void gageShapeBoundingBox(double min[3], double max[3], const gageShape *shape) { /* static const char me[]="gageShapeBoundingBox"; */ double minIdx[3], maxIdx[3], cornerIdx[8][3], tmp[3]; unsigned int ii; if (!( min && max && shape )) { return; } if (nrrdCenterNode == shape->center) { ELL_3V_SET(minIdx, 0, 0, 0); ELL_3V_SET(maxIdx, shape->size[0]-1, shape->size[1]-1, shape->size[2]-1); } else { ELL_3V_SET(minIdx, -0.5, -0.5, -0.5); ELL_3V_SET(maxIdx, shape->size[0]-0.5, shape->size[1]-0.5, shape->size[2]-0.5); } ELL_3V_SET(cornerIdx[0], minIdx[0], minIdx[1], minIdx[2]); ELL_3V_SET(cornerIdx[1], maxIdx[0], minIdx[1], minIdx[2]); ELL_3V_SET(cornerIdx[2], minIdx[0], maxIdx[1], minIdx[2]); ELL_3V_SET(cornerIdx[3], maxIdx[0], maxIdx[1], minIdx[2]); ELL_3V_SET(cornerIdx[4], minIdx[0], minIdx[1], maxIdx[2]); ELL_3V_SET(cornerIdx[5], maxIdx[0], minIdx[1], maxIdx[2]); ELL_3V_SET(cornerIdx[6], minIdx[0], maxIdx[1], maxIdx[2]); ELL_3V_SET(cornerIdx[7], maxIdx[0], maxIdx[1], maxIdx[2]); gageShapeItoW(shape, tmp, cornerIdx[0]); ELL_3V_COPY(min, tmp); ELL_3V_COPY(max, tmp); for (ii=1; ii<8; ii++) { gageShapeItoW(shape, tmp, cornerIdx[ii]); ELL_3V_MIN(min, min, tmp); ELL_3V_MAX(max, max, tmp); } return; }
int tenGlyphGen(limnObject *glyphsLimn, echoScene *glyphsEcho, tenGlyphParm *parm, const Nrrd *nten, const Nrrd *npos, const Nrrd *nslc) { static const char me[]="tenGlyphGen"; gageShape *shape; airArray *mop; float *tdata, eval[3], evec[9], *cvec, rotEvec[9], mA_f[16], absEval[3], glyphScl[3]; double pI[3], pW[3], cl, cp, sRot[16], mA[16], mB[16], msFr[9], tmpvec[3], R, G, B, qA, qB, qC, glyphAniso, sliceGray; unsigned int duh; int slcCoord[3], idx, glyphIdx, axis, numGlyphs, svRGBAfl=AIR_FALSE; limnLook *look; int lookIdx; echoObject *eglyph, *inst, *list=NULL, *split, *esquare; echoPos_t eM[16], originOffset[3], edge0[3], edge1[3]; char stmp[AIR_STRLEN_SMALL]; /* int eret; double tmp1[3], tmp2[3]; */ if (!( (glyphsLimn || glyphsEcho) && nten && parm)) { biffAddf(TEN, "%s: got NULL pointer", me); return 1; } mop = airMopNew(); shape = gageShapeNew(); shape->defaultCenter = nrrdCenterCell; airMopAdd(mop, shape, (airMopper)gageShapeNix, airMopAlways); if (npos) { if (!( 2 == nten->dim && 7 == nten->axis[0].size )) { biffAddf(TEN, "%s: nten isn't 2-D 7-by-N array", me); airMopError(mop); return 1; } if (!( 2 == npos->dim && 3 == npos->axis[0].size && nten->axis[1].size == npos->axis[1].size )) { biffAddf(TEN, "%s: npos isn't 2-D 3-by-%s array", me, airSprintSize_t(stmp, nten->axis[1].size)); airMopError(mop); return 1; } if (!( nrrdTypeFloat == nten->type && nrrdTypeFloat == npos->type )) { biffAddf(TEN, "%s: nten and npos must be %s, not %s and %s", me, airEnumStr(nrrdType, nrrdTypeFloat), airEnumStr(nrrdType, nten->type), airEnumStr(nrrdType, npos->type)); airMopError(mop); return 1; } } else { if (tenTensorCheck(nten, nrrdTypeFloat, AIR_TRUE, AIR_TRUE)) { biffAddf(TEN, "%s: didn't get a valid DT volume", me); airMopError(mop); return 1; } } if (tenGlyphParmCheck(parm, nten, npos, nslc)) { biffAddf(TEN, "%s: trouble", me); airMopError(mop); return 1; } if (!npos) { if (gageShapeSet(shape, nten, tenGageKind->baseDim)) { biffMovef(TEN, GAGE, "%s: trouble", me); airMopError(mop); return 1; } } if (parm->doSlice) { ELL_3V_COPY(edge0, shape->spacing); ELL_3V_COPY(edge1, shape->spacing); edge0[parm->sliceAxis] = edge1[parm->sliceAxis] = 0.0; switch(parm->sliceAxis) { case 0: edge0[1] = edge1[2] = 0; ELL_4M_ROTATE_Y_SET(sRot, AIR_PI/2); break; case 1: edge0[0] = edge1[2] = 0; ELL_4M_ROTATE_X_SET(sRot, AIR_PI/2); break; case 2: default: edge0[0] = edge1[1] = 0; ELL_4M_IDENTITY_SET(sRot); break; } ELL_3V_COPY(originOffset, shape->spacing); ELL_3V_SCALE(originOffset, -0.5, originOffset); originOffset[parm->sliceAxis] *= -2*parm->sliceOffset; } if (glyphsLimn) { /* create limnLooks for diffuse and ambient-only shading */ /* ??? */ /* hack: save old value of setVertexRGBAFromLook, and set to true */ svRGBAfl = glyphsLimn->setVertexRGBAFromLook; glyphsLimn->setVertexRGBAFromLook = AIR_TRUE; } if (glyphsEcho) { list = echoObjectNew(glyphsEcho, echoTypeList); } if (npos) { numGlyphs = AIR_UINT(nten->axis[1].size); } else { numGlyphs = shape->size[0] * shape->size[1] * shape->size[2]; } /* find measurement frame transform */ if (3 == nten->spaceDim && AIR_EXISTS(nten->measurementFrame[0][0])) { /* msFr nten->measurementFrame ** 0 1 2 [0][0] [1][0] [2][0] ** 3 4 5 [0][1] [1][1] [2][1] ** 6 7 8 [0][2] [1][2] [2][2] */ msFr[0] = nten->measurementFrame[0][0]; msFr[3] = nten->measurementFrame[0][1]; msFr[6] = nten->measurementFrame[0][2]; msFr[1] = nten->measurementFrame[1][0]; msFr[4] = nten->measurementFrame[1][1]; msFr[7] = nten->measurementFrame[1][2]; msFr[2] = nten->measurementFrame[2][0]; msFr[5] = nten->measurementFrame[2][1]; msFr[8] = nten->measurementFrame[2][2]; } else { ELL_3M_IDENTITY_SET(msFr); } for (idx=0; idx<numGlyphs; idx++) { tdata = (float*)(nten->data) + 7*idx; if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: hello %g %g %g %g %g %g %g\n", me, idx, numGlyphs, tdata[0], tdata[1], tdata[2], tdata[3], tdata[4], tdata[5], tdata[6]); } if (!( TEN_T_EXISTS(tdata) )) { /* there's nothing we can do here */ if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: non-existent data\n", me, idx, numGlyphs); } continue; } if (npos) { ELL_3V_COPY(pW, (float*)(npos->data) + 3*idx); if (!( AIR_EXISTS(pW[0]) && AIR_EXISTS(pW[1]) && AIR_EXISTS(pW[2]) )) { /* position doesn't exist- perhaps because its from the push library, which might kill points by setting coords to nan */ continue; } } else { NRRD_COORD_GEN(pI, shape->size, 3, idx); /* this does take into account full orientation */ gageShapeItoW(shape, pW, pI); if (parm->nmask) { if (!( nrrdFLookup[parm->nmask->type](parm->nmask->data, idx) >= parm->maskThresh )) { if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: doesn't meet mask thresh\n", me, idx, numGlyphs); } continue; } } } tenEigensolve_f(eval, evec, tdata); /* transform eigenvectors by measurement frame */ ELL_3MV_MUL(tmpvec, msFr, evec + 0); ELL_3V_COPY_TT(evec + 0, float, tmpvec); ELL_3MV_MUL(tmpvec, msFr, evec + 3); ELL_3V_COPY_TT(evec + 3, float, tmpvec); ELL_3MV_MUL(tmpvec, msFr, evec + 6); ELL_3V_COPY_TT(evec + 6, float, tmpvec); ELL_3V_CROSS(tmpvec, evec + 0, evec + 3); if (0 > ELL_3V_DOT(tmpvec, evec + 6)) { ELL_3V_SCALE(evec + 6, -1, evec + 6); } ELL_3M_TRANSPOSE(rotEvec, evec); if (parm->doSlice && pI[parm->sliceAxis] == parm->slicePos) { /* set sliceGray */ if (nslc) { /* we aren't masked by confidence, as anisotropy slice is */ for (duh=0; duh<parm->sliceAxis; duh++) { slcCoord[duh] = (int)(pI[duh]); } for (duh=duh<parm->sliceAxis; duh<2; duh++) { slcCoord[duh] = (int)(pI[duh+1]); } /* HEY: GLK has no idea what's going here */ slcCoord[0] = (int)(pI[0]); slcCoord[1] = (int)(pI[1]); slcCoord[2] = (int)(pI[2]); sliceGray = nrrdFLookup[nslc->type](nslc->data, slcCoord[0] + nslc->axis[0].size*slcCoord[1]); } else { if (!( tdata[0] >= parm->confThresh )) { if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d (slice): conf %g < thresh %g\n", me, idx, numGlyphs, tdata[0], parm->confThresh); } continue; } sliceGray = tenAnisoEval_f(eval, parm->sliceAnisoType); } if (parm->sliceGamma > 0) { sliceGray = AIR_AFFINE(0, sliceGray, 1, parm->sliceBias, 1); sliceGray = pow(sliceGray, 1.0/parm->sliceGamma); } else { sliceGray = AIR_AFFINE(0, sliceGray, 1, 0, 1-parm->sliceBias); sliceGray = 1.0 - pow(sliceGray, -1.0/parm->sliceGamma); } /* make slice contribution */ /* HEY: this is *NOT* aware of shape->fromOrientation */ if (glyphsLimn) { lookIdx = limnObjectLookAdd(glyphsLimn); look = glyphsLimn->look + lookIdx; ELL_4V_SET_TT(look->rgba, float, sliceGray, sliceGray, sliceGray, 1); ELL_3V_SET(look->kads, 1, 0, 0); look->spow = 0; glyphIdx = limnObjectSquareAdd(glyphsLimn, lookIdx); ELL_4M_IDENTITY_SET(mA); ell_4m_post_mul_d(mA, sRot); if (!npos) { ELL_4M_SCALE_SET(mB, shape->spacing[0], shape->spacing[1], shape->spacing[2]); } ell_4m_post_mul_d(mA, mB); ELL_4M_TRANSLATE_SET(mB, pW[0], pW[1], pW[2]); ell_4m_post_mul_d(mA, mB); ELL_4M_TRANSLATE_SET(mB, originOffset[0], originOffset[1], originOffset[2]); ell_4m_post_mul_d(mA, mB); ELL_4M_COPY_TT(mA_f, float, mA); limnObjectPartTransform(glyphsLimn, glyphIdx, mA_f); } if (glyphsEcho) { esquare = echoObjectNew(glyphsEcho,echoTypeRectangle); ELL_3V_ADD2(((echoRectangle*)esquare)->origin, pW, originOffset); ELL_3V_COPY(((echoRectangle*)esquare)->edge0, edge0); ELL_3V_COPY(((echoRectangle*)esquare)->edge1, edge1); echoColorSet(esquare, AIR_CAST(echoCol_t, sliceGray), AIR_CAST(echoCol_t, sliceGray), AIR_CAST(echoCol_t, sliceGray), 1); /* this is pretty arbitrary- but I want shadows to have some effect. Previously, the material was all ambient: (A,D,S) = (1,0,0), which avoided all shadow effects. */ echoMatterPhongSet(glyphsEcho, esquare, 0.4f, 0.6f, 0, 40); echoListAdd(list, esquare); } } if (parm->onlyPositive) { if (eval[2] < 0) { /* didn't have all positive eigenvalues, its outta here */ if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: not all evals %g %g %g > 0\n", me, idx, numGlyphs, eval[0], eval[1], eval[2]); } continue; } } if (!( tdata[0] >= parm->confThresh )) { if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: conf %g < thresh %g\n", me, idx, numGlyphs, tdata[0], parm->confThresh); } continue; } if (!( tenAnisoEval_f(eval, parm->anisoType) >= parm->anisoThresh )) { if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: aniso[%d] %g < thresh %g\n", me, idx, numGlyphs, parm->anisoType, tenAnisoEval_f(eval, parm->anisoType), parm->anisoThresh); } continue; } glyphAniso = tenAnisoEval_f(eval, parm->colAnisoType); /* fprintf(stderr, "%s: eret = %d; evals = %g %g %g\n", me, eret, eval[0], eval[1], eval[2]); ELL_3V_CROSS(tmp1, evec+0, evec+3); tmp2[0] = ELL_3V_LEN(tmp1); ELL_3V_CROSS(tmp1, evec+0, evec+6); tmp2[1] = ELL_3V_LEN(tmp1); ELL_3V_CROSS(tmp1, evec+3, evec+6); tmp2[2] = ELL_3V_LEN(tmp1); fprintf(stderr, "%s: crosses = %g %g %g\n", me, tmp2[0], tmp2[1], tmp2[2]); */ /* set transform (in mA) */ ELL_3V_ABS(absEval, eval); ELL_4M_IDENTITY_SET(mA); /* reset */ ELL_3V_SCALE(glyphScl, parm->glyphScale, absEval); /* scale by evals */ ELL_4M_SCALE_SET(mB, glyphScl[0], glyphScl[1], glyphScl[2]); ell_4m_post_mul_d(mA, mB); ELL_43M_INSET(mB, rotEvec); /* rotate by evecs */ ell_4m_post_mul_d(mA, mB); ELL_4M_TRANSLATE_SET(mB, pW[0], pW[1], pW[2]); /* translate */ ell_4m_post_mul_d(mA, mB); /* set color (in R,G,B) */ cvec = evec + 3*(AIR_CLAMP(0, parm->colEvec, 2)); R = AIR_ABS(cvec[0]); /* standard mapping */ G = AIR_ABS(cvec[1]); B = AIR_ABS(cvec[2]); /* desaturate by colMaxSat */ R = AIR_AFFINE(0.0, parm->colMaxSat, 1.0, parm->colIsoGray, R); G = AIR_AFFINE(0.0, parm->colMaxSat, 1.0, parm->colIsoGray, G); B = AIR_AFFINE(0.0, parm->colMaxSat, 1.0, parm->colIsoGray, B); /* desaturate some by anisotropy */ R = AIR_AFFINE(0.0, parm->colAnisoModulate, 1.0, R, AIR_AFFINE(0.0, glyphAniso, 1.0, parm->colIsoGray, R)); G = AIR_AFFINE(0.0, parm->colAnisoModulate, 1.0, G, AIR_AFFINE(0.0, glyphAniso, 1.0, parm->colIsoGray, G)); B = AIR_AFFINE(0.0, parm->colAnisoModulate, 1.0, B, AIR_AFFINE(0.0, glyphAniso, 1.0, parm->colIsoGray, B)); /* clamp and do gamma */ R = AIR_CLAMP(0.0, R, 1.0); G = AIR_CLAMP(0.0, G, 1.0); B = AIR_CLAMP(0.0, B, 1.0); R = pow(R, parm->colGamma); G = pow(G, parm->colGamma); B = pow(B, parm->colGamma); /* find axis, and superquad exponents qA and qB */ if (eval[2] > 0) { /* all evals positive */ cl = AIR_MIN(0.99, tenAnisoEval_f(eval, tenAniso_Cl1)); cp = AIR_MIN(0.99, tenAnisoEval_f(eval, tenAniso_Cp1)); if (cl > cp) { axis = 0; qA = pow(1-cp, parm->sqdSharp); qB = pow(1-cl, parm->sqdSharp); } else { axis = 2; qA = pow(1-cl, parm->sqdSharp); qB = pow(1-cp, parm->sqdSharp); } qC = qB; } else if (eval[0] < 0) { /* all evals negative */ float aef[3]; aef[0] = absEval[2]; aef[1] = absEval[1]; aef[2] = absEval[0]; cl = AIR_MIN(0.99, tenAnisoEval_f(aef, tenAniso_Cl1)); cp = AIR_MIN(0.99, tenAnisoEval_f(aef, tenAniso_Cp1)); if (cl > cp) { axis = 2; qA = pow(1-cp, parm->sqdSharp); qB = pow(1-cl, parm->sqdSharp); } else { axis = 0; qA = pow(1-cl, parm->sqdSharp); qB = pow(1-cp, parm->sqdSharp); } qC = qB; } else { #define OOSQRT2 0.70710678118654752440 #define OOSQRT3 0.57735026918962576451 /* double poleA[3]={OOSQRT3, OOSQRT3, OOSQRT3}; */ double poleB[3]={1, 0, 0}; double poleC[3]={OOSQRT2, OOSQRT2, 0}; double poleD[3]={OOSQRT3, -OOSQRT3, -OOSQRT3}; double poleE[3]={OOSQRT2, 0, -OOSQRT2}; double poleF[3]={OOSQRT3, OOSQRT3, -OOSQRT3}; double poleG[3]={0, -OOSQRT2, -OOSQRT2}; double poleH[3]={0, 0, -1}; /* double poleI[3]={-OOSQRT3, -OOSQRT3, -OOSQRT3}; */ double funk[3]={0,4,2}, thrn[3]={1,4,4}; double octa[3]={0,2,2}, cone[3]={1,2,2}; double evalN[3], tmp, bary[3]; double qq[3]; ELL_3V_NORM(evalN, eval, tmp); if (eval[1] >= -eval[2]) { /* inside B-F-C */ ell_3v_barycentric_spherical_d(bary, poleB, poleF, poleC, evalN); ELL_3V_SCALE_ADD3(qq, bary[0], octa, bary[1], thrn, bary[2], cone); axis = 2; } else if (eval[0] >= -eval[2]) { /* inside B-D-F */ if (eval[1] >= 0) { /* inside B-E-F */ ell_3v_barycentric_spherical_d(bary, poleB, poleE, poleF, evalN); ELL_3V_SCALE_ADD3(qq, bary[0], octa, bary[1], funk, bary[2], thrn); axis = 2; } else { /* inside B-D-E */ ell_3v_barycentric_spherical_d(bary, poleB, poleD, poleE, evalN); ELL_3V_SCALE_ADD3(qq, bary[0], cone, bary[1], thrn, bary[2], funk); axis = 0; } } else if (eval[0] < -eval[1]) { /* inside D-G-H */ ell_3v_barycentric_spherical_d(bary, poleD, poleG, poleH, evalN); ELL_3V_SCALE_ADD3(qq, bary[0], thrn, bary[1], cone, bary[2], octa); axis = 0; } else if (eval[1] < 0) { /* inside E-D-H */ ell_3v_barycentric_spherical_d(bary, poleE, poleD, poleH, evalN); ELL_3V_SCALE_ADD3(qq, bary[0], funk, bary[1], thrn, bary[2], octa); axis = 0; } else { /* inside F-E-H */ ell_3v_barycentric_spherical_d(bary, poleF, poleE, poleH, evalN); ELL_3V_SCALE_ADD3(qq, bary[0], thrn, bary[1], funk, bary[2], cone); axis = 2; } qA = qq[0]; qB = qq[1]; qC = qq[2]; #undef OOSQRT2 #undef OOSQRT3 } /* add the glyph */ if (parm->verbose >= 2) { fprintf(stderr, "%s: glyph %d/%d: the glyph stays!\n", me, idx, numGlyphs); } if (glyphsLimn) { lookIdx = limnObjectLookAdd(glyphsLimn); look = glyphsLimn->look + lookIdx; ELL_4V_SET_TT(look->rgba, float, R, G, B, 1); ELL_3V_SET(look->kads, parm->ADSP[0], parm->ADSP[1], parm->ADSP[2]); look->spow = 0; switch(parm->glyphType) { case tenGlyphTypeBox: glyphIdx = limnObjectCubeAdd(glyphsLimn, lookIdx); break; case tenGlyphTypeSphere: glyphIdx = limnObjectPolarSphereAdd(glyphsLimn, lookIdx, axis, 2*parm->facetRes, parm->facetRes); break; case tenGlyphTypeCylinder: glyphIdx = limnObjectCylinderAdd(glyphsLimn, lookIdx, axis, parm->facetRes); break; case tenGlyphTypeSuperquad: default: glyphIdx = limnObjectPolarSuperquadFancyAdd(glyphsLimn, lookIdx, axis, AIR_CAST(float, qA), AIR_CAST(float, qB), AIR_CAST(float, qC), 0, 2*parm->facetRes, parm->facetRes); break; } ELL_4M_COPY_TT(mA_f, float, mA); limnObjectPartTransform(glyphsLimn, glyphIdx, mA_f); } if (glyphsEcho) { switch(parm->glyphType) { case tenGlyphTypeBox: eglyph = echoObjectNew(glyphsEcho, echoTypeCube); /* nothing else to set */ break; case tenGlyphTypeSphere: eglyph = echoObjectNew(glyphsEcho, echoTypeSphere); echoSphereSet(eglyph, 0, 0, 0, 1); break; case tenGlyphTypeCylinder: eglyph = echoObjectNew(glyphsEcho, echoTypeCylinder); echoCylinderSet(eglyph, axis); break; case tenGlyphTypeSuperquad: default: eglyph = echoObjectNew(glyphsEcho, echoTypeSuperquad); echoSuperquadSet(eglyph, axis, qA, qB); break; } echoColorSet(eglyph, AIR_CAST(echoCol_t, R), AIR_CAST(echoCol_t, G), AIR_CAST(echoCol_t, B), 1); echoMatterPhongSet(glyphsEcho, eglyph, parm->ADSP[0], parm->ADSP[1], parm->ADSP[2], parm->ADSP[3]); inst = echoObjectNew(glyphsEcho, echoTypeInstance); ELL_4M_COPY(eM, mA); echoInstanceSet(inst, eM, eglyph); echoListAdd(list, inst); } } if (glyphsLimn) { glyphsLimn->setVertexRGBAFromLook = svRGBAfl; } if (glyphsEcho) { split = echoListSplit3(glyphsEcho, list, 10); echoObjectAdd(glyphsEcho, split); } airMopOkay(mop); return 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; }