/*
** exact same precautions about utility of this as with gageContextCopy!!!
** So: only after tenFiberUpdate, and don't touch anything, and don't
** call anything except tenFiberTrace and tenFiberContextNix
*/
tenFiberContext *
tenFiberContextCopy(tenFiberContext *oldTfx) {
char me[]="tenFiberContextCopy";
tenFiberContext *tfx;
if (oldTfx->useDwi) {
fprintf(stderr, "!%s: sorry, can't copy DWI contexts; bye.\n", me);
exit(1);
}
tfx = (tenFiberContext *)calloc(1, sizeof(tenFiberContext));
memcpy(tfx, oldTfx, sizeof(tenFiberContext));
tfx->ksp = nrrdKernelSpecCopy(oldTfx->ksp);
tfx->gtx = gageContextCopy(oldTfx->gtx);
tfx->pvl = tfx->gtx->pvl[0]; /* HEY! gage API sucks */
tfx->gageTen = gageAnswerPointer(tfx->gtx, tfx->pvl, tenGageTensor);
tfx->gageEval = gageAnswerPointer(tfx->gtx, tfx->pvl, tenGageEval0);
/* HEY: COPY AND PASTE */
tfx->gageEvec
= gageAnswerPointer(tfx->gtx, tfx->pvl,
(tenFiberTypeEvec0 == tfx->fiberType
? tenGageEvec0
: (tenFiberTypeEvec1 == tfx->fiberType
? tenGageEvec1
: tenGageEvec2)));
tfx->gageAnisoStop = gageAnswerPointer(tfx->gtx, tfx->pvl,
tfx->anisoStopType);
tfx->gageAnisoSpeed = (tfx->anisoSpeedType
? gageAnswerPointer(tfx->gtx, tfx->pvl,
tfx->anisoSpeedType)
: NULL);
return tfx;
}
int
gageDeconvolve(Nrrd *_nout, double *lastDiffP,
const Nrrd *nin, const gageKind *kind,
const NrrdKernelSpec *ksp, int typeOut,
unsigned int maxIter, int saveAnyway,
double step, double epsilon, int verbose) {
static const char me[]="gageDeconvolve";
gageContext *ctx[2];
gagePerVolume *pvl[2];
double *out[2], *val[2], alpha, (*lup)(const void *, size_t), meandiff=0;
const double *ans[2];
Nrrd *nout[2];
airArray *mop;
unsigned int sx, sy, sz, xi, yi, zi, anslen, thiz=0, last, inIdx, iter;
int E, valItem;
if (!(_nout && lastDiffP && nin && kind && ksp)) {
biffAddf(GAGE, "%s: got NULL pointer", me);
return 1;
}
if (!(nrrdTypeDefault == typeOut
|| !airEnumValCheck(nrrdType, typeOut))) {
biffAddf(GAGE, "%s: typeOut %d not valid", me, typeOut);
return 1;
}
if (!( maxIter >= 1 )) {
biffAddf(GAGE, "%s: need maxIter >= 1 (not %u)", me, maxIter);
return 1;
}
if (!( epsilon >= 0 )) {
biffAddf(GAGE, "%s: need epsilon >= 0.0 (not %g)", me, epsilon);
return 1;
}
/* this once changed from 0 to 1, but is unlikely to change again */
valItem = 1;
mop = airMopNew();
for (iter=0; iter<2; iter++) {
nout[iter] = nrrdNew();
airMopAdd(mop, nout[iter], (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(nout[iter], nin, nrrdTypeDouble)) {
biffMovef(GAGE, NRRD, "%s: couldn't allocate working buffer %u",
me, iter);
airMopError(mop); return 1;
}
ctx[iter] = gageContextNew();
airMopAdd(mop, ctx[iter], (airMopper)gageContextNix, airMopAlways);
E = 0;
if (!E) E |= !(pvl[iter] = gagePerVolumeNew(ctx[iter], nout[iter], kind));
if (!E) E |= gagePerVolumeAttach(ctx[iter], pvl[iter]);
if (!E) E |= gageKernelSet(ctx[iter], gageKernel00,
ksp->kernel, ksp->parm);
if (!E) E |= gageQueryItemOn(ctx[iter], pvl[iter], valItem);
if (!E) E |= gageUpdate(ctx[iter]);
if (E) {
biffAddf(GAGE, "%s: trouble setting up context %u", me, iter);
airMopError(mop); return 1;
}
out[iter] = AIR_CAST(double*, nout[iter]->data);
ans[iter] = gageAnswerPointer(ctx[iter], pvl[iter], valItem);
}
anslen = kind->table[valItem].answerLength;
lup = nrrdDLookup[nin->type];
alpha = ksp->kernel->eval1_d(0.0, ksp->parm);
sx = ctx[0]->shape->size[0];
sy = ctx[0]->shape->size[1];
sz = ctx[0]->shape->size[2];
for (iter=0; iter<maxIter; iter++) {
thiz = (iter+1) % 2;
last = (iter+0) % 2;
val[thiz] = out[thiz];
val[last] = out[last];
inIdx = 0;
meandiff = 0;
for (zi=0; zi<sz; zi++) {
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
unsigned int ai;
double in, aa;
gageProbe(ctx[last], xi, yi, zi);
for (ai=0; ai<anslen; ai++) {
in = lup(nin->data, ai + anslen*inIdx);
aa = ans[last][ai];
val[thiz][ai] = val[last][ai] + step*(in - aa)/alpha;
meandiff += 2*(in - aa)*(in - aa)/(DBL_EPSILON + in*in + aa*aa);
}
val[thiz] += anslen;
val[last] += anslen;
++inIdx;
}
}
}
meandiff /= sx*sy*sz;
if (verbose) {
fprintf(stderr, "%s: iter %u meandiff = %g\n", me, iter, meandiff);
}
if (meandiff < epsilon) {
/* we have indeed converged while iter < maxIter */
break;
}
}
if (iter == maxIter) {
if (!saveAnyway) {
biffAddf(GAGE, "%s: failed to converge in %u iterations, meandiff = %g",
me, maxIter, meandiff);
airMopError(mop); return 1;
} else {
if (verbose) {
fprintf(stderr, "%s: at maxIter %u; err %g still > thresh %g\n", me,
iter, meandiff, epsilon);
}
}
}
if (nrrdClampConvert(_nout, nout[thiz], (nrrdTypeDefault == typeOut
? nin->type
: typeOut))) {
biffAddf(GAGE, "%s: couldn't create output", me);
airMopError(mop); return 1;
}
*lastDiffP = meandiff;
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, done[13];
Nrrd *nin, *ndist, *nmask, *nupdate, *nout;
NrrdKernelSpec *k00, *k11, *k22;
int E;
unsigned int sx, sy, sz, xi, yi, zi, si, iter, maxIter;
gageContext *ctx;
gagePerVolume *pvl;
double dt, *dist, *mask, *update, thresh, eps, rmsMin;
const double *valu, *gmag, *mcrv;
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 volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &k00,
"tent", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &k11,
"cubicd:0,0.5", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "dt", "step", airTypeDouble, 1, 1, &dt, "0.17",
"time step size");
hestOptAdd(&hopt, "th", "val", airTypeDouble, 1, 1, &thresh, "0.0",
"the value to use for thresholding the input "
"volume, to create the binary constraint image.");
hestOptAdd(&hopt, "eps", "val", airTypeDouble, 1, 1, &eps, "0.05",
"width of value bracket around threshold, to constrain the "
"the update from letting to value, originally on either "
"side of the threshold, from getting too close.");
hestOptAdd(&hopt, "rms", "thresh", airTypeDouble, 1, 1, &rmsMin, "0.01",
"RMS change below this terminates updates.");
hestOptAdd(&hopt, "mi", "max", airTypeUInt, 1, 1, &maxIter, "100",
"maximum # iterations");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"fixed volume output");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, aaliasInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
ndist = nrrdNew();
nmask = nrrdNew();
nupdate = nrrdNew();
airMopAdd(mop, ndist, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nmask, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nupdate, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ndist, nin, nrrdTypeDouble)
|| nrrdConvert(nmask, nin, nrrdTypeDouble)
|| nrrdConvert(nupdate, nin, nrrdTypeDouble)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate buffers:\n%s", me, err);
airMopError(mop); return 1;
}
dist = AIR_CAST(double *, ndist->data);
mask = AIR_CAST(double *, nmask->data);
update = AIR_CAST(double *, nupdate->data);
ctx = gageContextNew();
airMopAdd(mop, ctx, (airMopper)gageContextNix, airMopAlways);
gageParmSet(ctx, gageParmRenormalize, AIR_TRUE);
gageParmSet(ctx, gageParmCheckIntegrals, AIR_TRUE);
E = 0;
if (!E) E |= !(pvl = gagePerVolumeNew(ctx, ndist, gageKindScl));
if (!E) E |= gagePerVolumeAttach(ctx, pvl);
if (!E) E |= gageKernelSet(ctx, gageKernel00, k00->kernel, k00->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel11, k11->kernel, k11->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel22, k22->kernel, k22->parm);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclValue);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradMag);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclMeanCurv);
if (!E) E |= gageUpdate(ctx);
if (E) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
valu = gageAnswerPointer(ctx, pvl, gageSclValue);
gmag = gageAnswerPointer(ctx, pvl, gageSclGradMag);
mcrv = gageAnswerPointer(ctx, pvl, gageSclMeanCurv);
sx = nin->axis[0].size;
sy = nin->axis[1].size;
sz = nin->axis[2].size;
for (iter=0; iter<maxIter; iter++) {
double rms;
unsigned count;
fprintf(stderr, "%s: iter %u: ", me, iter);
fflush(stderr);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
fflush(stderr);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
si = xi + sx*(yi + sy*zi);
gageProbe(ctx, xi, yi, zi);
update[si] = -dt*(*gmag)*(*mcrv);
}
}
}
rms = 0;
count = 0;
for (si=0; si<sx*sy*sz; si++) {
double newval;
if (update[si]) {
/* NOTE: this update behavior is only slightly different than
what's described in Equation 18 of the paper. That update
rule ensures that the value never changes "sign" (with
respect to the threshold value), by clamping the values
above or below to 0.0. But worst-case scenario is that two
adjacent samples that were on other side of the threshold
(i.e. 0), could then equal the threshold, which would
confuse a marching-cubes type algorithm. So the "eps"
enforces a small value range around the treshold, and keeps
the values on either side of it. */
newval = dist[si] + update[si];
if (mask[si] > thresh) {
newval = AIR_MAX(newval, thresh+eps/2);
} else {
newval = AIR_MIN(newval, thresh-eps/2);
}
rms += (dist[si] - newval)*(dist[si] - newval);
dist[si] = newval;
count++;
}
}
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
rms /= count;
rms = sqrt(rms);
if (rms < rmsMin) {
fprintf(stderr, "\n%s: RMS %g below threshold %g\n", me, rms, rmsMin);
break;
} else {
fprintf(stderr, " rms = %g > %g\n", rms, rmsMin);
}
}
if (iter == maxIter) {
fprintf(stderr, "%s: hit max iter %u\n", me, maxIter);
}
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, ndist)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
if (nrrdSave(outS, nout, 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
tenFiberAnisoSpeedSet(tenFiberContext *tfx, int aniso,
double lerp, double thresh, double soft) {
char me[]="tenFiberAnisoSpeedSet", err[BIFF_STRLEN];
int anisoGage;
if (!tfx) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(TEN, err); return 1;
}
if (tfx->useDwi) {
fprintf(stderr, "!%s: sorry, can't yet work on DWIs; bye.\n", me);
exit(1);
}
if (airEnumValCheck(tenAniso, aniso)) {
sprintf(err, "%s: aniso %d not valid", me, aniso);
biffAdd(TEN, err); return 1;
}
switch(aniso) {
case tenAniso_FA:
anisoGage = tenGageFA;
break;
case tenAniso_Cl1:
anisoGage = tenGageCl1;
break;
case tenAniso_Cp1:
anisoGage = tenGageCp1;
break;
case tenAniso_Ca1:
anisoGage = tenGageCa1;
break;
case tenAniso_Cl2:
anisoGage = tenGageCl2;
break;
case tenAniso_Cp2:
anisoGage = tenGageCp2;
break;
case tenAniso_Ca2:
anisoGage = tenGageCa2;
break;
default:
sprintf(err, "%s: sorry, currently don't have fast %s computation "
"via gage", me, airEnumStr(tenAniso, tfx->anisoStopType));
biffAdd(TEN, err); return 1;
break;
}
tfx->anisoSpeedType = aniso;
if (tfx->useDwi) {
/* actually, finding anisotropy in the context of 2-tensor
tracking is not currently done by gage */
} else {
GAGE_QUERY_ITEM_ON(tfx->query, anisoGage);
tfx->gageAnisoSpeed = gageAnswerPointer(tfx->gtx, tfx->pvl, anisoGage);
}
tfx->anisoSpeedFunc[0] = lerp;
tfx->anisoSpeedFunc[1] = thresh;
tfx->anisoSpeedFunc[2] = soft;
return 0;
}
/*
******** tenFiberStopSet
**
** how to set stop criteria and their parameters. a little tricky because
** of the use of varargs
**
** valid calls:
** tenFiberStopSet(tfx, tenFiberStopLength, double max)
** tenFiberStopSet(tfx, tenFiberStopMinLength, double min)
** tenFiberStopSet(tfx, tenFiberStopAniso, int anisoType, double anisoThresh)
** tenFiberStopSet(tfx, tenFiberStopNumSteps, unsigned int num)
** tenFiberStopSet(tfx, tenFiberStopMinNumSteps, unsigned int num)
** tenFiberStopSet(tfx, tenFiberStopConfidence, double conf)
** tenFiberStopSet(tfx, tenFiberStopRadius, double radius)
** tenFiberStopSet(tfx, tenFiberStopBounds)
** tenFiberStopSet(tfx, tenFiberStopFraction, double fraction)
** tenFiberStopSet(tfx, tenFiberStopStub)
*/
int
tenFiberStopSet(tenFiberContext *tfx, int stop, ...) {
char me[]="tenFiberStopSet", err[BIFF_STRLEN];
va_list ap;
int ret=0;
int anisoGage;
if (!tfx) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(TEN, err); return 1;
}
va_start(ap, stop);
switch(stop) {
case tenFiberStopAniso:
tfx->anisoStopType = va_arg(ap, int);
tfx->anisoThresh = va_arg(ap, double);
if (!(AIR_IN_OP(tenAnisoUnknown, tfx->anisoStopType, tenAnisoLast))) {
sprintf(err, "%s: given aniso stop type %d not valid", me,
tfx->anisoStopType);
biffAdd(TEN, err); ret = 1; goto end;
}
if (!(AIR_EXISTS(tfx->anisoThresh))) {
sprintf(err, "%s: given aniso threshold doesn't exist", me);
biffAdd(TEN, err); ret = 1; goto end;
}
if (tfx->useDwi) {
/* the tensor of which we measure anisotropy can come from lots of
places, not just a 1-tensor gage item, so there's no specific
item to turn on here... */
tfx->gageAnisoStop = NULL;
} else { /* using tensors */
switch(tfx->anisoStopType) {
case tenAniso_FA:
anisoGage = tenGageFA;
break;
case tenAniso_Cl1:
anisoGage = tenGageCl1;
break;
case tenAniso_Cp1:
anisoGage = tenGageCp1;
break;
case tenAniso_Ca1:
anisoGage = tenGageCa1;
break;
case tenAniso_Clpmin1:
anisoGage = tenGageClpmin1;
break;
case tenAniso_Cl2:
anisoGage = tenGageCl2;
break;
case tenAniso_Cp2:
anisoGage = tenGageCp2;
break;
case tenAniso_Ca2:
anisoGage = tenGageCa2;
break;
case tenAniso_Clpmin2:
anisoGage = tenGageClpmin2;
break;
default:
sprintf(err, "%s: sorry, currently don't have fast %s computation "
"via gage", me, airEnumStr(tenAniso, tfx->anisoStopType));
biffAdd(TEN, err); ret = 1; goto end;
break;
}
/* NOTE: we are no longer computing ALL anisotropy measures ...
GAGE_QUERY_ITEM_ON(tfx->query, tenGageAniso);
*/
GAGE_QUERY_ITEM_ON(tfx->query, anisoGage);
tfx->gageAnisoStop = gageAnswerPointer(tfx->gtx, tfx->pvl, anisoGage);
/*
fprintf(stderr, "!%s: stopping on aniso %s < %g\n", me,
airEnumStr(tenAniso, tfx->anisoStopType), tfx->anisoThresh);
*/
}
break;
case tenFiberStopLength:
tfx->maxHalfLen = va_arg(ap, double);
if (!( AIR_EXISTS(tfx->maxHalfLen) && tfx->maxHalfLen > 0.0 )) {
sprintf(err, "%s: given maxHalfLen %g doesn't exist or isn't > 0.0",
me, tfx->maxHalfLen);
biffAdd(TEN, err); ret = 1; goto end;
}
/* no query modifications needed */
break;
case tenFiberStopMinLength:
tfx->minWholeLen = va_arg(ap, double);
if (!( AIR_EXISTS(tfx->minWholeLen) && tfx->minWholeLen >= 0.0 )) {
sprintf(err, "%s: given minWholeLen %g doesn't exist or isn't >= 0.0",
me, tfx->minWholeLen);
biffAdd(TEN, err); ret = 1; goto end;
}
/* no query modifications needed */
break;
case tenFiberStopNumSteps:
tfx->maxNumSteps = va_arg(ap, unsigned int);
if (!( tfx->maxNumSteps > 0 )) {
sprintf(err, "%s: given maxNumSteps isn't > 0.0", me);
biffAdd(TEN, err); ret = 1; goto end;
}
/* no query modifications needed */
break;
case tenFiberStopMinNumSteps:
tfx->minNumSteps = va_arg(ap, unsigned int);
/* no query modifications needed */
break;
case tenFiberStopConfidence:
tfx->confThresh = va_arg(ap, double);
if (!( AIR_EXISTS(tfx->confThresh) )) {
sprintf(err, "%s: given confThresh doesn't exist", me);
biffAdd(TEN, err); ret = 1; goto end;
}
GAGE_QUERY_ITEM_ON(tfx->query, tenGageTensor);
break;
case tenFiberStopRadius:
tfx->minRadius = va_arg(ap, double);
if (!( AIR_EXISTS(tfx->minRadius) )) {
sprintf(err, "%s: given minimum radius doesn't exist", me);
biffAdd(TEN, err); ret = 1; goto end;
}
/* no query modifications needed */
break;
case tenFiberStopBounds:
/* nothing to set; always used as a stop criterion */
break;
case tenFiberStopFraction:
if (!tfx->useDwi) {
sprintf(err, "%s: can only use %s-based termination in DWI tractography",
me, airEnumStr(tenFiberStop, tenFiberStopFraction));
biffAdd(TEN, err); ret = 1; goto end;
}
tfx->minFraction = va_arg(ap, double);
if (!( AIR_EXISTS(tfx->minFraction) )) {
sprintf(err, "%s: given minimum fraction doesn't exist", me);
biffAdd(TEN, err); ret = 1; goto end;
}
/* no query modifications needed */
break;
case tenFiberStopStub:
/* no var-args to grab */
/* no query modifications needed */
break;
default:
sprintf(err, "%s: stop criterion %d not recognized", me, stop);
biffAdd(TEN, err); ret = 1; goto end;
}
tfx->stop = tfx->stop | (1 << stop);
end:
va_end(ap);
return ret;
}
int
tenFiberTypeSet(tenFiberContext *tfx, int ftype) {
char me[]="tenFiberTypeSet", err[BIFF_STRLEN];
if (!tfx) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(TEN, err); return 1;
}
if (tfx->useDwi) {
fprintf(stderr, "!%s(%d)--- hello\n", me, ftype);
switch (ftype) {
case tenDwiFiberType1Evec0:
GAGE_QUERY_ITEM_ON(tfx->query, tenDwiGageTensorLLS);
tfx->gageTen = gageAnswerPointer(tfx->gtx, tfx->pvl,
tenDwiGageTensorLLS);
tfx->gageTen2 = NULL;
break;
case tenDwiFiberType2Evec0:
GAGE_QUERY_ITEM_ON(tfx->query, tenDwiGage2TensorPeled);
tfx->gageTen = NULL;
tfx->gageTen2 = gageAnswerPointer(tfx->gtx, tfx->pvl,
tenDwiGage2TensorPeled);
break;
case tenDwiFiberType12BlendEvec0:
GAGE_QUERY_ITEM_ON(tfx->query, tenDwiGageTensorLLS);
tfx->gageTen = gageAnswerPointer(tfx->gtx, tfx->pvl,
tenDwiGageTensorLLS);
GAGE_QUERY_ITEM_ON(tfx->query, tenDwiGage2TensorPeled);
tfx->gageTen2 = gageAnswerPointer(tfx->gtx, tfx->pvl,
tenDwiGage2TensorPeled);
break;
default:
sprintf(err, "%s: unimplemented %s %d", me,
tenDwiFiberType->name, ftype);
biffAdd(TEN, err); return 1;
break;
}
tfx->gageEval = NULL;
tfx->gageEvec = NULL;
} else {
/* working with tensor volume */
switch(ftype) {
case tenFiberTypeEvec0:
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEvec0);
/* HEY: COPY AND PASTE */
tfx->gageEvec
= gageAnswerPointer(tfx->gtx, tfx->pvl,
(tenFiberTypeEvec0 == tfx->fiberType
? tenGageEvec0
: (tenFiberTypeEvec1 == tfx->fiberType
? tenGageEvec1
: tenGageEvec2)));
break;
case tenFiberTypeEvec1:
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEvec1);
/* HEY: COPY AND PASTE */
tfx->gageEvec
= gageAnswerPointer(tfx->gtx, tfx->pvl,
(tenFiberTypeEvec0 == tfx->fiberType
? tenGageEvec0
: (tenFiberTypeEvec1 == tfx->fiberType
? tenGageEvec1
: tenGageEvec2)));
break;
case tenFiberTypeEvec2:
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEvec2);
/* HEY: COPY AND PASTE */
tfx->gageEvec
= gageAnswerPointer(tfx->gtx, tfx->pvl,
(tenFiberTypeEvec0 == ftype
? tenGageEvec0
: (tenFiberTypeEvec1 == ftype
? tenGageEvec1
: tenGageEvec2)));
break;
case tenFiberTypeTensorLine:
GAGE_QUERY_ITEM_ON(tfx->query, tenGageTensor);
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEval0);
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEval1);
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEval2);
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEvec0);
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEvec1);
GAGE_QUERY_ITEM_ON(tfx->query, tenGageEvec2);
break;
case tenFiberTypePureLine:
GAGE_QUERY_ITEM_ON(tfx->query, tenGageTensor);
break;
case tenFiberTypeZhukov:
sprintf(err, "%s: sorry, Zhukov oriented tensors not implemented", me);
biffAdd(TEN, err); return 1;
break;
default:
sprintf(err, "%s: fiber type %d not recognized", me, ftype);
biffAdd(TEN, err); return 1;
break;
} /* switch */
if (tenFiberTypeEvec0 == ftype
|| tenFiberTypeEvec1 == ftype
|| tenFiberTypeEvec2 == ftype
|| tenFiberTypeTensorLine == ftype) {
tfx->gageTen = gageAnswerPointer(tfx->gtx, tfx->pvl, tenGageTensor);
tfx->gageEval = gageAnswerPointer(tfx->gtx, tfx->pvl, tenGageEval0);
tfx->gageEvec
= gageAnswerPointer(tfx->gtx, tfx->pvl,
(tenFiberTypeEvec0 == ftype
? tenGageEvec0
: (tenFiberTypeEvec1 == ftype
? tenGageEvec1
: (tenFiberTypeEvec2 == ftype
? tenGageEvec2
: tenGageEvec))));
tfx->gageTen2 = NULL;
}
tfx->ten2Which = 0;
}
tfx->fiberType = ftype;
return 0;
}
pullTask *
_pullTaskNew(pullContext *pctx, int threadIdx) {
char me[]="_pullTaskNew", err[BIFF_STRLEN];
pullTask *task;
unsigned int ii, offset;
task = (pullTask *)calloc(1, sizeof(pullTask));
if (!task) {
sprintf(err, "%s: couldn't allocate task", me);
biffAdd(PULL, err); return NULL;
}
task->pctx = pctx;
for (ii=0; ii<pctx->volNum; ii++) {
if (!(task->vol[ii] = _pullVolumeCopy(pctx->vol[ii]))) {
sprintf(err, "%s: trouble copying vol %u/%u", me, ii, pctx->volNum);
biffAdd(PULL, err); return NULL;
}
}
if (0) {
gagePerVolume *pvl;
const double *ans;
double pos[3];
int gret;
for (ii=0; ii<pctx->volNum; ii++) {
pvl = task->vol[ii]->gctx->pvl[0];
fprintf(stderr, "!%s: vol[%u] query:\n", me, ii);
gageQueryPrint(stderr, pvl->kind, pvl->query);
ans = gageAnswerPointer(task->vol[ii]->gctx, pvl, gageSclValue);
ELL_3V_SET(pos, 0.6, 0.6, 0.3);
gret = gageProbeSpace(task->vol[ii]->gctx, pos[0], pos[1], pos[2],
AIR_FALSE, AIR_TRUE);
fprintf(stderr, "!%s: (%d) val(%g,%g,%g) = %g\n", me, gret,
pos[0], pos[1], pos[2], *ans);
ELL_3V_SET(pos, 0.5, 0.0, 0.0);
gret = gageProbeSpace(task->vol[ii]->gctx, pos[0], pos[1], pos[2],
AIR_FALSE, AIR_TRUE);
fprintf(stderr, "!%s: (%d) val(%g,%g,%g) = %g\n", me, gret,
pos[0], pos[1], pos[2], *ans);
}
}
offset = 0;
for (ii=0; ii<=PULL_INFO_MAX; ii++) {
unsigned int volIdx;
if (pctx->ispec[ii]) {
volIdx = pctx->ispec[ii]->volIdx;
task->ans[ii] = gageAnswerPointer(task->vol[volIdx]->gctx,
task->vol[volIdx]->gpvl,
pctx->ispec[ii]->item);
fprintf(stderr, "!%s: task->ans[%u] = %p\n", me, ii, task->ans[ii]);
} else {
task->ans[ii] = NULL;
}
}
if (pctx->threadNum > 1) {
task->thread = airThreadNew();
}
task->threadIdx = threadIdx;
task->rng = airRandMTStateNew(pctx->rngSeed + threadIdx);
task->pointBuffer = pullPointNew(pctx);
pctx->idtagNext = 0; /* because pullPointNew incremented it */
task->neighPoint = AIR_CAST(pullPoint **, calloc(_PULL_NEIGH_MAXNUM,
sizeof(pullPoint*)));
task->returnPtr = NULL;
task->stuckNum = 0;
return task;
}
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
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, done[13];
Nrrd *nin, *nblur, *nout;
NrrdKernelSpec *kb0, *kb1, *k00, *k11, *k22;
NrrdResampleContext *rsmc;
int E;
unsigned int sx, sy, sz, xi, yi, zi, ai;
gageContext *ctx;
gagePerVolume *pvl;
const double *gvec, *gmag, *evec0, *eval;
double (*ins)(void *v, size_t I, double d);
double (*lup)(const void *v, size_t I);
double dotmax, dotpow, gmmax, evalshift, gmpow, _dotmax, _gmmax, scl, clamp;
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 volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "kb0", "kernel", airTypeOther, 1, 1, &kb0,
"guass:3,5", "kernel to use for pre-process blurring",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "kb1", "kernel", airTypeOther, 1, 1, &kb1,
"cubic:1.5,1,0", "kernel to use for pos-process blurring",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &k00,
"cubic:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &k11,
"cubicd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "dotmax", "dot", airTypeDouble, 1, 1, &dotmax, "5",
"max effective value of dot(gvec, evec0)");
hestOptAdd(&hopt, "evs", "shift", airTypeDouble, 1, 1, &evalshift, "0",
"negative shift to avoid changing mostly flat regions");
hestOptAdd(&hopt, "clamp", "clamp", airTypeDouble, 1, 1, &clamp, "nan",
"if it exists, data value can't be forced below this");
hestOptAdd(&hopt, "dotpow", "pow", airTypeDouble, 1, 1, &dotpow, "1",
"exponent for dot");
hestOptAdd(&hopt, "gmmax", "dot", airTypeDouble, 1, 1, &gmmax, "2",
"max effective value of gmag");
hestOptAdd(&hopt, "gmpow", "pow", airTypeDouble, 1, 1, &gmpow, "1",
"exponent for gmag");
hestOptAdd(&hopt, "scl", "scale", airTypeDouble, 1, 1, &scl, "0.1",
"how much to scale hack to decrease input value");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"fixed volume output");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, vhInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!( 3 == nin->dim
&& nrrdTypeBlock != nin->type )) {
fprintf(stderr, "%s: need a 3-D scalar nrrd (not %u-D %s)", me,
nin->dim, airEnumStr(nrrdType, nin->type));
airMopError(mop); return 1;
}
nblur = nrrdNew();
airMopAdd(mop, nblur, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nblur, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
fprintf(stderr, "%s: pre-blurring ... ", me);
fflush(stderr);
rsmc = nrrdResampleContextNew();
airMopAdd(mop, rsmc, (airMopper)nrrdResampleContextNix, airMopAlways);
E = AIR_FALSE;
if (!E) E |= nrrdResampleDefaultCenterSet(rsmc, nrrdCenterCell);
if (!E) E |= nrrdResampleNrrdSet(rsmc, nin);
for (ai=0; ai<3; ai++) {
if (!E) E |= nrrdResampleKernelSet(rsmc, ai, kb0->kernel, kb0->parm);
if (!E) E |= nrrdResampleSamplesSet(rsmc, ai, nin->axis[ai].size);
if (!E) E |= nrrdResampleRangeFullSet(rsmc, ai);
}
if (!E) E |= nrrdResampleBoundarySet(rsmc, nrrdBoundaryBleed);
if (!E) E |= nrrdResampleTypeOutSet(rsmc, nrrdTypeDefault);
if (!E) E |= nrrdResampleRenormalizeSet(rsmc, AIR_TRUE);
if (!E) E |= nrrdResampleExecute(rsmc, nblur);
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
fprintf(stderr, "done.\n");
ctx = gageContextNew();
airMopAdd(mop, ctx, (airMopper)gageContextNix, airMopAlways);
gageParmSet(ctx, gageParmRenormalize, AIR_TRUE);
gageParmSet(ctx, gageParmCheckIntegrals, AIR_TRUE);
E = 0;
if (!E) E |= !(pvl = gagePerVolumeNew(ctx, nblur, gageKindScl));
if (!E) E |= gagePerVolumeAttach(ctx, pvl);
if (!E) E |= gageKernelSet(ctx, gageKernel00, k00->kernel, k00->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel11, k11->kernel, k11->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel22, k22->kernel, k22->parm);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradVec);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradMag);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclHessEvec0);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclHessEval);
if (!E) E |= gageUpdate(ctx);
if (E) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
gvec = gageAnswerPointer(ctx, pvl, gageSclGradVec);
gmag = gageAnswerPointer(ctx, pvl, gageSclGradMag);
evec0 = gageAnswerPointer(ctx, pvl, gageSclHessEvec0);
eval = gageAnswerPointer(ctx, pvl, gageSclHessEval);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
if (!(nout->type == nin->type && nblur->type == nin->type)) {
fprintf(stderr, "%s: whoa, types (%s %s %s) not all equal\n", me,
airEnumStr(nrrdType, nin->type),
airEnumStr(nrrdType, nblur->type),
airEnumStr(nrrdType, nout->type));
}
ins = nrrdDInsert[nout->type];
lup = nrrdDLookup[nout->type];
sx = nin->axis[0].size;
sy = nin->axis[1].size;
sz = nin->axis[2].size;
gageProbe(ctx, 0, 0, 0);
_dotmax = ELL_3V_DOT(gvec, evec0);
_gmmax = *gmag;
fprintf(stderr, "%s: hacking ", me);
fflush(stderr);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
fflush(stderr);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
size_t si;
double dot, evl, gm, shift, in, out, mode;
gageProbe(ctx, xi, yi, zi);
si = xi + sx*(yi + sy*zi);
dot = ELL_3V_DOT(gvec, evec0);
_dotmax = AIR_MAX(_dotmax, dot);
dot = AIR_ABS(dot);
dot = 1 - AIR_MIN(dot, dotmax)/dotmax;
dot = pow(dot, dotpow);
evl = AIR_MAX(0, eval[0] - evalshift);
mode = airMode3_d(eval);
evl *= AIR_AFFINE(-1, mode, 1, 0, 1);
_gmmax = AIR_MAX(_gmmax, *gmag);
gm = 1 - AIR_MIN(*gmag, gmmax)/gmmax;
gm = pow(gm, gmpow);
shift = scl*gm*evl*dot;
if (AIR_EXISTS(clamp)) {
in = lup(nin->data, si);
out = in - shift;
out = AIR_MAX(out, clamp);
shift = AIR_MAX(0, in - out);
}
ins(nout->data, si, shift);
}
}
}
fprintf(stderr, "\n");
fprintf(stderr, "%s: max dot seen: %g\n", me, _dotmax);
fprintf(stderr, "%s: max gm seen: %g\n", me, _gmmax);
fprintf(stderr, "%s: post-blurring ... ", me);
fflush(stderr);
E = AIR_FALSE;
if (!E) E |= nrrdResampleNrrdSet(rsmc, nout);
for (ai=0; ai<3; ai++) {
if (!E) E |= nrrdResampleKernelSet(rsmc, ai, kb1->kernel, kb1->parm);
if (!E) E |= nrrdResampleSamplesSet(rsmc, ai, nout->axis[ai].size);
if (!E) E |= nrrdResampleRangeFullSet(rsmc, ai);
}
if (!E) E |= nrrdResampleExecute(rsmc, nblur);
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
fprintf(stderr, "done.\n");
for (zi=0; zi<sz; zi++) {
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
size_t si;
double in, shift;
si = xi + sx*(yi + sy*zi);
in = lup(nin->data, si);
shift = lup(nblur->data, si);
ins(nout->data, si, in - shift);
}
}
}
if (nrrdSave(outS, nout, 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);
}
