", airTypeFloat, 1, 1, &v0, NULL,
"data value at which to position bottom of triangle");
hestOptAdd(&opt, "g", "gthresh", airTypeFloat, 1, 1, &g0, "0.0",
"lowest grad mag to receive opacity");
hestOptAdd(&opt, "gw", "gwidth", airTypeFloat, 1, 1, &gwidth, "0.0",
"range of grad mag values over which to apply threshold "
"at low gradient magnitudes");
hestOptAdd(&opt, "top", "Vtop Gtop", airTypeFloat, 2, 2, top, NULL,
"data value and grad mag at center of top of triangle");
hestOptAdd(&opt, "w", "value width", airTypeFloat, 1, 1, &width, NULL,
"range of values to be spanned at top of triangle");
hestOptAdd(&opt, "mw", "value width", airTypeFloat, 1, 1, &mwidth, "0",
"range of values to be spanned at BOTTOM of triangle");
hestOptAdd(&opt, "step", NULL, airTypeInt, 0, 0, &step, NULL,
"instead of assigning opacity inside a triangular region, "
"make it more like a step function, in which opacity never "
"decreases in increasing data value");
hestOptAdd(&opt, "a", "max opac", airTypeFloat, 1, 1, &maxa, "1.0",
"highest opacity to assign");
hestOptAdd(&opt, "o", "opacOut", airTypeString, 1, 1, &out, NULL,
"output opacity function filename");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_baneGkms_txfInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
E = 0;
if (!E) E |= nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 3,
AIR_CAST(size_t, 1),
AIR_CAST(size_t, res[0]),
AIR_CAST(size_t, res[1]));
if (!E) E |= !(nout->axis[0].label = airStrdup("A"));
if (!E) E |= !(nout->axis[1].label = airStrdup("gage(scalar:v)"));
if (!E) nrrdAxisInfoSet_va(nout, nrrdAxisInfoMin,
AIR_NAN, (double)min[0], (double)min[1]);
if (!E) nrrdAxisInfoSet_va(nout, nrrdAxisInfoMax,
AIR_NAN, (double)max[0], (double)max[1]);
if (!E) E |= !(nout->axis[2].label = airStrdup("gage(scalar:gm)"));
if (E) {
sprintf(err, "%s: trouble creating opacity function nrrd", me);
biffMove(BANE, err, NRRD); airMopError(mop); return 1;
}
data = (float *)nout->data;
tvl = top[0] - width/2;
tvr = top[0] + width/2;
mwidth /= 2;
for (gi=0; gi<res[1]; gi++) {
g = AIR_CAST(float, NRRD_CELL_POS(min[1], max[1], res[1], gi));
for (vi=0; vi<res[0]; vi++) {
v = AIR_CAST(float, NRRD_CELL_POS(min[0], max[0], res[0], vi));
vl = AIR_CAST(float, AIR_AFFINE(0, g, top[1], v0-mwidth, tvl));
vr = AIR_CAST(float, AIR_AFFINE(0, g, top[1], v0+mwidth, tvr));
if (g > top[1]) {
data[vi + res[0]*gi] = 0;
continue;
}
tmp = AIR_CAST(float, (v - vl)/(0.00001 + vr - vl));
tmp = 1 - AIR_ABS(2*tmp - 1);
if (step && v > (vr + vl)/2) {
tmp = 1;
}
tmp = AIR_MAX(0, tmp);
data[vi + res[0]*gi] = tmp*maxa;
tmp = AIR_CAST(float, AIR_AFFINE(g0 - gwidth/2, g, g0 + gwidth/2,
0.0, 1.0));
tmp = AIR_CLAMP(0, tmp, 1);
data[vi + res[0]*gi] *= tmp;
}
}
if (nrrdSave(out, nout, NULL)) {
sprintf(err, "%s: trouble saving opacity function", me);
biffMove(BANE, err, NRRD); airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
miteRenderBegin(miteRender **mrrP, miteUser *muu) {
static const char me[]="miteRenderBegin";
gagePerVolume *pvl;
int E, T, pvlIdx;
gageQuery queryScl, queryVec, queryTen;
gageItemSpec isp;
unsigned int axi, thr;
if (!(mrrP && muu)) {
biffAddf(MITE, "%s: got NULL pointer", me);
return 1;
}
if (_miteUserCheck(muu)) {
biffAddf(MITE, "%s: problem with user-set parameters", me);
return 1;
}
if (!( *mrrP = _miteRenderNew() )) {
biffAddf(MITE, "%s: couldn't alloc miteRender", me);
return 1;
}
if (_miteNtxfAlphaAdjust(*mrrP, muu)) {
biffAddf(MITE, "%s: trouble copying and alpha-adjusting txfs", me);
return 1;
}
GAGE_QUERY_RESET(queryScl);
GAGE_QUERY_RESET(queryVec);
GAGE_QUERY_RESET(queryTen);
GAGE_QUERY_RESET((*mrrP)->queryMite);
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, (*mrrP)->queryMite, &isp);
}
}
miteVariableParse((*mrrP)->normalSpec, muu->normalStr);
miteQueryAdd(queryScl, queryVec, queryTen, (*mrrP)->queryMite,
(*mrrP)->normalSpec);
miteShadeSpecParse((*mrrP)->shadeSpec, muu->shadeStr);
miteShadeSpecQueryAdd(queryScl, queryVec, queryTen, (*mrrP)->queryMite,
(*mrrP)->shadeSpec);
(*mrrP)->queryMiteNonzero = GAGE_QUERY_NONZERO((*mrrP)->queryMite);
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,
muu->ksp[gageKernel00]->parm);
if (!E) E |= gageKernelSet(muu->gctx0, gageKernel11,
muu->ksp[gageKernel11]->kernel,
muu->ksp[gageKernel11]->parm);
if (!E) E |= gageKernelSet(muu->gctx0, gageKernel22,
muu->ksp[gageKernel22]->kernel,
muu->ksp[gageKernel22]->parm);
if (!E) E |= gageUpdate(muu->gctx0);
if (E) {
biffMovef(MITE, GAGE, "%s: gage trouble", me);
return 1;
}
fprintf(stderr, "!%s: kernel support = %d^3 samples\n",
me, 2*muu->gctx0->radius);
if (nrrdMaybeAlloc_va(muu->nout, mite_nt, 3,
AIR_CAST(size_t, 5) /* RGBAZ */ ,
AIR_CAST(size_t, muu->hctx->imgSize[0]),
AIR_CAST(size_t, muu->hctx->imgSize[1]))) {
biffMovef(MITE, NRRD, "%s: nrrd trouble", me);
return 1;
}
muu->nout->axis[1].center = nrrdCenterCell;
muu->nout->axis[1].min = muu->hctx->cam->uRange[0];
muu->nout->axis[1].max = muu->hctx->cam->uRange[1];
muu->nout->axis[2].center = nrrdCenterCell;
muu->nout->axis[2].min = muu->hctx->cam->vRange[0];
muu->nout->axis[2].max = muu->hctx->cam->vRange[1];
for (thr=0; thr<muu->hctx->numThreads; thr++) {
(*mrrP)->tt[thr] = miteThreadNew();
if (!((*mrrP)->tt[thr])) {
biffAddf(MITE, "%s: couldn't allocate thread[%d]", me, thr);
return 1;
}
airMopAdd((*mrrP)->rmop, (*mrrP)->tt[thr],
(airMopper)miteThreadNix, airMopAlways);
}
(*mrrP)->time0 = airTime();
return 0;
}
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;
}
int
unrrdu_acropMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
int pret;
airArray *mop;
size_t min[NRRD_DIM_MAX], max[NRRD_DIM_MAX];
unsigned int *axes, axesLen;
double frac;
int measr, offset;
Nrrd *nbounds;
char *boundsSave;
hestOptAdd(&opt, "a,axes", "ax0", airTypeUInt, 0, -1, &axes, "",
"the axes (if any) that should NOT be cropped", &axesLen);
hestOptAdd(&opt, "m,measure", "measr", airTypeEnum, 1, 1, &measr, NULL,
"How to measure slices (along axes to crop) as scalars, "
"to form 1-D array analyzed to determine cropping extent. "
"All the measures from \"unu project\" can be used, but "
"those that make more sense here include:\n "
"\b\bo \"max\", \"mean\", \"median\", "
"\"variance\": (self-explanatory)\n "
"\b\bo \"stdv\": standard deviation\n "
"\b\bo \"cov\": coefficient of variation\n "
"\b\bo \"product\", \"sum\": product or sum of all values\n "
"\b\bo \"L1\", \"L2\", \"NL2\", \"RMS\", \"Linf\": "
"different norms.", NULL, nrrdMeasure);
hestOptAdd(&opt, "f,frac", "frac", airTypeDouble, 1, 1, &frac, "0.1",
"threshold of cumulative sum of 1-D array at which to crop. "
"Needs to be in interval [0.0,0.5).");
hestOptAdd(&opt, "off,offset", "offset", airTypeInt, 1, 1, &offset, "1",
"how much to offset the numerically determined cropping; "
"positive offsets means expanding the interval of kept "
"indices (less cropping)");
hestOptAdd(&opt, "b,bounds", "filename", airTypeString, 1, 1,
&boundsSave, "",
"if a filename is given here, the automatically determined "
"min and max bounds for cropping are saved to this file "
"as a 2-D array; first scanline is for -min, second is for -max. "
"Unfortunately nothing using the \"m\" and \"M\" semantics "
"(above) can currently be saved in the bounds file.");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_acropInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCropAuto(nout, nin, min, max,
axes, axesLen,
measr, frac, offset)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error cropping nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
if (airStrlen(boundsSave)) {
unsigned int axi;
airULLong *bounds;
nbounds = nrrdNew();
airMopAdd(mop, nbounds, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nbounds, nrrdTypeULLong, 2,
AIR_CAST(airULLong, nin->dim),
AIR_CAST(airULLong, 2))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error allocating cropping bounds array:\n%s",
me, err);
airMopError(mop);
return 1;
}
bounds = AIR_CAST(airULLong*, nbounds->data);
for (axi=0; axi<nin->dim; axi++) {
bounds[axi + 0*(nin->dim)] = AIR_CAST(airULLong, min[axi]);
bounds[axi + 1*(nin->dim)] = AIR_CAST(airULLong, max[axi]);
}
if (nrrdSave(boundsSave, nbounds, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error saving cropping bounds array:\n%s",
me, err);
airMopError(mop);
return 1;
}
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
hestOpt *hopt=NULL;
hestParm *hparm;
Nrrd *nlight, *nmap, *ndebug;
const char *me;
char *outS, *errS, *debugS;
airArray *mop;
float amb[3], *linfo, *debug, *map, vscl;
unsigned li, ui, vi;
int qn, bits, method, doerr;
limnLight *light;
limnCamera *cam;
double u, v, r, w, V2W[9], diff, WW[3], VV[3];
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
cam = limnCameraNew();
airMopAdd(mop, cam, (airMopper)limnCameraNix, airMopAlways);
hestOptAdd(&hopt, "i", "nlight", airTypeOther, 1, 1, &nlight, NULL,
"input nrrd containing light information",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "# bits", airTypeInt, 1, 1, &bits, "16",
"number of bits to use for normal quantization, "
"between 8 and 16 inclusive. ");
hestOptAdd(&hopt, "amb", "ambient RGB", airTypeFloat, 3, 3, amb, "0 0 0",
"ambient light color");
hestOptAdd(&hopt, "fr", "from point", airTypeDouble, 3, 3, cam->from,"1 0 0",
"position of camera, used to determine view vector");
hestOptAdd(&hopt, "at", "at point", airTypeDouble, 3, 3, cam->at, "0 0 0",
"camera look-at point, used to determine view vector");
hestOptAdd(&hopt, "up", "up vector", airTypeDouble, 3, 3, cam->up, "0 0 1",
"camera pseudo-up vector, used to determine view coordinates");
hestOptAdd(&hopt, "rh", NULL, airTypeInt, 0, 0, &(cam->rightHanded), NULL,
"use a right-handed UVN frame (V points down)");
hestOptAdd(&hopt, "vs", "view-dir scaling", airTypeFloat, 1, 1, &vscl, "1",
"scaling along view-direction of location of "
"view-space lights");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, NULL,
"file to write output envmap to");
hestOptAdd(&hopt, "d", "filename", airTypeString, 1, 1, &debugS, "",
"Use this option to save out (to the given filename) a rendering "
"of the front (on the left) and back (on the right) of a sphere "
"as shaded with the new environment map. U increases "
"right-ward, V increases downward. The back sphere half is "
"rendered as though the front half was removed");
hestOptAdd(&hopt, "err", NULL, airTypeInt, 0, 0, &doerr, NULL,
"If using \"-d\", make the image represent the error between the "
"real and quantized vector");
hestParseOrDie(hopt, argc-1, argv+1, hparm, me, emapInfo,
AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
switch(bits) {
case 16:
method = limnQN16octa;
break;
case 15:
method = limnQN15octa;
break;
case 14:
method = limnQN14octa;
break;
case 13:
method = limnQN13octa;
break;
case 12:
method = limnQN12octa;
break;
case 11:
method = limnQN11octa;
break;
case 10:
method = limnQN10octa;
break;
case 9:
method = limnQN9octa;
break;
case 8:
method = limnQN8octa;
break;
default:
fprintf(stderr, "%s: requested #bits (%d) not in valid range [8,16]\n",
me, bits);
airMopError(mop);
return 1;
}
if (!(nrrdTypeFloat == nlight->type &&
2 == nlight->dim &&
7 == nlight->axis[0].size &&
LIMN_LIGHT_NUM >= nlight->axis[1].size)) {
fprintf(stderr, "%s: nlight isn't valid format for light specification, "
"must be: float type, 2-dimensional, 7\tx\tN size, N <= %d\n",
me, LIMN_LIGHT_NUM);
airMopError(mop);
return 1;
}
cam->neer = -0.000000001;
cam->dist = 0;
cam->faar = 0.0000000001;
cam->atRelative = AIR_TRUE;
if (limnCameraUpdate(cam)) {
airMopAdd(mop, errS = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: problem with camera:\n%s\n", me, errS);
airMopError(mop);
return 1;
}
light = limnLightNew();
airMopAdd(mop, light, (airMopper)limnLightNix, airMopAlways);
limnLightAmbientSet(light, amb[0], amb[1], amb[2]);
for (li=0; li<nlight->axis[1].size; li++) {
int vsp;
float lxyz[3];
linfo = (float *)(nlight->data) + 7*li;
vsp = !!linfo[0];
ELL_3V_COPY(lxyz, linfo + 4);
if (vsp) {
lxyz[2] *= vscl;
}
limnLightSet(light, li, vsp,
linfo[1], linfo[2], linfo[3], lxyz[0], lxyz[1], lxyz[2]);
}
if (limnLightUpdate(light, cam)) {
airMopAdd(mop, errS = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: problem with lights:\n%s\n", me, errS);
airMopError(mop);
return 1;
}
nmap=nrrdNew();
airMopAdd(mop, nmap, (airMopper)nrrdNuke, airMopAlways);
if (limnEnvMapFill(nmap, limnLightDiffuseCB, method, light)) {
airMopAdd(mop, errS = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: problem making environment map:\n%s\n", me, errS);
airMopError(mop);
return 1;
}
map = (float *)nmap->data;
if (nrrdSave(outS, nmap, NULL)) {
fprintf(stderr, "%s: trouble:\n%s", me, errS = biffGetDone(NRRD));
free(errS);
return 1;
}
if (airStrlen(debugS)) {
ELL_34M_EXTRACT(V2W, cam->V2W);
ndebug = nrrdNew();
nrrdMaybeAlloc_va(ndebug, nrrdTypeFloat, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, 1024),
AIR_CAST(size_t, 512));
airMopAdd(mop, ndebug, (airMopper)nrrdNuke, airMopAlways);
debug = (float *)ndebug->data;
for (vi=0; vi<=511; vi++) {
v = AIR_AFFINE(0, vi, 511, -0.999, 0.999);
for (ui=0; ui<=511; ui++) {
u = AIR_AFFINE(0, ui, 511, -0.999, 0.999);
r = sqrt(u*u + v*v);
if (r > 1) {
continue;
}
w = sqrt(1 - r*r);
/* first, the near side of the sphere */
ELL_3V_SET(VV, u, v, -w);
ELL_3MV_MUL(WW, V2W, VV);
qn = limnVtoQN_d[method](WW);
if (doerr) {
limnQNtoV_d[method](VV, qn);
ELL_3V_SUB(WW, WW, VV);
diff = ELL_3V_LEN(WW);
ELL_3V_SET_TT(debug + 3*(ui + 1024*vi), float,
diff, diff, diff);
} else {
ELL_3V_COPY(debug + 3*(ui + 1024*vi), map + 3*qn);
}
/* second, the far side of the sphere */
ELL_3V_SET(VV, u, v, w);
ELL_3MV_MUL(WW, V2W, VV);
qn = limnVtoQN_d[method](WW);
if (doerr) {
limnQNtoV_d[method](VV, qn);
ELL_3V_SUB(WW, WW, VV);
diff = ELL_3V_LEN(WW);
ELL_3V_SET_TT(debug + 3*(ui + 512 + 1024*vi), float,
diff, diff, diff);
} else {
ELL_3V_COPY(debug + 3*(ui + 512 + 1024*vi), map + 3*qn);
}
}
}
int
doit(Nrrd *nout, Nrrd *nin, int smart, float amount) {
char me[]="doit", err[BIFF_STRLEN];
Nrrd *nproj[3];
airArray *mop;
int axis, srl, sap, ssi, E, margin, which;
size_t min[3];
if (!(nout && nin)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(NINSPECT, err);
return 1;
}
if (!(3 == nin->dim)) {
sprintf(err, "%s: given nrrd has dimension %d, not 3\n", me, nin->dim);
biffAdd(NINSPECT, err);
return 1;
}
mop = airMopNew();
airMopAdd(mop, nproj[0]=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nproj[1]=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nproj[2]=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
/* how much space to put between and around the projections */
margin = 6;
/* do projections for each axis, with some progress indication to sterr */
for (axis=0; axis<=2; axis++) {
fprintf(stderr, "%s: doing axis %d projections ... ", me, axis);
fflush(stderr);
if (ninspect_proj(nproj[axis], nin, axis, smart, amount)) {
fprintf(stderr, "ERROR\n");
sprintf(err, "%s: trouble doing projections for axis %d", me, axis);
biffAdd(NINSPECT, err);
airMopError(mop); return 1;
}
fprintf(stderr, "done\n");
}
if (nrrdSpaceRightAnteriorSuperior == nin->space) {
if (fixproj(nproj, nin)) {
fprintf(stderr, "ERROR\n");
sprintf(err, "%s: trouble orienting projections", me);
biffAdd(NINSPECT, err);
airMopError(mop); return 1;
}
}
srl = nproj[1]->axis[0+1].size;
sap = nproj[0]->axis[0+1].size;
ssi = nproj[1]->axis[1+1].size;
/* allocate output as 8-bit color image. We know output type is
nrrdTypeUChar because ninspect_proj finishes each projection
with nrrdQuantize to 8-bits */
if (nrrdMaybeAlloc_va(nout, nrrdTypeUChar, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, srl + 3*margin + sap),
AIR_CAST(size_t, ssi + 3*margin + sap))) {
sprintf(err, "%s: couldn't allocate output", me);
biffMove(NINSPECT, err, NRRD);
airMopError(mop); return 1;
}
min[0] = 0;
E = 0;
which = 0;
if (!E) { min[1] = margin; min[2] = margin; which = 1; }
if (!E) E |= nrrdInset(nout, nout, nproj[1], min);
if (!E) { min[1] = margin; min[2] = 2*margin + ssi; which = 2; }
if (!E) E |= nrrdInset(nout, nout, nproj[2], min);
if (!E) { min[1] = 2*margin + srl; min[2] = margin; which = 3; }
if (!E) E |= nrrdInset(nout, nout, nproj[0], min);
if (E) {
sprintf(err, "%s: couldn't composite output (which = %d)",
me, which);
biffMove(NINSPECT, err, NRRD);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
/*
******** limnCameraPathMake
**
** uses limnSplines to do camera paths based on key-frames
**
** output: cameras at all "numFrames" frames are set in the
** PRE-ALLOCATED array of output cameras, "cam".
**
** input:
** keycam: array of keyframe cameras
** time: times associated with the key frames
** ---> both of these arrays are length "numKeys" <---
** trackWhat: takes values from the limnCameraPathTrack* enum
** quatType: spline to control camera orientations. This is needed for
** tracking at or from, but not needed for limnCameraPathTrackBoth.
** This is the only limnSplineTypeSpec* argument that can be NULL.
** posType: spline to control whichever of from, at, and up are needed for
** the given style of tracking.
** distType: spline to control neer, faar, dist: positions of near clipping,
** far clipping, and image plane, as well as the
** distance between from and at (which is used if not doing
** limnCameraPathTrackBoth)
** viewType: spline to control fov (and aspect, if you're crazy)
**
** NOTE: The "atRelative", "orthographic", and "rightHanded" fields
** are copied from keycam[0] into all output cam[i], but you still need
** to correctly set them for all keycam[i] for limnCameraUpdate to work
** as expected. Also, for the sake of simplicity, this function only works
** with fov and aspect, instead of {u,v}Range, and hence both "fov" and
** "aspect" need to set in *all* the keycams, even if neither of them
** ever changes!
*/
int
limnCameraPathMake(limnCamera *cam, int numFrames,
limnCamera *keycam, double *time, int numKeys,
int trackWhat,
limnSplineTypeSpec *quatType,
limnSplineTypeSpec *posType,
limnSplineTypeSpec *distType,
limnSplineTypeSpec *viewType) {
static const char me[]="limnCameraPathMake";
char which[AIR_STRLEN_MED];
airArray *mop;
Nrrd *nquat, *nfrom, *natpt, *nupvc, *ndist, *nfova, *ntime, *nsample;
double fratVec[3], *quat, *from, *atpt, *upvc, *dist, *fova,
W2V[9], N[3], fratDist;
limnSpline *timeSpline, *quatSpline, *fromSpline, *atptSpline, *upvcSpline,
*distSpline, *fovaSpline;
limnSplineTypeSpec *timeType;
int ii, E;
if (!( cam && keycam && time && posType && distType && viewType )) {
biffAddf(LIMN, "%s: got NULL pointer", me);
return 1;
}
if (!( AIR_IN_OP(limnCameraPathTrackUnknown, trackWhat,
limnCameraPathTrackLast) )) {
biffAddf(LIMN, "%s: trackWhat %d not in valid range [%d,%d]", me,
trackWhat, limnCameraPathTrackUnknown+1,
limnCameraPathTrackLast-1);
return 1;
}
if (limnCameraPathTrackBoth != trackWhat && !quatType) {
biffAddf(LIMN, "%s: need the quaternion limnSplineTypeSpec if not "
"doing trackBoth", me);
return 1;
}
/* create and allocate nrrds. For the time being, we're allocating
more different nrrds, and filling their contents, than we need
to-- nquat is not needed if we're doing limnCameraPathTrackBoth,
for example. However, we do make an effort to only do the spline
evaluation on the things we actually need to know. */
mop = airMopNew();
airMopAdd(mop, nquat = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nfrom = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, natpt = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nupvc = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, ndist = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nfova = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, ntime = nrrdNew(), (airMopper)nrrdNix, airMopAlways);
if (nrrdWrap_va(ntime, time, nrrdTypeDouble, 1,
AIR_CAST(size_t, numKeys))) {
biffMovef(LIMN, NRRD, "%s: trouble wrapping time values", me);
airMopError(mop); return 1;
}
airMopAdd(mop, nsample = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
timeType = limnSplineTypeSpecNew(limnSplineTypeTimeWarp);
airMopAdd(mop, timeType, (airMopper)limnSplineTypeSpecNix, airMopAlways);
if (nrrdMaybeAlloc_va(nquat, nrrdTypeDouble, 2,
AIR_CAST(size_t, 4), AIR_CAST(size_t, numKeys))
|| nrrdMaybeAlloc_va(nfrom, nrrdTypeDouble, 2,
AIR_CAST(size_t, 3), AIR_CAST(size_t, numKeys))
|| nrrdMaybeAlloc_va(natpt, nrrdTypeDouble, 2,
AIR_CAST(size_t, 3), AIR_CAST(size_t, numKeys))
|| nrrdMaybeAlloc_va(nupvc, nrrdTypeDouble, 2,
AIR_CAST(size_t, 3), AIR_CAST(size_t, numKeys))
|| nrrdMaybeAlloc_va(ndist, nrrdTypeDouble, 2,
AIR_CAST(size_t, 4), AIR_CAST(size_t, numKeys))
|| nrrdMaybeAlloc_va(nfova, nrrdTypeDouble, 2,
AIR_CAST(size_t, 2), AIR_CAST(size_t, numKeys))) {
biffMovef(LIMN, NRRD, "%s: couldn't allocate buffer nrrds", me);
airMopError(mop); return 1;
}
quat = (double*)(nquat->data);
from = (double*)(nfrom->data);
atpt = (double*)(natpt->data);
upvc = (double*)(nupvc->data);
dist = (double*)(ndist->data);
fova = (double*)(nfova->data);
/* check cameras, and put camera information into nrrds */
for (ii=0; ii<numKeys; ii++) {
if (limnCameraUpdate(keycam + ii)) {
biffAddf(LIMN, "%s: trouble with camera at keyframe %d\n", me, ii);
airMopError(mop); return 1;
}
if (!( AIR_EXISTS(keycam[ii].fov) && AIR_EXISTS(keycam[ii].aspect) )) {
biffAddf(LIMN, "%s: fov, aspect not both defined on keyframe %d",
me, ii);
airMopError(mop); return 1;
}
ell_4m_to_q_d(quat + 4*ii, keycam[ii].W2V);
if (ii) {
if (0 > ELL_4V_DOT(quat + 4*ii, quat + 4*(ii-1))) {
ELL_4V_SCALE(quat + 4*ii, -1, quat + 4*ii);
}
}
ELL_3V_COPY(from + 3*ii, keycam[ii].from);
ELL_3V_COPY(atpt + 3*ii, keycam[ii].at);
ELL_3V_COPY(upvc + 3*ii, keycam[ii].up);
ELL_3V_SUB(fratVec, keycam[ii].from, keycam[ii].at);
fratDist = ELL_3V_LEN(fratVec);
ELL_4V_SET(dist + 4*ii, fratDist,
keycam[ii].neer, keycam[ii].dist, keycam[ii].faar);
ELL_2V_SET(fova + 2*ii, keycam[ii].fov, keycam[ii].aspect);
}
/* create splines from nrrds */
if (!( (strcpy(which, "quaternion"), quatSpline =
limnSplineCleverNew(nquat, limnSplineInfoQuaternion, quatType))
&& (strcpy(which, "from point"), fromSpline =
limnSplineCleverNew(nfrom, limnSplineInfo3Vector, posType))
&& (strcpy(which, "at point"), atptSpline =
limnSplineCleverNew(natpt, limnSplineInfo3Vector, posType))
&& (strcpy(which, "up vector"), upvcSpline =
limnSplineCleverNew(nupvc, limnSplineInfo3Vector, posType))
&& (strcpy(which, "plane distances"), distSpline =
limnSplineCleverNew(ndist, limnSplineInfo4Vector, distType))
&& (strcpy(which, "field-of-view"), fovaSpline =
limnSplineCleverNew(nfova, limnSplineInfo2Vector, viewType))
&& (strcpy(which, "time warp"), timeSpline =
limnSplineCleverNew(ntime, limnSplineInfoScalar, timeType)) )) {
biffAddf(LIMN, "%s: trouble creating %s spline", me, which);
airMopError(mop); return 1;
}
airMopAdd(mop, quatSpline, (airMopper)limnSplineNix, airMopAlways);
airMopAdd(mop, fromSpline, (airMopper)limnSplineNix, airMopAlways);
airMopAdd(mop, atptSpline, (airMopper)limnSplineNix, airMopAlways);
airMopAdd(mop, upvcSpline, (airMopper)limnSplineNix, airMopAlways);
airMopAdd(mop, distSpline, (airMopper)limnSplineNix, airMopAlways);
airMopAdd(mop, fovaSpline, (airMopper)limnSplineNix, airMopAlways);
airMopAdd(mop, timeSpline, (airMopper)limnSplineNix, airMopAlways);
/* evaluate splines */
E = AIR_FALSE;
if (!E) E |= limnSplineSample(nsample, timeSpline,
limnSplineMinT(timeSpline), numFrames,
limnSplineMaxT(timeSpline));
quat = NULL;
from = NULL;
atpt = NULL;
upvc = NULL;
switch(trackWhat) {
case limnCameraPathTrackAt:
if (!E) E |= limnSplineNrrdEvaluate(natpt, atptSpline, nsample);
if (!E) atpt = (double*)(natpt->data);
if (!E) E |= limnSplineNrrdEvaluate(nquat, quatSpline, nsample);
if (!E) quat = (double*)(nquat->data);
break;
case limnCameraPathTrackFrom:
if (!E) E |= limnSplineNrrdEvaluate(nfrom, fromSpline, nsample);
if (!E) from = (double*)(nfrom->data);
if (!E) E |= limnSplineNrrdEvaluate(nquat, quatSpline, nsample);
if (!E) quat = (double*)(nquat->data);
break;
case limnCameraPathTrackBoth:
if (!E) E |= limnSplineNrrdEvaluate(nfrom, fromSpline, nsample);
if (!E) from = (double*)(nfrom->data);
if (!E) E |= limnSplineNrrdEvaluate(natpt, atptSpline, nsample);
if (!E) atpt = (double*)(natpt->data);
if (!E) E |= limnSplineNrrdEvaluate(nupvc, upvcSpline, nsample);
if (!E) upvc = (double*)(nupvc->data);
break;
}
dist = NULL;
if (!E) E |= limnSplineNrrdEvaluate(ndist, distSpline, nsample);
if (!E) dist = (double*)(ndist->data);
fova = NULL;
if (!E) E |= limnSplineNrrdEvaluate(nfova, fovaSpline, nsample);
if (!E) fova = (double*)(nfova->data);
if (E) {
biffAddf(LIMN, "%s: trouble evaluating splines", me);
airMopError(mop); return 1;
}
/* copy information from nrrds back into cameras */
for (ii=0; ii<numFrames; ii++) {
cam[ii].atRelative = keycam[0].atRelative;
cam[ii].orthographic = keycam[0].orthographic;
cam[ii].rightHanded = keycam[0].rightHanded;
if (limnCameraPathTrackBoth == trackWhat) {
ELL_3V_COPY(cam[ii].from, from + 3*ii);
ELL_3V_COPY(cam[ii].at, atpt + 3*ii);
ELL_3V_COPY(cam[ii].up, upvc + 3*ii);
} else {
fratDist = (dist + 4*ii)[0];
ell_q_to_3m_d(W2V, quat + 4*ii);
ELL_3MV_ROW1_GET(cam[ii].up, W2V);
if (cam[ii].rightHanded) {
ELL_3V_SCALE(cam[ii].up, -1, cam[ii].up);
}
ELL_3MV_ROW2_GET(N, W2V);
if (limnCameraPathTrackFrom == trackWhat) {
ELL_3V_COPY(cam[ii].from, from + 3*ii);
ELL_3V_SCALE_ADD2(cam[ii].at, 1.0, cam[ii].from, fratDist, N);
} else {
ELL_3V_COPY(cam[ii].at, atpt + 3*ii);
ELL_3V_SCALE_ADD2(cam[ii].from, 1.0, cam[ii].at, -fratDist, N);
}
}
cam[ii].neer = (dist + 4*ii)[1];
cam[ii].dist = (dist + 4*ii)[2];
cam[ii].faar = (dist + 4*ii)[3];
cam[ii].fov = (fova + 2*ii)[0];
cam[ii].aspect = (fova + 2*ii)[1];
if (limnCameraUpdate(cam + ii)) {
biffAddf(LIMN, "%s: trouble with output camera %d\n", me, ii);
airMopError(mop); return 1;
}
}
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
const char *me;
char *err, *outS;
hestOpt *hopt=NULL;
airArray *mop;
int xi, yi, zi, samp;
float *tdata;
double clp[2], xyz[3], q[4], len;
double mD[9], mRF[9], mRI[9], mT[9];
Nrrd *nten;
mop = airMopNew();
me = argv[0];
hestOptAdd(&hopt, "n", "# samples", airTypeInt, 1, 1, &samp, "4",
"number of samples along each edge of cube");
hestOptAdd(&hopt, "c", "cl cp", airTypeDouble, 2, 2, clp, NULL,
"shape of tensor to use; \"cl\" and \"cp\" are cl1 "
"and cp1 values, both in [0.0,1.0]");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output file to save tensors into");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nten = nrrdNew();
airMopAdd(mop, nten, (airMopper)nrrdNuke, airMopAlways);
_clp2xyz(xyz, clp);
fprintf(stderr, "%s: want evals = %g %g %g\n", me, xyz[0], xyz[1], xyz[2]);
if (nrrdMaybeAlloc_va(nten, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7),
AIR_CAST(size_t, samp),
AIR_CAST(size_t, samp),
AIR_CAST(size_t, samp))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
ELL_3M_IDENTITY_SET(mD);
ELL_3M_DIAG_SET(mD, xyz[0], xyz[1], xyz[2]);
tdata = (float*)nten->data;
for (zi=0; zi<samp; zi++) {
for (yi=0; yi<samp; yi++) {
for (xi=0; xi<samp; xi++) {
q[0] = 1.0;
q[1] = AIR_AFFINE(-0.5, (float)xi, samp-0.5, -1, 1);
q[2] = AIR_AFFINE(-0.5, (float)yi, samp-0.5, -1, 1);
q[3] = AIR_AFFINE(-0.5, (float)zi, samp-0.5, -1, 1);
len = ELL_4V_LEN(q);
ELL_4V_SCALE(q, 1.0/len, q);
washQtoM3(mRF, q);
ELL_3M_TRANSPOSE(mRI, mRF);
ELL_3M_IDENTITY_SET(mT);
ell_3m_post_mul_d(mT, mRI);
ell_3m_post_mul_d(mT, mD);
ell_3m_post_mul_d(mT, mRF);
tdata[0] = 1.0;
TEN_M2T(tdata, mT);
tdata += 7;
}
}
}
if (nrrdSave(outS, nten, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt=NULL;
airArray *mop;
char *errS, *outS, *covarS;
Nrrd *_nodf, *nvec, *nhist, *ncovar;
int bins;
size_t size[NRRD_DIM_MAX];
float min;
mop = airMopNew();
me = argv[0];
hestOptAdd(&hopt, "i", "odf", airTypeOther, 1, 1, &_nodf, NULL,
"ODF volume to analyze", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "v", "odf", airTypeOther, 1, 1, &nvec, NULL,
"list of vectors by which odf is sampled",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "min", "min", airTypeFloat, 1, 1, &min, "0.0",
"ODF values below this are ignored, and per-voxel ODF is "
"normalized to have sum 1.0. Use \"nan\" to subtract out "
"the per-voxel min.");
hestOptAdd(&hopt, "b", "bins", airTypeInt, 1, 1, &bins, "128",
"number of bins in histograms");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output file");
hestOptAdd(&hopt, "co", "covariance out", airTypeString, 1, 1,
&covarS, "covar.nrrd", "covariance output file");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!( nrrdTypeFloat == nvec->type )) {
fprintf(stderr, "%s vector type (%s) not %s\n", me,
airEnumStr(nrrdType, nvec->type),
airEnumStr(nrrdType, nrrdTypeFloat));
airMopError(mop); return 1;
}
if (!( 2 == nvec->dim && 3 == nvec->axis[0].size )) {
fprintf(stderr, "%s: nvec not a 2-D 3-by-N array\n", me);
airMopError(mop); return 1;
}
if (!( _nodf->axis[0].size == nvec->axis[1].size )) {
fprintf(stderr, "%s mismatch of _nodf->axis[0].size (%d) vs. "
"nvec->axis[1].size (%d)\n", me,
(int)_nodf->axis[0].size, (int)nvec->axis[1].size);
airMopError(mop); return 1;
}
nrrdAxisInfoGet_nva(_nodf, nrrdAxisInfoSize, size);
size[0] = bins;
nhist = nrrdNew();
airMopAdd(mop, nhist, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_nva(nhist, nrrdTypeFloat, _nodf->dim, size)) {
airMopAdd(mop, errS = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating output:\n%s", me, errS);
airMopError(mop); return 1;
}
ncovar = nrrdNew();
airMopAdd(mop, ncovar, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(ncovar, nrrdTypeFloat, 2,
AIR_CAST(size_t, bins),
AIR_CAST(size_t, bins))) {
airMopAdd(mop, errS = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating covariance output:\n%s", me, errS);
airMopError(mop); return 1;
}
{
/* we modify the lengths of the vectors here */
int NN, VV, ii, jj=0, kk, *anglut;
float *odf, *hist, *covar, *vec, *vi, *vj, tmp, pvmin;
double *mean;
Nrrd *nodf, *nanglut;
VV = nvec->axis[1].size;
NN = nrrdElementNumber(_nodf)/VV;
nanglut = nrrdNew();
airMopAdd(mop, nanglut, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nanglut, nrrdTypeInt, 2,
AIR_CAST(size_t, VV),
AIR_CAST(size_t, VV))) {
airMopAdd(mop, errS = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating lookup table:\n%s", me, errS);
airMopError(mop); return 1;
}
if (nrrdTypeFloat == _nodf->type) {
nodf = _nodf;
} else {
nodf = nrrdNew();
airMopAdd(mop, nodf, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(nodf, _nodf, nrrdTypeFloat)) {
airMopAdd(mop, errS = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble converting input:\n%s", me, errS);
airMopError(mop); return 1;
}
}
/* normalize lengths (MODIFIES INPUT) */
vec = (float*)nvec->data;
for (ii=0; ii<=jj; ii++) {
vi = vec + 3*ii;
ELL_3V_NORM(vi, vi, tmp);
}
/* pre-compute pair-wise angles */
anglut = (int*)nanglut->data;
for (jj=0; jj<VV; jj++) {
vj = vec + 3*jj;
for (ii=0; ii<=jj; ii++) {
vi = vec + 3*ii;
tmp = ELL_3V_DOT(vi, vj);
tmp = AIR_ABS(tmp);
tmp = acos(tmp)/(AIR_PI/2.0);
anglut[ii + VV*jj] = airIndex(0.0, tmp, 1.0, bins);
}
}
/* process all samples (MODIFIES INPUT if input was already float) */
odf = (float*)nodf->data;
hist = (float*)nhist->data;
for (kk=0; kk<NN; kk++) {
if (!(kk % 100)) {
fprintf(stderr, "%d/%d\n", kk, NN);
}
tmp = 0;
if (AIR_EXISTS(min)) {
for (ii=0; ii<VV; ii++) {
odf[ii] = AIR_MAX(0.0, odf[ii]-min);
tmp += odf[ii];
}
} else {
/* we do the more sketchy per-voxel min subtraction */
pvmin = airFPGen_f(airFP_POS_INF);
for (ii=0; ii<VV; ii++) {
pvmin = AIR_MIN(pvmin, odf[ii]);
}
for (ii=0; ii<VV; ii++) {
odf[ii] -= pvmin;
tmp += odf[ii];
}
}
if (tmp) {
/* something left after subtracting out baseline isotropic */
for (ii=0; ii<VV; ii++) {
odf[ii] /= tmp;
}
/* odf[] is normalized to 1.0 sum */
for (jj=0; jj<VV; jj++) {
for (ii=0; ii<=jj; ii++) {
tmp = odf[ii]*odf[jj];
hist[anglut[ii + VV*jj]] += tmp;
}
}
}
odf += VV;
hist += bins;
}
odf = NULL;
hist = NULL;
/* find mean value of each bin (needed for covariance) */
mean = (double*)calloc(bins, sizeof(double));
if (!mean) {
fprintf(stderr, "%s: couldn't allocate mean array", me);
airMopError(mop); return 1;
}
hist = (float*)nhist->data;
for (kk=0; kk<NN; kk++) {
for (ii=0; ii<bins; ii++) {
mean[ii] += hist[ii];
}
hist += bins;
}
hist = NULL;
for (ii=0; ii<bins; ii++) {
mean[ii] /= NN;
}
/* make covariance matrix of from all histograms */
covar = (float*)ncovar->data;
hist = (float*)nhist->data;
for (kk=0; kk<NN; kk++) {
for (jj=0; jj<bins; jj++) {
for (ii=0; ii<jj; ii++) {
tmp = (hist[ii] - mean[ii])*(hist[jj] - mean[jj]);
covar[ii + bins*jj] += tmp;
covar[jj + bins*ii] += tmp;
}
covar[jj + bins*jj] += (hist[jj] - mean[jj])*(hist[jj] - mean[jj]);
}
hist += bins;
}
hist = NULL;
}
if (nrrdSave(outS, nhist, NULL)) {
airMopAdd(mop, errS = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s\n", me, errS);
airMopError(mop); return 1;
}
if (nrrdSave(covarS, ncovar, NULL)) {
airMopAdd(mop, errS = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save covariance output:\n%s\n", me, errS);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}