int
probeParseKind(void *ptr, char *str, char err[AIR_STRLEN_HUGE]) {
char me[] = "probeParseKind";
gageKind **kindP;
if (!(ptr && str)) {
sprintf(err, "%s: got NULL pointer", me);
return 1;
}
kindP = (gageKind **)ptr;
airToLower(str);
if (!strcmp(gageKindScl->name, str)) {
*kindP = gageKindScl;
} else if (!strcmp(gageKindVec->name, str)) {
*kindP = gageKindVec;
} else if (!strcmp(tenGageKind->name, str)) {
*kindP = tenGageKind;
} else if (!strcmp(TEN_DWI_GAGE_KIND_NAME, str)) {
*kindP = tenDwiGageKindNew();
} else {
sprintf(err, "%s: not \"%s\", \"%s\", \"%s\", or \"%s\"", me,
gageKindScl->name, gageKindVec->name,
tenGageKind->name, TEN_DWI_GAGE_KIND_NAME);
return 1;
}
return 0;
}
int
probeParseKind(void *ptr, char *str, char err[AIR_STRLEN_HUGE]) {
char me[] = "probeParseKind";
gageKind **kindP;
if (!(ptr && str)) {
sprintf(err, "%s: got NULL pointer", me);
return 1;
}
kindP = (gageKind **)ptr;
airToLower(str);
if (!strcmp("scalar", str)) {
*kindP = gageKindScl;
} else if (!strcmp("vector", str)) {
*kindP = gageKindVec;
} else if (!strcmp("tensor", str)) {
*kindP = tenGageKind;
} else if (!strcmp("dwi", str)) {
*kindP = tenDwiGageKindNew();
} else {
sprintf(err, "%s: not \"scalar\", \"vector\", \"tensor\", or \"dwi\"", me);
return 1;
}
return 0;
}
gageKind *
_meetGageKindParse(const char *_str, int constOnly) {
char *str;
gageKind *ret;
if (!_str) {
return NULL;
}
str = airToLower(airStrdup(_str));
if (!str) {
return NULL;
}
if (!strcmp(gageKindScl->name, str)) {
ret = gageKindScl;
} else if (!strcmp(gageKindVec->name, str)) {
ret = gageKindVec;
} else if (!strcmp(tenGageKind->name, str)) {
ret = tenGageKind;
} else if (!constOnly && !strcmp(TEN_DWI_GAGE_KIND_NAME, str)) {
ret = tenDwiGageKindNew();
} else {
ret = NULL;
}
airFree(str);
return ret;
}
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;
}