pullVolume *
pullVolumeNew() {
pullVolume *vol;
vol = AIR_CAST(pullVolume *, calloc(1, sizeof(pullVolume)));
if (vol) {
vol->name = NULL;
vol->kind = NULL;
vol->ninSingle = NULL;
vol->ninScale = NULL;
vol->scaleNum = 0;
vol->scalePos = NULL;
vol->ksp00 = nrrdKernelSpecNew();
vol->ksp11 = nrrdKernelSpecNew();
vol->ksp22 = nrrdKernelSpecNew();
vol->kspSS = nrrdKernelSpecNew();
vol->gctx = gageContextNew();
vol->gpvl = NULL;
vol->seedOnly = AIR_TRUE;
}
return vol;
}
int
_nrrdHestKernelSpecParse(void *ptr, char *str, char err[AIR_STRLEN_HUGE]) {
NrrdKernelSpec **ksP;
char me[]="_nrrdHestKernelSpecParse", *nerr;
if (!(ptr && str)) {
sprintf(err, "%s: got NULL pointer", me);
return 1;
}
ksP = (NrrdKernelSpec **)ptr;
*ksP = nrrdKernelSpecNew();
if (nrrdKernelParse(&((*ksP)->kernel), (*ksP)->parm, str)) {
nerr = biffGetDone(NRRD);
airStrcpy(err, AIR_STRLEN_HUGE, nerr);
free(nerr);
return 1;
}
return 0;
}
static
tenFiberContext *
_tenFiberContextCommonNew(const Nrrd *vol, int useDwi,
double thresh, double soft, double valueMin,
int ten1method, int ten2method) {
char me[]="_tenFiberContextCommonNew", err[BIFF_STRLEN];
tenFiberContext *tfx;
gageKind *kind;
if (!( tfx = (tenFiberContext *)calloc(1, sizeof(tenFiberContext)) )) {
sprintf(err, "%s: couldn't allocate new context", me);
biffAdd(TEN, err); return NULL;
}
if (useDwi) {
Nrrd *ngrad=NULL, *nbmat=NULL;
double bval=0;
unsigned int *skip, skipNum;
tfx->useDwi = AIR_TRUE;
/* default fiber type */
tfx->fiberType = tenDwiFiberTypeUnknown;
if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &bval, &skip, &skipNum, vol)) {
sprintf(err, "%s: trouble parsing DWI info", me );
biffAdd(TEN, err); return NULL;
}
if (skipNum) {
sprintf(err, "%s: sorry, can't do DWI skipping here", me);
biffAdd(TEN, err); return NULL;
}
kind = tenDwiGageKindNew();
if (tenDwiGageKindSet(kind,
thresh, soft, bval, valueMin,
ngrad, NULL,
ten1method, ten2method, 42)) {
sprintf(err, "%s: trouble setting DWI kind", me);
biffAdd(TEN, err); return NULL;
}
} else {
/* it should be a tensor volume */
tfx->useDwi = AIR_FALSE;
/* default fiber type */
tfx->fiberType = tenFiberTypeUnknown;
if (tenTensorCheck(vol, nrrdTypeUnknown, AIR_TRUE, AIR_TRUE)) {
sprintf(err, "%s: didn't get a tensor volume", me);
biffAdd(TEN, err); return NULL;
}
kind = tenGageKind;
}
if ( !(tfx->gtx = gageContextNew())
|| !(tfx->pvl = gagePerVolumeNew(tfx->gtx, vol, kind))
|| (gagePerVolumeAttach(tfx->gtx, tfx->pvl)) ) {
sprintf(err, "%s: gage trouble", me);
biffMove(TEN, err, GAGE); free(tfx); return NULL;
}
tfx->nin = vol;
tfx->ksp = nrrdKernelSpecNew();
if (nrrdKernelSpecParse(tfx->ksp, tenDefFiberKernel)) {
sprintf(err, "%s: couldn't parse tenDefFiberKernel \"%s\"",
me, tenDefFiberKernel);
biffMove(TEN, err, NRRD); return NULL;
}
if (tenFiberKernelSet(tfx, tfx->ksp->kernel, tfx->ksp->parm)) {
sprintf(err, "%s: couldn't set default kernel", me);
biffAdd(TEN, err); return NULL;
}
/* looks to GK like GK says that we must set some stop criterion */
tfx->intg = tenDefFiberIntg;
tfx->anisoStopType = tenDefFiberAnisoStopType;
tfx->anisoSpeedType = tenAnisoUnknown;
tfx->stop = 0;
tfx->anisoThresh = tenDefFiberAnisoThresh;
/* so I'm not using the normal default mechanism, shoot me */
tfx->anisoSpeedFunc[0] = 0;
tfx->anisoSpeedFunc[1] = 0;
tfx->anisoSpeedFunc[2] = 0;
tfx->maxNumSteps = tenDefFiberMaxNumSteps;
tfx->minNumSteps = 0;
tfx->useIndexSpace = tenDefFiberUseIndexSpace;
tfx->verbose = 0;
tfx->stepSize = tenDefFiberStepSize;
tfx->maxHalfLen = tenDefFiberMaxHalfLen;
tfx->minWholeLen = 0.0;
tfx->confThresh = 0.5; /* why do I even bother setting these- they'll
only get read if the right tenFiberStopSet has
been called, in which case they'll be set... */
tfx->minRadius = 1; /* above lament applies here as well */
tfx->minFraction = 0.5; /* and here */
tfx->wPunct = tenDefFiberWPunct;
GAGE_QUERY_RESET(tfx->query);
tfx->mframe[0] = vol->measurementFrame[0][0];
tfx->mframe[1] = vol->measurementFrame[1][0];
tfx->mframe[2] = vol->measurementFrame[2][0];
tfx->mframe[3] = vol->measurementFrame[0][1];
tfx->mframe[4] = vol->measurementFrame[1][1];
tfx->mframe[5] = vol->measurementFrame[2][1];
tfx->mframe[6] = vol->measurementFrame[0][2];
tfx->mframe[7] = vol->measurementFrame[1][2];
tfx->mframe[8] = vol->measurementFrame[2][2];
if (ELL_3M_EXISTS(tfx->mframe)) {
tfx->mframeUse = AIR_TRUE;
ELL_3M_TRANSPOSE(tfx->mframeT, tfx->mframe);
} else {
tfx->mframeUse = AIR_FALSE;
}
tfx->gageAnisoStop = NULL;
tfx->gageAnisoSpeed = NULL;
tfx->ten2AnisoStop = AIR_NAN;
/* ... don't really see the point of initializing the ten2 stuff here;
its properly done in tenFiberTraceSet() ... */
tfx->radius = AIR_NAN;
return tfx;
}
int
main(int argc, char *argv[]) {
char *me, *kS, *minS, *stepS, *maxS, *outS, *err, kstr[AIR_STRLEN_LARGE];
const NrrdKernel *k;
NrrdKernelSpec *ksp;
double parm[NRRD_KERNEL_PARMS_NUM], min, step, max, integral,
*dom_d, *ran_d;
float *dom_f, *ran_f, v, r_f, r_d;
FILE *fout;
int i, len;
airArray *mop;
me = argv[0];
if (6 != argc) {
usage(me);
}
kS = argv[1];
minS = argv[2];
stepS = argv[3];
maxS = argv[4];
outS = argv[5];
mop = airMopNew();
if (nrrdKernelParse(&k, parm, kS)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop);
exit(1);
}
ksp = nrrdKernelSpecNew();
airMopAdd(mop, ksp, (airMopper)nrrdKernelSpecNix, airMopAlways);
nrrdKernelSpecSet(ksp, k, parm);
if (nrrdKernelSpecSprint(kstr, ksp)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop);
exit(1);
}
printf("%s: printed kernel as \"%s\"\n", me, kstr);
if (3 != (sscanf(minS, "%lf", &min) +
sscanf(stepS, "%lf", &step) +
sscanf(maxS, "%lf", &max))) {
fprintf(stderr, "%s: couldn't parse \"%s\", \"%s\", \"%s\" as 3 doubles\n",
me, minS, stepS, maxS);
exit(1);
}
if (!( min <= -k->support(parm) && max >= k->support(parm) )) {
fprintf(stderr, "%s: WARNING: support=%g => lower min (%g) or raise max (%g)\n",
me, k->support(parm), min, max);
}
/* see how many values are in the interval */
len = 0;
for (v=min; v<=max; v+=step) {
len++;
}
/* allocate domain and range for both float and double */
if (!( (dom_d = (double *)calloc(len, sizeof(double))) &&
(ran_d = (double *)calloc(len, sizeof(double))) &&
(dom_f = (float *)calloc(len, sizeof(float))) &&
(ran_f = (float *)calloc(len, sizeof(float))) )) {
fprintf(stderr, "%s: PANIC: couldn't allocate buffers\n", me);
exit(1);
}
airMopAdd(mop, dom_d, airFree, airMopAlways);
airMopAdd(mop, ran_d, airFree, airMopAlways);
airMopAdd(mop, dom_f, airFree, airMopAlways);
airMopAdd(mop, ran_f, airFree, airMopAlways);
/* set values in both domains */
i=0;
for (v=min; v<=max; v+=step) {
/* note that the value stored in dom_d[i] is only a
single-precision float, so that it is really equal to dom_f[i] */
dom_d[i] = v;
dom_f[i] = v;
i++;
}
/* do the vector evaluations */
k->evalN_f(ran_f, dom_f, len, parm);
k->evalN_d(ran_d, dom_d, len, parm);
/* do the single evaluations, and make sure everything agrees */
i = 0;
integral = 0;
for (v=min; v<=max; v+=step) {
/* compare two single evaluations */
r_f = k->eval1_f(v, parm);
r_d = k->eval1_d(v, parm);
if (!CLOSE(r_f,r_d)) {
fprintf(stderr, "%s: (eval1_f(%g)== %f) != (eval1_d(%g)== %f)\n",
me, v, r_f, v, r_d);
}
/* compare single float with vector float */
if (!CLOSE(r_f,ran_f[i])) {
fprintf(stderr, "%s: (eval1_f(%g)== %f) != (evalN_f[%d]== %f)\n",
me, v, r_f, i, ran_f[i]);
}
/* compare single float with vector double */
r_d = ran_d[i];
if (!CLOSE(r_f,r_d)) {
fprintf(stderr, "%s: (eval1_f(%g)== %f) != (evalN_d[%d]== %f)\n",
me, v, r_f, i, r_d);
}
integral += step*ran_d[i];
i++;
}
if (!KINDACLOSE(integral, k->integral(parm))) {
fprintf(stderr,
"discrete integral %f != %f\n", integral, k->integral(parm));
/* not a fatal error */
}
/* it all checks out; write the file */
if (!(fout = fopen(outS, "w"))) {
fprintf(stderr, "%s: couldn't open \"%s\" for writing\n", me, outS);
exit(1);
}
for (i=0; i<=len-1; i++) {
fprintf(fout, "%g %g\n", dom_f[i], ran_f[i]);
}
fclose(fout);
fprintf(stderr, "(for matlab:)\n");
fprintf(stderr, "x = dlmread(\'%s\', \' \'); plot(x(:,1), x(:,2));\n", outS);
airMopOkay(mop);
exit(0);
}
int
main(int argc, char *argv[]) {
char *me, *kernS[2], *minS, *stepS, *maxS, *outS, *err, kstr[AIR_STRLEN_LARGE];
const NrrdKernel *kern[2];
NrrdKernelSpec *ksp[2];
double parm[NRRD_KERNEL_PARMS_NUM], min, step, max, integral,
*dom_d, *ran_d;
float *dom_f, *ran_f, val, r_f, r_d;
FILE *fout;
int i, len;
airArray *mop;
unsigned int kii;
me = argv[0];
if (!( 6 == argc || 7 == argc )) {
usage(me);
}
kernS[0] = argv[1];
minS = argv[2];
stepS = argv[3];
maxS = argv[4];
outS = argv[5];
if (7 == argc) {
kernS[1] = argv[6];
} else {
kernS[1] = NULL;
}
if (3 != (sscanf(minS, "%lf", &min) +
sscanf(stepS, "%lf", &step) +
sscanf(maxS, "%lf", &max))) {
fprintf(stderr, "%s: couldn't parse \"%s\", \"%s\", \"%s\" as 3 doubles\n",
me, minS, stepS, maxS);
exit(1);
}
mop = airMopNew();
for (kii=0; kii<=(kernS[1] ? 1 : 0); kii++) {
if (nrrdKernelParse(&(kern[kii]), parm, kernS[kii])) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: (kii %u) trouble:\n%s\n", me, kii, err);
airMopError(mop);
exit(1);
}
ksp[kii] = nrrdKernelSpecNew();
airMopAdd(mop, ksp[kii], (airMopper)nrrdKernelSpecNix, airMopAlways);
nrrdKernelSpecSet(ksp[kii], kern[kii], parm);
if (nrrdKernelSpecSprint(kstr, ksp[kii])) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop);
exit(1);
}
fprintf(stderr, "%s: printed kernel as \"%s\"\n", me, kstr);
if (!( min <= -kern[kii]->support(parm)
&& max >= kern[kii]->support(parm) )) {
fprintf(stderr, "%s: WARNING: support=%g => lower min (%g) or raise max (%g)\n",
me, kern[kii]->support(parm), min, max);
}
fprintf(stderr, "%s: support(%s) = %g\n", me, kstr, kern[kii]->support(parm));
}
/* see how many values are in the interval */
len = 0;
for (val=min; val<=max; val+=step) {
len++;
}
/* allocate domain and range for both float and double */
if (!( (dom_d = (double *)calloc(len, sizeof(double))) &&
(ran_d = (double *)calloc(len, sizeof(double))) &&
(dom_f = (float *)calloc(len, sizeof(float))) &&
(ran_f = (float *)calloc(len, sizeof(float))) )) {
fprintf(stderr, "%s: PANIC: couldn't allocate buffers\n", me);
exit(1);
}
airMopAdd(mop, dom_d, airFree, airMopAlways);
airMopAdd(mop, ran_d, airFree, airMopAlways);
airMopAdd(mop, dom_f, airFree, airMopAlways);
airMopAdd(mop, ran_f, airFree, airMopAlways);
/* set values in both domains */
i=0;
for (val=min; val<=max; val+=step) {
/* note that the value stored in dom_d[i] is only a
single-precision float, so that it is really equal to dom_f[i] */
dom_d[i] = val;
dom_f[i] = val;
i++;
}
/* do the vector evaluations */
kern[0]->evalN_f(ran_f, dom_f, len, parm);
kern[0]->evalN_d(ran_d, dom_d, len, parm);
/* do the single evaluations, and make sure everything agrees */
i = 0;
integral = 0;
for (val=min; val<=max; val+=step) {
/* compare two single evaluations */
r_f = kern[0]->eval1_f(val, parm);
r_d = kern[0]->eval1_d(val, parm);
if (!CLOSE(r_f,r_d, 0.00001)) {
fprintf(stderr, "%s: (eval1_f(%g)== %f) != (eval1_d(%g)== %f)\n",
me, val, r_f, val, r_d);
}
/* compare single float with vector float */
if (!CLOSE(r_f,ran_f[i], 0.00001)) {
fprintf(stderr, "%s: (eval1_f(%g)== %f) != (evalN_f[%d]== %f)\n",
me, val, r_f, i, ran_f[i]);
}
/* compare single float with vector double */
r_d = ran_d[i];
if (!CLOSE(r_f,r_d, 0.00001)) {
fprintf(stderr, "%s: (eval1_f(%g)== %f) != (evalN_d[%d]== %f)\n",
me, val, r_f, i, r_d);
}
integral += step*ran_d[i];
/* possibly check on given derivatives */
if (kern[1]) {
double numd;
numd = (kern[0]->eval1_d(val+step/2, parm)
- kern[0]->eval1_d(val-step/2, parm))/step;
if (!CLOSE(numd, kern[1]->eval1_d(val+step, parm), 0.005)) {
fprintf(stderr, "%s: |numerical f'(%g) %g - true %g| = %g > 0.005\n",
me, val, numd, kern[1]->eval1_d(val+step, parm),
fabs(numd - kern[1]->eval1_d(val+step, parm)));
/* exit(1); */
}
}
i++;
}
if (!CLOSE(integral, kern[0]->integral(parm), 0.0005)) {
fprintf(stderr, "%s: HEY HEY HEY HEY HEY HEY!\n", me);
fprintf(stderr,
"%s: discrete integral %f != %f\n", me, integral, kern[0]->integral(parm));
/* exit(1); */
}
/* it all checks out; write the file */
if (!(fout = airFopen(outS, stdout, "w"))) {
fprintf(stderr, "%s: couldn't open \"%s\" for writing\n", me, outS);
exit(1);
}
for (i=0; i<=len-1; i++) {
fprintf(fout, "%g %g\n", dom_f[i], ran_f[i]);
}
fclose(fout);
airMopOkay(mop);
exit(0);
}
