int
main(int argc, char *argv[]) {
char *me, *err;
FILE *file;
limnPolyData *lmpd;
AIR_UNUSED(argc);
me = argv[0];
lmpd = limnPolyDataNew();
file = fopen("in.lmpd", "r");
if (limnPolyDataReadLMPD(lmpd, file)) {
err = biffGetDone(LIMN),
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
return 1;
}
fclose(file);
file = fopen("out.vtk", "w");
if (limnPolyDataWriteVTK(file, lmpd)) {
err = biffGetDone(LIMN);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
return 1;
}
fclose(file);
return 0;
}
/* Creates an elfMaximaContext, which can then be used to find all
* maxima of a symmetric even-order 3D tensor of the given type.
* Returns NULL if type is not even-order 3D symmetric.
*
* The initial maximum sampling is at the vertices of a subdivided
* icosahedron - level=3 (321 unique directions) should be
* sufficient. Larger levels reduce the risk of missing one of two (or
* more) very close maxima, at increased computational cost. */
elfMaximaContext *elfMaximaContextNew(const tijk_type *type,
unsigned int level) {
elfMaximaContext *retval;
limnPolyData *sphere;
unsigned int vert;
if (type==NULL || type->dim!=3 || type->sym==NULL || type->order%2!=0)
return NULL; /* elfMaxima cannot be used with this tensor type */
sphere = limnPolyDataNew();
limnPolyDataIcoSphere(sphere, 0, level);
retval = (elfMaximaContext*) malloc(sizeof(elfMaximaContext));
retval->num = sphere->xyzwNum;
retval->type = type;
retval->parm = NULL;
retval->refine = 1;
/* extract neighborhood info (needed to take discrete maxima) */
limnPolyDataNeighborArray(&(retval->neighbors), &(retval->nbstride), sphere);
/* copy over vertices in single and double precision */
retval->vertices_f = (float*) malloc(sizeof(float)*3*(sphere->xyzwNum/2));
for (vert=0; vert<sphere->xyzwNum; vert+=2) {
ELL_3V_COPY(retval->vertices_f+3*(vert/2), sphere->xyzw+4*vert);
}
retval->vertices_d = NULL;
sphere=limnPolyDataNix(sphere);
return retval;
}
int
main(int argc, const char **argv) {
const char *me;
char *err;
hestOpt *hopt=NULL;
hestParm *hparm;
airArray *mop;
/* variables learned via hest */
Nrrd *nin;
float camfr[3], camat[3], camup[3], camnc, camfc, camFOV;
int camortho, hitandquit;
unsigned int camsize[2];
double isovalue, sliso, isomin, isomax;
/* boilerplate hest code */
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hparm->respFileEnable = AIR_TRUE;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
/* setting up the command-line options */
hparm->respFileEnable = AIR_TRUE;
hestOptAdd(&hopt, "i", "volume", airTypeOther, 1, 1, &nin, NULL,
"input volume to isosurface", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "v", "isovalue", airTypeDouble, 1, 1, &isovalue, "nan",
"isovalue at which to run Marching Cubes");
hestOptAdd(&hopt, "fr", "x y z", airTypeFloat, 3, 3, camfr, "3 4 5",
"look-from point");
hestOptAdd(&hopt, "at", "x y z", airTypeFloat, 3, 3, camat, "0 0 0",
"look-at point");
hestOptAdd(&hopt, "up", "x y z", airTypeFloat, 3, 3, camup, "0 0 1",
"up direction");
hestOptAdd(&hopt, "nc", "dist", airTypeFloat, 1, 1, &(camnc), "-2",
"at-relative near clipping distance");
hestOptAdd(&hopt, "fc", "dist", airTypeFloat, 1, 1, &(camfc), "2",
"at-relative far clipping distance");
hestOptAdd(&hopt, "fov", "angle", airTypeFloat, 1, 1, &(camFOV), "20",
"vertical field-of-view, in degrees. Full vertical "
"extent of image plane subtends this angle.");
hestOptAdd(&hopt, "sz", "s0 s1", airTypeUInt, 2, 2, &(camsize), "640 480",
"# samples (horz vert) of image plane. ");
hestOptAdd(&hopt, "ortho", NULL, airTypeInt, 0, 0, &(camortho), NULL,
"use orthographic instead of (the default) "
"perspective projection ");
hestOptAdd(&hopt, "haq", NULL, airTypeBool, 0, 0, &(hitandquit), NULL,
"save a screenshot rather than display the viewer");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, "demo program", AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
/* learn value range, and set initial isovalue if needed */
NrrdRange *range = nrrdRangeNewSet(nin, AIR_FALSE);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
isomin = range->min;
isomax = range->max;
if (!AIR_EXISTS(isovalue)) {
isovalue = (isomin + isomax)/2;
}
/* first, make sure we can isosurface ok */
limnPolyData *lpld = limnPolyDataNew();
seekContext *sctx = seekContextNew();
airMopAdd(mop, sctx, (airMopper)seekContextNix, airMopAlways);
sctx->pldArrIncr = nrrdElementNumber(nin);
seekVerboseSet(sctx, 0);
seekNormalsFindSet(sctx, AIR_TRUE);
if (seekDataSet(sctx, nin, NULL, 0)
|| seekTypeSet(sctx, seekTypeIsocontour)
|| seekIsovalueSet(sctx, isovalue)
|| seekUpdate(sctx)
|| seekExtract(sctx, lpld)) {
airMopAdd(mop, err=biffGetDone(SEEK), airFree, airMopAlways);
fprintf(stderr, "trouble with isosurfacing:\n%s", err);
airMopError(mop);
return 1;
}
if (!lpld->xyzwNum) {
fprintf(stderr, "%s: warning: No isocontour generated at isovalue %g\n",
me, isovalue);
}
/* then create empty scene */
Hale::init();
Hale::Scene scene;
/* then create viewer (in order to create the OpenGL context) */
Hale::Viewer viewer(camsize[0], camsize[1], "Iso", &scene);
viewer.lightDir(glm::vec3(-1.0f, 1.0f, 3.0f));
viewer.camera.init(glm::vec3(camfr[0], camfr[1], camfr[2]),
glm::vec3(camat[0], camat[1], camat[2]),
glm::vec3(camup[0], camup[1], camup[2]),
camFOV, (float)camsize[0]/camsize[1],
camnc, camfc, camortho);
viewer.refreshCB((Hale::ViewerRefresher)render);
viewer.refreshData(&viewer);
sliso = isovalue;
viewer.slider(&sliso, isomin, isomax);
viewer.current();
/* then create geometry, and add it to scene */
Hale::Polydata hply(lpld, true, // hply now owns lpld
Hale::ProgramLib(Hale::preprogramAmbDiff2SideSolid));
scene.add(&hply);
scene.drawInit();
render(&viewer);
if (hitandquit) {
seekIsovalueSet(sctx, isovalue);
seekUpdate(sctx);
seekExtract(sctx, lpld);
hply.rebuffer();
render(&viewer);
glfwWaitEvents();
render(&viewer);
viewer.snap();
Hale::done();
airMopOkay(mop);
return 0;
}
while(!Hale::finishing){
glfwWaitEvents();
if (viewer.sliding() && sliso != isovalue) {
isovalue = sliso;
printf("%s: isosurfacing at %g\n", me, isovalue);
seekIsovalueSet(sctx, isovalue);
seekUpdate(sctx);
seekExtract(sctx, lpld);
hply.rebuffer();
}
render(&viewer);
}
/* clean exit; all okay */
Hale::done();
airMopOkay(mop);
return 0;
}
int
limnpu_pselMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *hopt = NULL;
char *err, *perr;
airArray *mop;
int pret;
limnPolyData *pldIn, *pldOut;
unsigned int prange[2], pi;
Nrrd *nsel;
double *sel;
char *out;
size_t size[NRRD_DIM_MAX];
hestOptAdd(&hopt, "r", "range", airTypeUInt, 2, 2, prange, NULL,
"range of indices of primitives to select");
hestOptAdd(&hopt, NULL, "input", airTypeOther, 1, 1, &pldIn, NULL,
"input polydata filename",
NULL, NULL, limnHestPolyDataLMPD);
hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
"output polydata filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(myinfo);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!( prange[0] <= pldIn->primNum-1 &&
prange[1] <= pldIn->primNum-1 )) {
fprintf(stderr, "%s: prange[0] %u or [1] %u outside range [0,%u]", me,
prange[0], prange[1], pldIn->primNum-1);
airMopError(mop);
return 1;
}
if (!( prange[0] <= prange[1] )) {
fprintf(stderr, "%s: need prange[0] %u <= [1] %u", me,
prange[0], prange[1]);
airMopError(mop);
return 1;
}
nsel = nrrdNew();
airMopAdd(mop, nsel, (airMopper)nrrdNuke, airMopAlways);
size[0] = pldIn->primNum;
if (nrrdMaybeAlloc_nva(nsel, nrrdTypeDouble, 1, size)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating buffer:%s", me, err);
airMopError(mop);
return 1;
}
sel = AIR_CAST(double *, nsel->data);
for (pi=prange[0]; pi<=prange[1]; pi++) {
sel[pi] = 1;
}
pldOut = limnPolyDataNew();
airMopAdd(mop, pldOut, (airMopper)limnPolyDataNix, airMopAlways);
if (limnPolyDataPrimitiveSelect(pldOut, pldIn, nsel)
|| limnPolyDataSave(out, pldOut)) {
airMopAdd(mop, err = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:%s", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
const char *me;
char *err, *outS;
hestOpt *hopt=NULL;
airArray *mop;
limnPolyData *pld, *pldSub;
gageContext *gctx=NULL;
gagePerVolume *pvl;
Nrrd *nin, *nmeas;
double kparm[3], strength, scaling[3];
seekContext *sctx;
FILE *file;
unsigned int ncc;
size_t samples[3];
gageKind *kind;
char *itemGradS; /* , *itemEvalS[2], *itemEvecS[2]; */
int itemGrad; /* , itemEval[2], itemEvec[2]; */
int E;
me = argv[0];
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume to analyze",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
"\"kind\" of volume (\"scalar\", \"vector\", \"tensor\")",
NULL, NULL, &probeKindHestCB);
hestOptAdd(&hopt, "s", "strength", airTypeDouble, 1, 1, &strength, "0.01",
"strength");
hestOptAdd(&hopt, "gi", "grad item", airTypeString, 1, 1, &itemGradS, NULL,
"item for gradient vector");
hestOptAdd(&hopt, "c", "scaling", airTypeDouble, 3, 3, scaling, "1 1 1",
"amount by which to up/down-sample on each spatial axis");
hestOptAdd(&hopt, "n", "# CC", airTypeUInt, 1, 1, &ncc, "0",
"if non-zero, number of CC to save");
hestOptAdd(&hopt, "o", "output LMPD", airTypeString, 1, 1, &outS, "out.lmpd",
"output file to save LMPD into");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
itemGrad = airEnumVal(kind->enm, itemGradS);
pld = limnPolyDataNew();
airMopAdd(mop, pld, (airMopper)limnPolyDataNix, airMopAlways);
pldSub = limnPolyDataNew();
airMopAdd(mop, pldSub, (airMopper)limnPolyDataNix, airMopAlways);
file = airFopen(outS, stdout, "w");
airMopAdd(mop, file, (airMopper)airFclose, airMopAlways);
sctx = seekContextNew();
airMopAdd(mop, sctx, (airMopper)seekContextNix, airMopAlways);
gctx = gageContextNew();
airMopAdd(mop, gctx, (airMopper)gageContextNix, airMopAlways);
ELL_3V_SET(kparm, 1, 1.0, 0.0);
if (!(pvl = gagePerVolumeNew(gctx, nin, kind))
|| gagePerVolumeAttach(gctx, pvl)
|| gageKernelSet(gctx, gageKernel00, nrrdKernelBCCubic, kparm)
|| gageKernelSet(gctx, gageKernel11, nrrdKernelBCCubicD, kparm)
|| gageKernelSet(gctx, gageKernel22, nrrdKernelBCCubicDD, kparm)
|| gageQueryItemOn(gctx, pvl, itemGrad)
|| gageQueryItemOn(gctx, pvl, gageSclHessEval)
|| gageQueryItemOn(gctx, pvl, gageSclHessEval2)
|| gageQueryItemOn(gctx, pvl, gageSclHessEvec)
|| gageQueryItemOn(gctx, pvl, gageSclHessEvec2)
|| gageUpdate(gctx)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
seekVerboseSet(sctx, 10);
E = 0;
if (!E) E |= seekDataSet(sctx, NULL, gctx, 0);
ELL_3V_SET(samples,
scaling[0]*nin->axis[kind->baseDim + 0].size,
scaling[1]*nin->axis[kind->baseDim + 1].size,
scaling[2]*nin->axis[kind->baseDim + 2].size);
if (!E) E |= seekSamplesSet(sctx, samples);
if (!E) E |= seekItemGradientSet(sctx, itemGrad);
if (!E) E |= seekItemEigensystemSet(sctx, gageSclHessEval,
gageSclHessEvec);
if (!E) E |= seekItemNormalSet(sctx, gageSclHessEvec2);
if (!E) E |= seekStrengthUseSet(sctx, AIR_TRUE);
if (!E) E |= seekStrengthSet(sctx, -1, strength);
if (!E) E |= seekItemStrengthSet(sctx, gageSclHessEval2);
if (!E) E |= seekNormalsFindSet(sctx, AIR_TRUE);
if (!E) E |= seekTypeSet(sctx, seekTypeRidgeSurface);
if (!E) E |= seekUpdate(sctx);
if (!E) E |= seekExtract(sctx, pld);
if (E) {
airMopAdd(mop, err = biffGetDone(SEEK), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
fprintf(stderr, "%s: extraction time = %g\n", me, sctx->time);
nmeas = nrrdNew();
airMopAdd(mop, nmeas, (airMopper)nrrdNuke, airMopAlways);
if (limnPolyDataVertexWindingFix(pld, AIR_TRUE)
|| limnPolyDataVertexWindingFlip(pld)
|| limnPolyDataVertexNormals(pld)
|| limnPolyDataCCFind(pld)
|| limnPolyDataPrimitiveArea(nmeas, pld)
|| limnPolyDataPrimitiveSort(pld, nmeas)) {
err = biffGetDone(LIMN);
fprintf(stderr, "%s: trouble sorting:\n%s", me, err);
free(err);
}
if (ncc > 1) {
double *meas;
unsigned int ccIdx;
nrrdSave("meas.nrrd", nmeas, NULL);
ncc = AIR_MIN(ncc, nmeas->axis[0].size);
meas = AIR_CAST(double *, nmeas->data);
for (ccIdx=ncc; ccIdx<nmeas->axis[0].size; ccIdx++) {
meas[ccIdx] = 0.0;
}
if (!E) E |= limnPolyDataPrimitiveSelect(pldSub, pld, nmeas);
if (!E) E |= limnPolyDataWriteLMPD(file, pldSub);
} else {
