/*
******** tenGradientJitter
**
** moves all gradients by amount dist on tangent plane, in a random
** direction, and then renormalizes. The distance is a fraction
** of the ideal edge length (via tenGradientIdealEdge)
*/
int
tenGradientJitter(Nrrd *nout, const Nrrd *nin, double dist) {
static const char me[]="tenGradientJitter";
double *grad, perp0[3], perp1[3], len, theta, cc, ss, edge;
unsigned int gi, num;
if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
biffMovef(TEN, NRRD, "%s: trouble converting input to double", me);
return 1;
}
if (tenGradientCheck(nout, nrrdTypeDouble, 3)) {
biffAddf(TEN, "%s: didn't get valid gradients", me);
return 1;
}
grad = AIR_CAST(double*, nout->data);
num = AIR_UINT(nout->axis[1].size);
/* HEY: possible confusion between single and not */
edge = tenGradientIdealEdge(num, AIR_FALSE);
for (gi=0; gi<num; gi++) {
ELL_3V_NORM(grad, grad, len);
ell_3v_perp_d(perp0, grad);
ELL_3V_CROSS(perp1, perp0, grad);
theta = AIR_AFFINE(0, airDrandMT(), 1, 0, 2*AIR_PI);
cc = dist*edge*cos(theta);
ss = dist*edge*sin(theta);
ELL_3V_SCALE_ADD3(grad, 1.0, grad, cc, perp0, ss, perp1);
ELL_3V_NORM(grad, grad, len);
grad += 3;
}
return 0;
}
int
tend_msimMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
tenExperSpec *espec;
const tenModel *model;
int E, seed, keyValueSet, outType, plusB0, insertB0;
Nrrd *nin, *nT2, *_ngrad, *ngrad, *nout;
char *outS, *modS;
double bval, sigma;
/* maybe this can go in tend.c, but for some reason its explicitly
set to AIR_FALSE there */
hparm->elideSingleOtherDefault = AIR_TRUE;
hestOptAdd(&hopt, "sigma", "sigma", airTypeDouble, 1, 1, &sigma, "0.0",
"Gaussian/Rician noise parameter");
hestOptAdd(&hopt, "seed", "seed", airTypeInt, 1, 1, &seed, "42",
"seed value for RNG which creates noise");
hestOptAdd(&hopt, "g", "grad list", airTypeOther, 1, 1, &_ngrad, NULL,
"gradient list, one row per diffusion-weighted image",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b0", "b0 image", airTypeOther, 1, 1, &nT2, "",
"reference non-diffusion-weighted (\"B0\") image, which "
"may be needed if it isn't part of give model param image",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "i", "model image", airTypeOther, 1, 1, &nin, "-",
"input model image", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "m", "model", airTypeString, 1, 1, &modS, NULL,
"model with which to simulate DWIs, which must be specified if "
"it is not indicated by the first axis in input model image.");
hestOptAdd(&hopt, "ib0", "bool", airTypeBool, 1, 1, &insertB0, "false",
"insert a non-DW B0 image at the beginning of the experiment "
"specification (useful if the given gradient list doesn't "
"already have one) and hence also insert a B0 image at the "
"beginning of the output simulated DWIs");
hestOptAdd(&hopt, "b", "b", airTypeDouble, 1, 1, &bval, "1000",
"b value for simulated scan");
hestOptAdd(&hopt, "kvp", "bool", airTypeBool, 1, 1, &keyValueSet, "true",
"generate key/value pairs in the NRRD header corresponding "
"to the input b-value and gradients.");
hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &outType, "float",
"output type of DWIs", NULL, nrrdType);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output dwis");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_msimInfoL);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
espec = tenExperSpecNew();
airMopAdd(mop, espec, (airMopper)tenExperSpecNix, airMopAlways);
airSrandMT(seed);
if (nrrdTypeDouble == _ngrad->type) {
ngrad = _ngrad;
} else {
ngrad = nrrdNew();
airMopAdd(mop, ngrad, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ngrad, _ngrad, nrrdTypeDouble)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble converting grads to %s:\n%s\n", me,
airEnumStr(nrrdType, nrrdTypeDouble), err);
airMopError(mop); return 1;
}
}
plusB0 = AIR_FALSE;
if (airStrlen(modS)) {
if (tenModelParse(&model, &plusB0, AIR_FALSE, modS)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing model \"%s\":\n%s\n",
me, modS, err);
airMopError(mop); return 1;
}
} else if (tenModelFromAxisLearnPossible(nin->axis + 0)) {
if (tenModelFromAxisLearn(&model, &plusB0, nin->axis + 0)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing model frmo axis 0 of nin:\n%s\n",
me, err);
airMopError(mop); return 1;
}
} else {
fprintf(stderr, "%s: need model specified either via \"-m\" or input "
"model image axis 0\n", me);
airMopError(mop); return 1;
}
/* we have learned plusB0, but we don't actually need it;
either: it describes the given model param image
(which is courteous but not necessary since the logic inside
tenModeSimulate will see this),
or: it is trying to say something about including B0 amongst
model parameters (which isn't actually meaningful in the
context of simulated DWIs */
E = 0;
if (!E) E |= tenGradientCheck(ngrad, nrrdTypeDouble, 1);
if (!E) E |= tenExperSpecGradSingleBValSet(espec, insertB0, bval,
AIR_CAST(const double *,
ngrad->data),
ngrad->axis[1].size);
if (!E) E |= tenModelSimulate(nout, outType, espec,
model, nT2, nin, keyValueSet);
if (E) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
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;
}
/*
******** tenGradientDistribute
**
** Takes the given list of gradients, normalizes their lengths,
** optionally jitters their positions, does point repulsion, and then
** (optionally) selects a combination of directions with minimum vector sum.
**
** The complicated part of this is the point repulsion, which uses a
** gradient descent with variable set size. The progress of the system
** is measured by decrease in potential (when its measurement doesn't
** overflow to infinity) or an increase in the minimum angle. When a
** step results in negative progress, the step size is halved, and the
** iteration is attempted again. Based on the observation that at
** some points the step size must be made very small to get progress,
** the step size is cautiously increased ("nudged") at every
** iteration, to try to avoid using an overly small step. The amount
** by which the step is nudged is halved everytime the step is halved,
** to avoid endless cycling through step sizes.
*/
int
tenGradientDistribute(Nrrd *nout, const Nrrd *nin,
tenGradientParm *tgparm) {
static const char me[]="tenGradientDistribute";
char filename[AIR_STRLEN_SMALL];
unsigned int ii, num, iter, oldIdx, newIdx, edgeShrink;
airArray *mop;
Nrrd *npos[2];
double *pos, len, meanVelocity, pot, potNew, potD,
edge, edgeMin, angle, angleNew;
int E;
if (!nout || tenGradientCheck(nin, nrrdTypeUnknown, 2) || !tgparm) {
biffAddf(TEN, "%s: got NULL pointer or invalid input", me);
return 1;
}
num = AIR_UINT(nin->axis[1].size);
mop = airMopNew();
npos[0] = nrrdNew();
npos[1] = nrrdNew();
airMopAdd(mop, npos[0], (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, npos[1], (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(npos[0], nin, nrrdTypeDouble)
|| nrrdConvert(npos[1], nin, nrrdTypeDouble)) {
biffMovef(TEN, NRRD, "%s: trouble allocating temp buffers", me);
airMopError(mop); return 1;
}
pos = (double*)(npos[0]->data);
for (ii=0; ii<num; ii++) {
ELL_3V_NORM(pos, pos, len);
pos += 3;
}
if (tgparm->jitter) {
if (tenGradientJitter(npos[0], npos[0], tgparm->jitter)) {
biffAddf(TEN, "%s: problem jittering input", me);
airMopError(mop); return 1;
}
}
/* initialize things prior to first iteration; have to
make sure that loop body tests pass 1st time around */
meanVelocity = 2*tgparm->minVelocity;
potD = -2*tgparm->minPotentialChange;
oldIdx = 0;
newIdx = 1;
tgparm->step = tgparm->initStep;
tgparm->nudge = 0.1;
tenGradientMeasure(&pot, &angle, NULL,
npos[oldIdx], tgparm, AIR_TRUE);
for (iter = 0;
((!!tgparm->minIteration && iter < tgparm->minIteration)
||
(iter < tgparm->maxIteration
&& (!tgparm->minPotentialChange
|| !AIR_EXISTS(potD)
|| -potD > tgparm->minPotentialChange)
&& (!tgparm->minVelocity
|| meanVelocity > tgparm->minVelocity)
&& tgparm->step > FLT_MIN));
iter++) {
/* copy positions from old to new */
memcpy(npos[newIdx]->data, npos[oldIdx]->data, 3*num*sizeof(double));
edge = tenGradientIdealEdge(num, tgparm->single);
edgeShrink = 0;
/* try to do a position update, which will fail if repulsion values
explode, from having an insufficiently small edge normalization,
so retry with smaller edge next time */
do {
E = _tenGradientUpdate(&meanVelocity, &edgeMin,
npos[newIdx], edge, tgparm);
if (E) {
if (edgeShrink > tgparm->maxEdgeShrink) {
biffAddf(TEN, "%s: %u > %u edge shrinks (%g), update still failed",
me, edgeShrink, tgparm->maxEdgeShrink, edge);
airMopError(mop); return 1;
}
edgeShrink++;
/* re-initialize positions (HEY ugly code logic) */
memcpy(npos[newIdx]->data, npos[oldIdx]->data, 3*num*sizeof(double));
edge = edgeMin;
}
} while (E);
tenGradientMeasure(&potNew, &angleNew, NULL,
npos[newIdx], tgparm, AIR_TRUE);
if ((AIR_EXISTS(pot) && AIR_EXISTS(potNew) && potNew <= pot)
|| angleNew >= angle) {
/* there was progress of some kind, either through potential
decrease, or angle increase */
potD = 2*(potNew - pot)/(potNew + pot);
if (!(iter % tgparm->report) && tgparm->verbose) {
fprintf(stderr, "%s(%d): . . . . . . step = %g, edgeShrink = %u\n"
" velo = %g<>%g, phi = %g ~ %g<>%g, angle = %g ~ %g\n",
me, iter, tgparm->step, edgeShrink,
meanVelocity, tgparm->minVelocity,
pot, potD, tgparm->minPotentialChange,
angle, angleNew - angle);
}
if (tgparm->snap && !(iter % tgparm->snap)) {
sprintf(filename, "%05d.nrrd", iter/tgparm->snap);
if (tgparm->verbose) {
fprintf(stderr, "%s(%d): . . . . . . saving %s\n",
me, iter, filename);
}
if (nrrdSave(filename, npos[newIdx], NULL)) {
char *serr;
serr = biffGetDone(NRRD);
if (tgparm->verbose) { /* perhaps shouldn't have this check */
fprintf(stderr, "%s: iter=%d, couldn't save snapshot:\n%s"
"continuing ...\n", me, iter, serr);
}
free(serr);
}
}
tgparm->step *= 1 + tgparm->nudge;
tgparm->step = AIR_MIN(tgparm->initStep, tgparm->step);
pot = potNew;
angle = angleNew;
/* swap buffers */
newIdx = 1 - newIdx;
oldIdx = 1 - oldIdx;
} else {
/* oops, did not make progress; back off and try again */
if (tgparm->verbose) {
fprintf(stderr, "%s(%d): ######## step %g --> %g\n"
" phi = %g --> %g ~ %g, angle = %g --> %g\n",
me, iter, tgparm->step, tgparm->step/2,
pot, potNew, potD, angle, angleNew);
}
tgparm->step /= 2;
tgparm->nudge /= 2;
}
}
/* when the for-loop test fails, we stop before computing the next
iteration (which starts with copying from npos[oldIdx] to
npos[newIdx]) ==> the final results are in npos[oldIdx] */
if (tgparm->verbose) {
fprintf(stderr, "%s: .......................... done distribution:\n"
" (%d && %d) || (%d \n"
" && (%d || %d || %d) \n"
" && (%d || %d) \n"
" && %d) is false\n", me,
!!tgparm->minIteration, iter < tgparm->minIteration,
iter < tgparm->maxIteration,
!tgparm->minPotentialChange,
!AIR_EXISTS(potD), AIR_ABS(potD) > tgparm->minPotentialChange,
!tgparm->minVelocity, meanVelocity > tgparm->minVelocity,
tgparm->step > FLT_MIN);
fprintf(stderr, " iter=%d, velo = %g<>%g, phi = %g ~ %g<>%g;\n",
iter, meanVelocity, tgparm->minVelocity, pot,
potD, tgparm->minPotentialChange);
fprintf(stderr, " minEdge = %g; idealEdge = %g\n",
2*sin(angle/2), tenGradientIdealEdge(num, tgparm->single));
}
tenGradientMeasure(&pot, NULL, NULL, npos[oldIdx], tgparm, AIR_FALSE);
tgparm->potential = pot;
tenGradientMeasure(&pot, &angle, &edge, npos[oldIdx], tgparm, AIR_TRUE);
tgparm->potentialNorm = pot;
tgparm->angle = angle;
tgparm->edge = edge;
tgparm->itersUsed = iter;
if ((tgparm->minMeanImprovement || tgparm->minMean)
&& !tgparm->single) {
if (tgparm->verbose) {
fprintf(stderr, "%s: optimizing balance:\n", me);
}
if (tenGradientBalance(nout, npos[oldIdx], tgparm)) {
biffAddf(TEN, "%s: failed to minimize vector sum of gradients", me);
airMopError(mop); return 1;
}
if (tgparm->verbose) {
fprintf(stderr, "%s: .......................... done balancing.\n", me);
}
} else {
if (tgparm->verbose) {
fprintf(stderr, "%s: .......................... (no balancing)\n", me);
}
if (nrrdConvert(nout, npos[oldIdx], nrrdTypeDouble)) {
biffMovef(TEN, NRRD, "%s: couldn't set output", me);
airMopError(mop); return 1;
}
}
airMopOkay(mop);
return 0;
}
/*
** parties until the gradients settle down
*/
int
tenGradientBalance(Nrrd *nout, const Nrrd *nin,
tenGradientParm *tgparm) {
static const char me[]="tenGradientBalance";
double len, lastLen, improv;
airRandMTState *rstate;
Nrrd *ncopy;
unsigned int iter, maxIter;
int done;
airArray *mop;
if (!nout || tenGradientCheck(nin, nrrdTypeUnknown, 2) || !tgparm) {
biffAddf(TEN, "%s: got NULL pointer (%p,%p) or invalid nin", me,
AIR_VOIDP(nout), AIR_VOIDP(tgparm));
return 1;
}
if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
biffMovef(TEN, NRRD, "%s: can't initialize output with input", me);
return 1;
}
mop = airMopNew();
ncopy = nrrdNew();
airMopAdd(mop, ncopy, (airMopper)nrrdNuke, airMopAlways);
rstate = airRandMTStateNew(tgparm->seed);
airMopAdd(mop, rstate, (airMopper)airRandMTStateNix, airMopAlways);
/* HEY: factor of 100 is an approximate hack */
maxIter = 100*tgparm->maxIteration;
lastLen = 1.0;
done = AIR_FALSE;
do {
iter = 0;
do {
iter++;
len = party(nout, rstate);
} while (len > lastLen && iter < maxIter);
if (iter >= maxIter) {
if (tgparm->verbose) {
fprintf(stderr, "%s: stopping at max iter %u\n", me, maxIter);
}
if (nrrdCopy(nout, ncopy)) {
biffMovef(TEN, NRRD, "%s: trouble copying", me);
airMopError(mop); return 1;
}
done = AIR_TRUE;
} else {
if (nrrdCopy(ncopy, nout)) {
biffMovef(TEN, NRRD, "%s: trouble copying", me);
airMopError(mop); return 1;
}
improv = lastLen - len;
lastLen = len;
if (tgparm->verbose) {
fprintf(stderr, "%s: (iter %u) improvement: %g (mean length = %g)\n",
me, iter, improv, len);
}
done = (improv <= tgparm->minMeanImprovement
|| len < tgparm->minMean);
}
} while (!done);
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *err;
hestOpt *hopt=NULL;
airArray *mop;
char *outTenS, *outCovarS, *outRmvS;
int seed, E;
unsigned int NN;
Nrrd *_ninTen, *ninTen, *ngrad, *_ninB0, *ninB0, *nmask,
*noutCovar, *noutTen, *noutRmv, *ntbuff;
float sigma, bval;
size_t sizeX, sizeY, sizeZ;
tenEstimateContext *tec;
int axmap[NRRD_DIM_MAX], randrot;
mop = airMopNew();
me = argv[0];
hestOptAdd(&hopt, "i", "ten", airTypeOther, 1, 1, &_ninTen, NULL,
"input tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "n", "#sim", airTypeUInt, 1, 1, &NN, "100",
"number of simulations to run");
hestOptAdd(&hopt, "seed", "seed", airTypeInt, 1, 1, &seed, "42",
"seed value for RNG which creates noise");
hestOptAdd(&hopt, "r", "reference field", airTypeOther, 1, 1, &_ninB0, NULL,
"reference anatomical scan, with no diffusion weighting",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "rr", NULL, airTypeOther, 0, 0, &randrot, NULL,
"randomize gradient set orientation");
hestOptAdd(&hopt, "g", "grad list", airTypeOther, 1, 1, &ngrad, "",
"gradient list, one row per diffusion-weighted image",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "b", airTypeFloat, 1, 1, &bval, "1000",
"b value for simulated scan");
hestOptAdd(&hopt, "sigma", "sigma", airTypeFloat, 1, 1, &sigma, "0.0",
"Rician noise parameter");
hestOptAdd(&hopt, "ot", "filename", airTypeString, 1, 1, &outTenS,
"tout.nrrd", "file to write output tensor nrrd to");
hestOptAdd(&hopt, "oc", "filename", airTypeString, 1, 1, &outCovarS,
"cout.nrrd", "file to write output covariance nrrd to");
hestOptAdd(&hopt, "or", "filename", airTypeString, 1, 1, &outRmvS,
"rout.nrrd", "file to write output R_i means, variances to");
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 (tenGradientCheck(ngrad, nrrdTypeDefault, 7)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: problem with gradient list:\n%s\n", me, err);
airMopError(mop);
return 1;
}
if (tenTensorCheck(_ninTen, nrrdTypeDefault, AIR_TRUE, AIR_TRUE)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: didn't like input:\n%s\n", me, err);
airMopError(mop);
return 1;
}
sizeX = _ninTen->axis[1].size;
sizeY = _ninTen->axis[2].size;
sizeZ = _ninTen->axis[3].size;
if (!(3 == _ninB0->dim &&
sizeX == _ninB0->axis[0].size &&
sizeY == _ninB0->axis[1].size &&
sizeZ == _ninB0->axis[2].size)) {
fprintf(stderr, "%s: given B0 (%u-D) volume not 3-D " _AIR_SIZE_T_CNV
"x" _AIR_SIZE_T_CNV "x" _AIR_SIZE_T_CNV, me, _ninB0->dim,
sizeX, sizeY, sizeZ);
airMopError(mop);
return 1;
}
ninTen = nrrdNew();
airMopAdd(mop, ninTen, (airMopper)nrrdNuke, airMopOnError);
nmask = nrrdNew();
airMopAdd(mop, nmask, (airMopper)nrrdNuke, airMopOnError);
ninB0 = nrrdNew();
airMopAdd(mop, ninB0, (airMopper)nrrdNuke, airMopOnError);
noutCovar = nrrdNew();
airMopAdd(mop, noutCovar, (airMopper)nrrdNuke, airMopOnError);
noutTen = nrrdNew();
airMopAdd(mop, noutTen, (airMopper)nrrdNuke, airMopOnError);
noutRmv = nrrdNew();
airMopAdd(mop, noutRmv, (airMopper)nrrdNuke, airMopOnError);
ntbuff = nrrdNew();
airMopAdd(mop, ntbuff, (airMopper)nrrdNuke, airMopOnError);
if (nrrdConvert(ninTen, _ninTen, nrrdTypeDouble)
|| nrrdSlice(nmask, ninTen, 0, 0)
|| nrrdConvert(ninB0, _ninB0, nrrdTypeDouble)
|| nrrdMaybeAlloc_va(noutTen, nrrdTypeDouble, 4,
AIR_CAST(size_t, 7), sizeX, sizeY, sizeZ)
|| nrrdMaybeAlloc_va(noutCovar, nrrdTypeDouble, 4,
AIR_CAST(size_t, 21), sizeX, sizeY, sizeZ)
|| nrrdMaybeAlloc_va(noutRmv, nrrdTypeDouble, 4,
AIR_CAST(size_t, 6), sizeX, sizeY, sizeZ)
|| nrrdMaybeAlloc_va(ntbuff, nrrdTypeDouble, 2,
AIR_CAST(size_t, 7), NN)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble setting up tec:\n%s\n", me, err);
airMopError(mop);
return 1;
}
tec = tenEstimateContextNew();
airMopAdd(mop, tec, (airMopper)tenEstimateContextNix, airMopAlways);
E = 0;
if (!E) E |= tenEstimateMethodSet(tec, tenEstimate1MethodLLS);
if (!E) E |= tenEstimateValueMinSet(tec, 0.000000001);
if (!E) E |= tenEstimateGradientsSet(tec, ngrad, bval, AIR_TRUE);
if (!E) E |= tenEstimateThresholdSet(tec, 0, 0);
if (!E) E |= tenEstimateUpdate(tec);
if (E) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble setting up tec:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airSrandMT(seed);
fprintf(stderr, "!%s: randrot = %d\n", me, randrot);
if (1) {
unsigned int II;
unsigned int nsamp;
double *inTen, *outTen, *outCovar, *outRmv,
*dwibuff, (*lup)(const void *, size_t);
char doneStr[AIR_STRLEN_SMALL];
dwibuff = AIR_CAST(double *, calloc(ngrad->axis[1].size, sizeof(double)));
airMopAdd(mop, dwibuff, airFree, airMopAlways);
nsamp = sizeX*sizeY*sizeZ;
inTen = AIR_CAST(double *, ninTen->data);
lup = nrrdDLookup[nrrdTypeDouble];
outTen = AIR_CAST(double *, noutTen->data);
outCovar = AIR_CAST(double *, noutCovar->data);
outRmv = AIR_CAST(double *, noutRmv->data);
fprintf(stderr, "!%s: simulating ... ", me);
fflush(stderr);
for (II=0; II<nsamp; II++) {
if (!(II % sizeX)) {
fprintf(stderr, "%s", airDoneStr(0, II, nsamp, doneStr));
fflush(stderr);
}
if (csimDo(outTen, outCovar, outRmv + 0, outRmv + 3, ntbuff,
tec, dwibuff, sigma,
bval, lup(ninB0->data, II), NN, randrot, inTen)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop);
return 1;
}
inTen += 7;
outTen += 7;
outCovar += 21;
outRmv += 6;
}
fprintf(stderr, "%s\n", airDoneStr(0, II, nsamp, doneStr));
}