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[Teem-commit] SF.net SVN: teem:[7085] teem/trunk/src/bin/puller.c
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From: <kin...@us...> - 2023-07-13 11:59:34
|
Revision: 7085
http://sourceforge.net/p/teem/code/7085
Author: kindlmann
Date: 2023-07-13 11:59:32 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
removing Deft code and updating hest usage
Modified Paths:
--------------
teem/trunk/src/bin/puller.c
Modified: teem/trunk/src/bin/puller.c
===================================================================
--- teem/trunk/src/bin/puller.c 2023-07-13 11:41:02 UTC (rev 7084)
+++ teem/trunk/src/bin/puller.c 2023-07-13 11:59:32 UTC (rev 7085)
@@ -19,26 +19,9 @@
Fifth Floor, Boston, MA 02110-1301 USA
*/
-/*
-** NOTE: all the "#ifdef DEFT" directives refer to an FLTK2-based GUI
-** for some parts of Teem called "Deft". Unfortunately FLTK2 has been
-** abandoned, and Deft is not released or supported in any way. The
-** Deft-related code is preserved for legacy purposes.
-*/
+/* for Teem v2 the Deft stuff was removed from this file; see
+ puller-with-Deft.c for that code */
-#ifdef DEFT
-# include "Deft.h"
-# include "Contour.h"
-# include "Viewer.h"
-# include "ViewerUI.h"
-# include "TensorGlyph.h"
-# include "TensorGlyphUI.h"
-# include "Slider.h"
-# include "TriPlane.h"
-# include "TriPlaneUI.h"
-
-#endif
-
#include <teem/pull.h>
#include <teem/meet.h>
@@ -52,645 +35,6 @@
"\t\tParticles. IEEE Trans. on Visualization and Computer Graphics,\n "
"\t\t15(6):1415-1424 (2009).");
-#ifdef DEFT
-typedef struct {
- fltk::FloatInput *scaleVecInput[3];
- fltk::ValueInput *glyphScaleRadInput;
- Deft::Slider *isoval;
- Deft::Slider *strength;
- Deft::Slider *quality;
- Deft::Slider *alpha, *beta, *cwell, *gamma;
- /* Deft::Slider *height; */
- Deft::Slider *ccSelect, *rho, *sclMean, *sclWind;
- fltk::CheckButton *ccSingle;
- Deft::Contour *contour;
- Deft::Scene *scene;
- Deft::Viewer *viewer;
- Deft::TensorGlyph *glyph, *hedge;
- fltk::IntInput *iters;
- fltk::FloatInput *radius;
- fltk::ValueInput *verbose;
- pullContext *pctx;
- Nrrd *nPosOut, *nTenOut, *nFrcOut, *nten, *ntmp, *nenr, *nscl, *nidcc, *nstrn, *nqual,
- *ncovar, *ntcovar, *nstab, *nintern, *nstuck, *nfrcOld, *nfrcNew, *nposOld, *nposNew,
- *nrgb, *nccrgb, *ncval, *ncmap, *ncmapOut, *nblur;
- NrrdResampleContext *rsmc;
- const Nrrd *norig;
- NrrdRange *cvalRange;
- limnPolyData *phistLine, *phistTube;
- Deft::PolyData *phistSurf;
- double icvalr[2], sclMin, sclMax, strnMin, qualMin, scaleVec[3], glyphScaleRad,
- energyIncreasePermitFrac;
-} pullBag;
-
-void
-verbose_cb(fltk::Widget *widget, pullBag *bag) {
- fltk::ValueInput *val;
-
- val = (fltk::ValueInput *)widget;
- pullVerboseSet(bag->pctx, (int)val->value());
-}
-/* ... DEFT ... */
-void
-isovalue_cb(fltk::Widget *widget, pullBag *bag) {
- Deft::Slider *slider;
-
- slider = (Deft::Slider *)widget;
- if (bag->contour) {
- bag->contour->extract(slider->value());
- }
- bag->viewer->redraw();
-}
-
-void
-outputGet(pullBag *bag) {
- static const char me[] = "outputGet";
- char *err;
- size_t cropMin[2], cropMax[2];
-
- if (pullOutputGet(bag->nPosOut, bag->nTenOut, bag->nstrn, /* may be NULL */
- bag->scaleVec, bag->glyphScaleRad, bag->pctx)
- || pullPropGet(bag->nscl, pullPropScale, bag->pctx)
- || (bag->pctx->ispec[pullInfoQuality]
- ? pullInfoGet(bag->nqual, pullInfoQuality, bag->pctx)
- : 0)
- || pullPropGet(bag->nenr, pullPropEnergy, bag->pctx)
- || pullPropGet(bag->nidcc, pullPropIdCC, bag->pctx)
- || pullPropGet(bag->nstuck, pullPropStuck, bag->pctx)
- || pullPropGet(bag->ncovar, pullPropNeighCovar7Ten, bag->pctx)
-# if PULL_TANCOVAR
- || pullPropGet(bag->ntcovar, pullPropNeighTanCovar, bag->pctx)
-# endif
- || pullPropGet(bag->nstab, pullPropStability, bag->pctx)
- || pullPropGet(bag->nintern, pullPropNeighInterNum, bag->pctx)
- || pullPropGet(bag->nFrcOut, pullPropForce, bag->pctx)
- || (pullPhistEnabled ? pullPositionHistoryGet(bag->phistLine, bag->pctx) : 0)) {
- err = biffGetDone(PULL);
- fprintf(stderr, "%s: error getting pull output:\n%s\n", me, err);
- free(err);
- exit(1);
- }
- /* ... DEFT ... */
- cropMin[0] = 0;
- cropMin[1] = 0;
- cropMax[0] = 2;
- cropMax[1] = bag->nPosOut->axis[1].size - 1;
- if ((!bag->pctx->iter ? 0
- : (nrrdCopy(bag->nfrcOld, bag->nfrcNew)
- || nrrdCopy(bag->nposOld, bag->nposNew)))
- || nrrdConvert(bag->nten, bag->nTenOut, nrrdTypeFloat)
- /* hacks to visualize the (tan) covariance tensors
- || nrrdCopy(bag->nten, bag->ncovar)
- || nrrdCopy(bag->nten, bag->ntcovar)
- */
- || nrrdCrop(bag->ntmp, bag->nPosOut, cropMin, cropMax)
- || nrrdConvert(bag->nposNew, bag->ntmp, nrrdTypeFloat)
- || nrrdCrop(bag->ntmp, bag->nFrcOut, cropMin, cropMax)
- || nrrdConvert(bag->nfrcNew, bag->ntmp, nrrdTypeFloat)
- || (!bag->pctx->iter ? (nrrdCopy(bag->nfrcOld, bag->nfrcNew)
- || nrrdCopy(bag->nposOld, bag->nposNew))
- : 0)) {
- err = biffGetDone(NRRD);
- fprintf(stderr, "%s: another error 0\n%s\n", me, err);
- free(err);
- exit(1);
- }
-}
-/* ... DEFT ... */
-void
-outputShow(pullBag *bag) {
- static const char me[] = "outputShow";
- char *err;
- float *rgb;
- unsigned int ii, nn, *idcc;
- unsigned char *stuck;
- int first;
- double *cval, emean, estdv, *pos;
-
- /*
- if (limnPolyDataSpiralTubeWrap(bag->phistTube, bag->phistLine,
- (1 << limnPolyDataInfoRGBA)
- | (1 << limnPolyDataInfoNorm),
- NULL,
- 8, 8, bag->glyph->glyphScale()/5)) {
- err = biffGetDone(LIMN);
- fprintf(stderr, "%s: another error 1\n%s\n", me, err);
- free(err);
- exit(1);
- }
- */
-
- if (pullPhistEnabled) {
- bag->phistSurf->changed();
- }
-
- bag->ncval = bag->nenr;
- /* bag->ncval = bag->nstrn; */
- /* bag->ncval = bag->nstuck; */
- /* bag->ncval = bag->nscl; */
-
- /* ... DEFT ... */
- if (bag->ncval) {
- nrrdRangeSet(bag->cvalRange, bag->ncval, AIR_FALSE);
- } else {
- bag->cvalRange->min = AIR_NAN;
- bag->cvalRange->max = AIR_NAN;
- }
- if (bag->ncval) {
- cval = AIR_CAST(double *, bag->ncval->data);
- } else {
- cval = NULL;
- }
- if (cval) {
- nn = bag->ncval->axis[0].size;
- emean = 0;
- for (ii = 0; ii < nn; ii++) {
- emean += cval[ii];
- }
- emean /= nn;
- estdv = 0;
- for (ii = 0; ii < nn; ii++) {
- estdv += (emean - cval[ii]) * (emean - cval[ii]);
- }
- estdv = sqrt(estdv / nn);
- if (bag->cvalRange->hasNonExist) {
- fprintf(stderr, "!%s: cval range %g -- %g (%s), mean %g, stdv %g\n", me,
- bag->cvalRange->min, bag->cvalRange->max,
- bag->cvalRange->hasNonExist ? "HAS non-exist" : "no non-exist", emean,
- estdv);
- }
- bag->cvalRange->min = AIR_LERP(0.7, bag->cvalRange->min, emean - 2 * estdv);
- bag->cvalRange->max = AIR_LERP(0.7, bag->cvalRange->max, emean + 2 * estdv);
- }
- /* ... DEFT ... */
- float *cmapOut;
- if (bag->ncmap && bag->ncval && AIR_EXISTS(bag->cvalRange->min)
- && AIR_EXISTS(bag->cvalRange->max)) {
- /* double mmin, mmax; */
- fprintf(stderr, "!%s: cval cmap range %g %g ----------- \n", me, bag->cvalRange->min,
- bag->cvalRange->max);
- /*
- mmin = -0.0342937;
- mmax = -0.0105725;
- */
- /* */
- /*
- bag->cvalRange->min = AIR_LERP(0.05, mmin, mmax);
- bag->cvalRange->max = AIR_LERP(0.3, mmin, mmax);
- */
- /* */
- if (nrrdApply1DRegMap(bag->ncmapOut, bag->ncval, bag->cvalRange, bag->ncmap,
- nrrdTypeFloat, AIR_TRUE)) {
- err = biffGetDone(NRRD);
- fprintf(stderr, "%s: cmap error\n%s\n", me, err);
- free(err);
- exit(1);
- }
- cmapOut = AIR_CAST(float *, bag->ncmapOut->data);
- } else {
- cmapOut = NULL;
- }
-
- /* ... DEFT ... */
-
- idcc = AIR_CAST(unsigned int *, bag->nidcc->data);
- stuck = AIR_CAST(unsigned char *, bag->nstuck->data);
- nn = bag->nPosOut->axis[1].size;
- pos = AIR_CAST(double *, bag->nPosOut->data);
-
- first = bag->nrgb->axis[1].size != bag->nPosOut->axis[1].size;
- /*
- fprintf(stderr, "!%s: %u %u -> %d\n", me,
- AIR_UINT(bag->nrgb->axis[1].size),
- AIR_UINT(bag->nPosOut->axis[1].size), first);
- */
- if (first) {
- if (nrrdMaybeAlloc_va(bag->nrgb, nrrdTypeFloat, 2, AIR_CAST(size_t, 3),
- bag->nPosOut->axis[1].size)) {
- err = biffGetDone(NRRD);
- fprintf(stderr, "%s: error creating RGB:\n%s\n", me, err);
- free(err);
- exit(1);
- }
- }
- bag->icvalr[0] = bag->cvalRange->min;
- bag->icvalr[1] = bag->cvalRange->max;
-
- /* ... DEFT ... */
-
- double *strnOut;
- strnOut = (bag->nstrn ? AIR_CAST(double *, bag->nstrn->data) : NULL);
- double *qualOut;
- qualOut = (bag->nqual ? AIR_CAST(double *, bag->nqual->data) : NULL);
- rgb = (float *)bag->nrgb->data;
- for (ii = 0; ii < nn; ii++) {
- float ee, *ccrgb;
- ccrgb = (float *)bag->nccrgb->data;
- /* ee = bag->cvalRange->min - (bag->icvalr[1] - bag->icvalr[0])/50;*/
- ee = bag->cvalRange->min;
- if (bag->pctx->CCNum && ccrgb) {
- rgb[0 + 3 * ii] = ccrgb[0 + 3 * idcc[ii]];
- rgb[1 + 3 * ii] = ccrgb[1 + 3 * idcc[ii]];
- rgb[2 + 3 * ii] = ccrgb[2 + 3 * idcc[ii]];
- } else if (cmapOut) {
- ELL_3V_COPY(rgb + 3 * ii, cmapOut + 3 * ii);
- } else {
- ELL_3V_SET(rgb + 3 * ii, 0.95, 0.95, 0.95);
- /*
- if (AIR_EXISTS(cval[ii])) {
- rgb[1 + 3*ii] = AIR_AFFINE(ee, cval[ii], bag->cvalRange->max, 0, 1);
- rgb[1 + 3*ii] = sqrt(rgb[1 + 3*ii]);
- rgb[0 + 3*ii] = rgb[1 + 3*ii];
- } else {
- rgb[1 + 3*ii] = 0;
- rgb[0 + 3*ii] = 1;
- }
- rgb[2 + 3*ii] = stuck[ii];
- */
- }
- }
-
- /* ... DEFT ... */
-
- if (1) {
- float *ten, *pos;
- double *posOut;
- ten = AIR_CAST(float *, bag->nten->data);
- posOut = AIR_CAST(double *, bag->nPosOut->data);
- pos = AIR_CAST(float *, bag->nposNew->data);
- for (ii = 0; ii < nn; ii++) {
- if (!(AIR_IN_CL(bag->sclMin - 0.00001, posOut[3], bag->sclMax + 0.00001))) {
- ten[0] = 0;
- } else if (strnOut && strnOut[ii] < bag->strnMin) {
- ten[0] = 0;
- } else if (qualOut && qualOut[ii] < bag->qualMin - 0.000001) {
- ten[0] = 0;
- } else if (bag->pctx->CCNum
- && (bag->ccSingle->value() ? idcc[ii] != bag->ccSelect->value()
- : idcc[ii] > bag->ccSelect->value())) {
- ten[0] = 0;
- } else {
- ten[0] = 1;
- }
- /*
- if (4589 == ii) {
- fprintf(stderr, "!%s: point %u/%u at (%g,%g,%g)=(%g,%g,%g,%g) got ten[0] %g\n",
- me, ii, nn,
- pos[0], pos[1], pos[1],
- posOut[0], posOut[1], posOut[2], posOut[3],
- ten[0]);
- }
- */
- pos += 3;
- posOut += 4;
- ten += 7;
- }
- }
-
- /* ... DEFT ... */
-
- if (bag->nPosOut->axis[1].size) {
- bag->glyph->dataSet(bag->nPosOut->axis[1].size, (float *)bag->nten->data, 7,
- (float *)bag->nposNew->data, 3, rgb, 3, NULL);
- bag->glyph->update();
- /*
- bag->hedge->dataSet(bag->nPosOut->axis[1].size,
- (float*)bag->nfrcNew->data, 3,
- (float*)bag->nposOld->data, 3, rgb, 3, NULL);
- bag->hedge->update();
- */
- bag->viewer->redraw();
- fltk::flush();
- } else {
- fprintf(stderr, "!%s: got zero tensors out!\n", me);
- }
- return;
-}
-
-void
-iter_cb(void *_bag) {
- pullBag *bag;
- bag = AIR_CAST(pullBag *, _bag);
- outputGet(bag);
- outputShow(bag);
-}
-
-/* ... DEFT ... */
-
-void
-step_cb(fltk::Widget *, pullBag *bag) {
- /* static double lastthresh = -42; */
- static const char me[] = "step_cb";
- char *err;
- static unsigned int itersTotal = 0;
-
- unsigned int iters = bag->iters->ivalue();
- bag->pctx->iterParm.max += iters;
- if (pullRun(bag->pctx)) {
- err = biffGetDone(PULL);
- fprintf(stderr, "%s: error running pull:\n%s\n", me, err);
- free(err);
- exit(1);
- }
- itersTotal += iters;
- fprintf(stderr, "!%s: enr = %g; time = %g sec; %u iters (%g iters/sec)\n", me,
- bag->pctx->energy, bag->pctx->timeRun, itersTotal,
- itersTotal / bag->pctx->timeRun);
- outputGet(bag);
- outputShow(bag);
- for (unsigned int ci = pullCountUnknown + 1; ci < pullCountLast; ci++) {
- if (bag->pctx->count[ci]) {
- fprintf(stderr, " %u: %s\n", bag->pctx->count[ci], airEnumStr(pullCount, ci));
- }
- }
-}
-
-/* ... DEFT ... */
-
-void
-gammaSet_cb(fltk::Widget *, pullBag *bag) {
- static const char me[] = "gammaSet_cb";
-
- if (pullGammaLearn(bag->pctx)) {
- char *err = biffGetDone(PULL);
- fprintf(stderr, "%s: problem learning gamma:\n%s", me, err);
- free(err);
- }
- if (bag->pctx->sysParm.gamma > bag->gamma->maximum()) {
- bag->gamma->maximum(2 * bag->pctx->sysParm.gamma);
- }
- bag->gamma->value(bag->pctx->sysParm.gamma);
-}
-
-/* ... DEFT ... */
-
-void
-cc_cb(fltk::Widget *, pullBag *bag) {
- static const char me[] = "cc_cb";
- unsigned int cc;
- float *rgb;
-
- if (pullCCFind(bag->pctx)
- || pullCCSort(bag->pctx, (bag->pctx->ispec[pullInfoQuality] ? pullInfoQuality : 0),
- bag->rho->value())) {
- char *err = biffGetDone(PULL);
- fprintf(stderr, "%s: problem finding/sorting CCs:\n%s", me, err);
- free(err);
- }
- printf("%s: found %u CCs\n", me, bag->pctx->CCNum);
- bag->ccSelect->range(0, bag->pctx->CCNum - 1);
- if (bag->nccrgb->axis[1].size != bag->pctx->CCNum) {
- airSrandMT(AIR_UINT(airTime()));
- if (nrrdMaybeAlloc_va(bag->nccrgb, nrrdTypeFloat, 2, AIR_CAST(size_t, 3),
- AIR_CAST(size_t, bag->pctx->CCNum))) {
- char *err = biffGetDone(NRRD);
- fprintf(stderr, "%s: problem alloc'ing cc rgb:\n%s", me, err);
- free(err);
- }
- rgb = (float *)bag->nccrgb->data;
- ELL_3V_SET(rgb + 0 * 3, 0.95, 0.95, 0.95);
- for (cc = 0; cc < bag->pctx->CCNum; cc++) {
- rgb[0 + 3 * cc] = AIR_AFFINE(0, airDrandMT(), 1, 0.3, 1.0);
- rgb[1 + 3 * cc] = AIR_AFFINE(0, airDrandMT(), 1, 0.3, 1.0);
- rgb[2 + 3 * cc] = AIR_AFFINE(0, airDrandMT(), 1, 0.3, 1.0);
- }
- }
- outputGet(bag);
- outputShow(bag);
-}
-
-/* ... DEFT ... */
-
-void
-ccSelect_cb(fltk::Widget *, pullBag *bag) {
-
- outputShow(bag);
-}
-
-void
-scaleGlyph_cb(fltk::Widget *, pullBag *bag) {
-
- bag->scaleVec[0] = bag->scaleVecInput[0]->fvalue();
- bag->scaleVec[1] = bag->scaleVecInput[1]->fvalue();
- bag->scaleVec[2] = bag->scaleVecInput[2]->fvalue();
- bag->glyphScaleRad = bag->glyphScaleRadInput->value();
- outputGet(bag);
- outputShow(bag);
-}
-
-/* ... DEFT ... */
-
-void
-reblur_cb(fltk::Widget *, pullBag *bag) {
- static const char me[] = "reblur_cb";
- double kparm[NRRD_KERNEL_PARMS_NUM], scl;
- int E;
-
- if (!bag->pctx->haveScale) {
- return;
- }
- scl = bag->sclMean->value();
- if (bag->pctx->flag.scaleIsTau) {
- kparm[0] = gageSigOfTau(scl);
- printf("!%s: tau = %g ---> sigma = %g\n", me, scl, kparm[0]);
- } else {
- kparm[0] = scl;
- printf("!%s: sigma = %g\n", me, kparm[0]);
- }
- kparm[1] = 3;
- E = 0;
- for (unsigned int axi = 0; axi < 3; axi++) {
- if (!E)
- E |= nrrdResampleKernelSet(bag->rsmc, axi, nrrdKernelDiscreteGaussian, kparm);
- }
- if (!E) E |= nrrdResampleExecute(bag->rsmc, bag->nblur);
- if (E) {
- char *err = biffGetDone(NRRD);
- fprintf(stderr, "%s: problem resampling to scale %g:\n%s", me, bag->sclMean->value(),
- err);
- free(err);
- }
- outputShow(bag);
- return;
-}
-
-/* ... DEFT ... */
-
-void
-scale_cb(fltk::Widget *, pullBag *bag) {
- double sclMean, sclWind;
-
- if (bag->pctx->haveScale) {
- sclMean = bag->sclMean->value();
- sclWind = bag->sclWind->value();
- bag->sclMin = sclMean - sclWind / 2;
- bag->sclMax = sclMean + sclWind / 2;
- } else {
- bag->sclMin = 0;
- bag->sclMax = 0;
- }
- outputShow(bag);
- return;
-}
-
-void
-alpha_cb(fltk::Widget *, pullBag *bag) {
-
- pullSysParmSet(bag->pctx, pullSysParmAlpha, bag->alpha->value());
-}
-
-void
-beta_cb(fltk::Widget *, pullBag *bag) {
-
- pullSysParmSet(bag->pctx, pullSysParmBeta, bag->beta->value());
-}
-
-/* ... DEFT ... */
-
-void
-cwell_cb(fltk::Widget *, pullBag *bag) {
- double *parm;
-
- parm = bag->pctx->energySpecR->parm;
- parm[1] = bag->cwell->value();
- pullSysParmSet(bag->pctx, pullSysParmEnergyIncreasePermit,
- bag->energyIncreasePermitFrac * bag->cwell->value());
- {
- unsigned int ii, nn;
- double xx, yy, de;
- FILE *file;
-
- if ((file = fopen("eplot.txt", "w"))) {
- nn = 800;
- for (ii = 0; ii < nn; ii++) {
- xx = AIR_AFFINE(0, ii, nn - 1, 0.0, 1.0);
- yy = bag->pctx->energySpecR->energy->eval(&de, xx, parm);
- fprintf(file, "%f %f\n", xx, yy);
- }
- fclose(file);
- }
- }
-}
-
-void
-gamma_cb(fltk::Widget *, pullBag *bag) {
-
- pullSysParmSet(bag->pctx, pullSysParmGamma, bag->gamma->value());
-}
-
-/* ... DEFT ... */
-
-void
-strength_cb(fltk::Widget *, pullBag *bag) {
-
- bag->strnMin = bag->strength->value();
- outputShow(bag);
-}
-
-void
-quality_cb(fltk::Widget *, pullBag *bag) {
-
- bag->qualMin = bag->quality->value();
- outputShow(bag);
-}
-
-void
-save_cb(fltk::Widget *, pullBag *bag) {
- static const char me[] = "save_cb";
- unsigned int ii, nn, count;
- float *ten;
- Nrrd *nPosSel, *nStrnSel;
- double *posSel, *posAll, *strnSel, *strnAll;
-
- if (!(0.0 == ELL_3V_LEN(bag->scaleVec))) {
- fprintf(stderr, "%s: refusing to save with non-zero scaleVec %g %g %g\n", me,
- bag->scaleVec[0], bag->scaleVec[1], bag->scaleVec[2]);
- return;
- }
-
- /* ... DEFT ... */
-
- nPosSel = nrrdNew();
- if (bag->nstrn) {
- nStrnSel = nrrdNew();
- } else {
- nStrnSel = NULL;
- }
- outputGet(bag);
- outputShow(bag); /* will exploit its masking of ten[0] */
- count = 0;
- nn = bag->nPosOut->axis[1].size;
- ten = AIR_CAST(float *, bag->nten->data);
- for (ii = 0; ii < nn; ii++) {
- count += !!ten[0];
- ten += 7;
- }
- nrrdMaybeAlloc_va(nPosSel, nrrdTypeDouble, 2, AIR_CAST(size_t, 4),
- AIR_CAST(size_t, count));
- posAll = AIR_CAST(double *, bag->nPosOut->data);
- posSel = AIR_CAST(double *, nPosSel->data);
- if (bag->nstrn) {
- nrrdMaybeAlloc_va(nStrnSel, nrrdTypeDouble, 1, AIR_CAST(size_t, count));
- strnAll = AIR_CAST(double *, bag->nstrn->data);
- strnSel = AIR_CAST(double *, nStrnSel->data);
- } else {
- strnSel = NULL;
- strnAll = NULL;
- }
- ten = AIR_CAST(float *, bag->nten->data);
- count = 0;
- for (ii = 0; ii < nn; ii++) {
- if (ten[0]) {
- ELL_4V_COPY(posSel, posAll);
- if (strnSel && strnAll) {
- strnSel[count] = strnAll[ii];
- }
- posSel += 4;
- count++;
- }
- posAll += 4;
- ten += 7;
- }
-
- /* ... DEFT ... */
-
- nrrdSave("pos-all.nrrd", bag->nPosOut, NULL);
- if (0) {
- nrrdSave("pos-sel.nrrd", nPosSel, NULL);
- } else {
- char fname[512];
- FILE *ff;
- unsigned int ii = 0;
-
- for (ii = 0, ff = NULL; AIR_TRUE; ii++) {
- ff = airFclose(ff);
- sprintf(fname, "pos-sel-%03u.nrrd", ii);
- if (!(ff = fopen(fname, "rb"))) {
- break;
- }
- }
- ff = airFclose(ff);
- nrrdSave(fname, nPosSel, NULL);
- }
- nrrdSave("covar-all.nrrd", bag->ncovar, NULL);
-# if PULL_TANCOVAR
- nrrdSave("tcovar-all.nrrd", bag->ntcovar, NULL);
-# endif
- nrrdSave("stab-all.nrrd", bag->nstab, NULL);
- nrrdSave("intern-all.nrrd", bag->nintern, NULL);
- if (bag->nstrn) {
- nrrdSave("strn-all.nrrd", bag->nstrn, NULL);
- nrrdSave("strn-sel.nrrd", nStrnSel, NULL);
- }
- nrrdNuke(nPosSel);
- if (bag->nstrn) {
- nrrdNuke(nStrnSel);
- }
- return;
-}
-
-#endif /* DEFT */
-
int
main(int argc, const char **argv) {
hestOpt *hopt = NULL;
@@ -698,17 +42,6 @@
airArray *mop;
const char *me;
-#ifdef DEFT
- float fr[3], at[3], up[3], fovy, neer, faar, dist, bg[3];
- int imgSize[2], ortho, rght, atrel, camkeep;
-
- float anisoThresh, anisoThreshMin, glyphScale, haloTraceBound, glyphHaloWidth,
- glyphNormPow, glyphEvalPow, sqdSharp;
- int glyphType, glyphFacetRes, aniso;
- double ssrange[2];
- pullBag bag;
-#endif
-
char *err, *outS, *extraOutBaseS, *addLogS, *cachePathSS;
FILE *addLog;
meetPullVol **vspec;
@@ -747,287 +80,188 @@
hparm->respectDashDashHelp = AIR_TRUE;
me = argv[0];
-#ifdef DEFT
- unsigned int baryRes;
- int saveAndQuit, fog;
+ hestOptAdd_1_Enum(&hopt, "int", "int", &interType, "justr",
+ "inter-particle energy type", pullInterType);
+ hestOptAdd_1_Other(&hopt, "enr", "spec", &enspR, "cotan",
+ "inter-particle energy, radial component", pullHestEnergySpec);
+ hestOptAdd_1_Other(&hopt, "ens", "spec", &enspS, "zero",
+ "inter-particle energy, scale component", pullHestEnergySpec);
+ hestOptAdd_1_Other(&hopt, "enw", "spec", &enspWin, "butter:16,0.8",
+ "windowing to create locality with additive "
+ "scale-space interaction (\"-int add\")",
+ pullHestEnergySpec);
+ hestOptAdd_1_Bool(&hopt, "zz", "bool", &zeroZ, "false",
+ "always constrain Z=0, to process 2D images");
+ hestOptAdd_1_Bool(&hopt, "efs", "bool", &energyFromStrength, "false",
+ "whether or not strength contributes to particle-image energy");
+ hestOptAdd_1_Bool(&hopt, "nave", "bool", &nixAtVolumeEdgeSpace, "false",
+ "whether or not to nix points at edge of volume, where gage had "
+ "to invent values for kernel support");
+ hestOptAdd_1_Bool(&hopt, "cbst", "bool", &constraintBeforeSeedThresh, "false",
+ "during initialization, try constraint satisfaction before "
+ "testing seedThresh");
+ hestOptAdd_Flag(&hopt, "noadd", &noAdd, "turn off adding during population control");
+ hestOptAdd_1_Bool(&hopt, "usa", "bool", &unequalShapesAllow, "false",
+ "allow volumes to have different shapes (false is safe as "
+ "different volume sizes are often accidental)");
+ hestOptAdd_1_Bool(&hopt, "pcet", "bool", &popCntlEnoughTest, "true",
+ "use neighbor-counting \"enough\" heuristic to "
+ "bail out of pop cntl");
+ hestOptAdd_1_Bool(&hopt, "cipc", "bool", &convergenceIgnoresPopCntl, "false",
+ "convergence test doesn't care if there has been "
+ "recent changes due to population control");
+ hestOptAdd_Flag(&hopt, "nobin", &binSingle,
+ "turn off spatial binning (which prevents multi-threading "
+ "from being useful), for debugging or speed-up measurement");
+ hestOptAdd_1_Bool(&hopt, "lti", "bool", &liveThresholdOnInit, "true",
+ "impose liveThresh on initialization");
+ hestOptAdd_1_Bool(&hopt, "por", "bool", &permuteOnRebin, "true",
+ "permute points during rebinning");
+ hestOptAdd_1_Bool(&hopt, "npcwza", "bool", &noPopCntlWithZeroAlpha, "false",
+ "no pop cntl with zero alpha");
+ hestOptAdd_1_Bool(&hopt, "ubfgl", "bool", &useBetaForGammaLearn, "false",
+ "use beta for gamma learning");
+ hestOptAdd_1_Bool(&hopt, "ratb", "bool", &restrictiveAddToBins, "true",
+ "be choosy when adding points to bins to avoid overlap");
+ hestOptAdd_3_Double(&hopt, "svec", "vec", scaleVec, "0 0 0",
+ "if non-zero (length), vector to use for displaying scale "
+ "in 3-space");
+ hestOptAdd_1_Double(&hopt, "gssr", "rad", &glyphScaleRad, "0.0",
+ "if non-zero (length), scaling of scale to cylindrical tensors");
+ hestOptAdd_1_Int(&hopt, "v", "verbosity", &verbose, "1", "verbosity level");
+ hestOptAdd_Nv_Other(&hopt, "vol", "vol0 vol1", 1, -1, &vspec, NULL,
+ "input volumes, in format <filename>:<kind>:<volname>", &vspecNum,
+ meetHestPullVol);
+ hestOptAdd_Nv_Other(&hopt, "info", "info0 info1", 1, -1, &idef, NULL,
+ "info definitions, in format "
+ "<info>[-c]:<volname>:<item>[:<zero>:<scale>]",
+ &idefNum, meetHestPullInfo);
- hestOptAdd(&hopt, "csqvmm", "min max", airTypeDouble, 2, 2,
- Deft::colorSclQuantityValueMinMax, "nan nan",
- "min/max values for cutting planes of scalar values");
- hestOptAdd(&hopt, "saq", "save & quit", airTypeInt, 0, 0, &saveAndQuit, NULL,
- "save image and quit, for batch processing");
- hestOptAdd(&hopt, "cmap", "nin", airTypeOther, 1, 1, &(bag.ncmap), "",
- "colormap for particles", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "fr", "from point", airTypeFloat, 3, 3, fr, "3 4 5",
- "position of camera, used to determine view vector");
- hestOptAdd(&hopt, "at", "at point", airTypeFloat, 3, 3, at, "0 0 0",
- "camera look-at point, used to determine view vector");
- hestOptAdd(&hopt, "up", "up vector", airTypeFloat, 3, 3, up, "0 0 1",
- "camera pseudo-up vector, used to determine view coordinates");
- hestOptAdd(&hopt, "rh", NULL, airTypeInt, 0, 0, &rght, NULL,
- "normally, use a right-handed UVN frame (V points down), "
- "but in Deft this is always true");
- hestOptAdd(&hopt, "fv", "fov", airTypeFloat, 1, 1, &fovy, "20",
- "vertical field-of-view, in degrees");
- hestOptAdd(&hopt, "or", NULL, airTypeInt, 0, 0, &ortho, NULL,
- "use orthogonal projection instead of perspective");
- hestOptAdd(&hopt, "dn", "near clip", airTypeFloat, 1, 1, &neer, "-2",
- "position of near clipping plane, relative to look-at point");
- hestOptAdd(&hopt, "di", "image", airTypeFloat, 1, 1, &dist, "0.0",
- "normally, distance to image plane, "
- "but in Deft this is always 0.0");
- hestOptAdd(&hopt, "df", "far clip", airTypeFloat, 1, 1, &faar, "2",
- "position of far clipping plane, relative to look-at point");
- hestOptAdd(&hopt, "ar", NULL, airTypeInt, 0, 0, &atrel, NULL,
- "normally: near, image, and far plane distances are relative to "
- "the *at* point, instead of the eye point, "
- "but for Deft, this is always true");
- hestOptAdd(&hopt, "usecam", NULL, airTypeInt, 0, 0, &camkeep, NULL,
- "hack: by default, a camera reset is done to put the volume "
- "in view. Use this to say that the camera specified by the "
- "flags above should be preserved and used");
- hestOptAdd(&hopt, "bg", "R G B", airTypeFloat, 3, 3, bg, "0.2 0.3 0.4",
- "background color");
- hestOptAdd(&hopt, "fog", NULL, airTypeInt, 0, 0, &fog, NULL, "hack: turn on fog");
- hestOptAdd(&hopt, "is", "su sv", airTypeInt, 2, 2, imgSize, "640 480",
- "initial window size");
- /* ... DEFT ... */
- /* this tensor stuff is here because we're hijacking the tensor glyph
- object for doing the particle display ... */
- hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &aniso, NULL,
- "anisotropy metric to make volume of", NULL, tenAniso);
- hestOptAdd(&hopt, "atr", "aniso thresh", airTypeFloat, 1, 1, &anisoThresh, "0.85",
- "Glyphs will be drawn only for tensors with anisotropy "
- "greater than this threshold");
- hestOptAdd(&hopt, "atrm", "aniso thresh min", airTypeFloat, 1, 1, &anisoThreshMin,
- "0.4", "lower bound on aniso thresh");
- hestOptAdd(&hopt, "g", "glyph shape", airTypeEnum, 1, 1, &glyphType, "sqd",
- "shape of glyph to use for display. Possibilities "
- "include \"box\", \"sphere\"=\"sph\", \"cylinder\"=\"cyl\", and "
- "\"superquad\"=\"sqd\"",
- NULL, tenGlyphType);
- hestOptAdd(&hopt, "gsc", "scale", airTypeFloat, 1, 1, &glyphScale, "0.25",
- "over-all glyph size");
- hestOptAdd(&hopt, "htb", "trace", airTypeFloat, 1, 1, &haloTraceBound, "1.0",
- "halo trace bound");
- hestOptAdd(&hopt, "ghw", "hwidth", airTypeFloat, 1, 1, &glyphHaloWidth, "0.0",
- "glyph halo width");
- hestOptAdd(&hopt, "gnp", "npow", airTypeFloat, 1, 1, &glyphNormPow, "1.0",
- "pow() exponent for compressing range of norms");
- hestOptAdd(&hopt, "gep", "epow", airTypeFloat, 1, 1, &glyphEvalPow, "1.0",
- "pow() exponent for compressing single eigenvalues");
- hestOptAdd(&hopt, "br", "barycentric res", airTypeInt, 1, 1, &baryRes, "50",
- "resolution of sampling of tensor shape palette");
- hestOptAdd(&hopt, "gr", "glyph res", airTypeInt, 1, 1, &glyphFacetRes, "7",
- "resolution of polygonalization of glyphs (other than box)");
- hestOptAdd(&hopt, "sh", "sharpness", airTypeFloat, 1, 1, &sqdSharp, "2.5",
- "for superquadric glyphs, how much to sharp edges form as a "
- "function of differences between eigenvalues. Higher values "
- "mean that edges form more easily");
-#endif /* DEFT */
+ hestOptAdd_1_Other(&hopt, "k00", "kern00", &k00, "cubic:1,0",
+ "kernel for gageKernel00", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k11", "kern11", &k11, "cubicd:1,0",
+ "kernel for gageKernel11", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k22", "kern22", &k22, "cubicdd:1,0",
+ "kernel for gageKernel22", nrrdHestKernelSpec);
- hestOptAdd(&hopt, "int", "int", airTypeEnum, 1, 1, &interType, "justr",
- "inter-particle energy type", NULL, pullInterType);
- hestOptAdd(&hopt, "enr", "spec", airTypeOther, 1, 1, &enspR, "cotan",
- "inter-particle energy, radial component", NULL, NULL, pullHestEnergySpec);
- hestOptAdd(&hopt, "ens", "spec", airTypeOther, 1, 1, &enspS, "zero",
- "inter-particle energy, scale component", NULL, NULL, pullHestEnergySpec);
- hestOptAdd(&hopt, "enw", "spec", airTypeOther, 1, 1, &enspWin, "butter:16,0.8",
- "windowing to create locality with additive "
- "scale-space interaction (\"-int add\")",
- NULL, NULL, pullHestEnergySpec);
- hestOptAdd(&hopt, "zz", "bool", airTypeBool, 1, 1, &zeroZ, "false",
- "always constrain Z=0, to process 2D images");
- hestOptAdd(&hopt, "efs", "bool", airTypeBool, 1, 1, &energyFromStrength, "false",
- "whether or not strength contributes to particle-image energy");
- hestOptAdd(&hopt, "nave", "bool", airTypeBool, 1, 1, &nixAtVolumeEdgeSpace, "false",
- "whether or not to nix points at edge of volume, where gage had "
- "to invent values for kernel support");
- hestOptAdd(&hopt, "cbst", "bool", airTypeBool, 1, 1, &constraintBeforeSeedThresh,
- "false",
- "during initialization, try constraint satisfaction before "
- "testing seedThresh");
- hestOptAdd(&hopt, "noadd", NULL, airTypeBool, 0, 0, &noAdd, NULL,
- "turn off adding during population control");
- hestOptAdd(&hopt, "usa", "bool", airTypeBool, 1, 1, &unequalShapesAllow, "false",
- "allow volumes to have different shapes (false is safe as "
- "different volume sizes are often accidental)");
- hestOptAdd(&hopt, "pcet", "bool", airTypeBool, 1, 1, &popCntlEnoughTest, "true",
- "use neighbor-counting \"enough\" heuristic to "
- "bail out of pop cntl");
- hestOptAdd(&hopt, "cipc", "bool", airTypeBool, 1, 1, &convergenceIgnoresPopCntl,
- "false",
- "convergence test doesn't care if there has been "
- "recent changes due to population control");
- hestOptAdd(&hopt, "nobin", NULL, airTypeBool, 0, 0, &binSingle, NULL,
- "turn off spatial binning (which prevents multi-threading "
- "from being useful), for debugging or speed-up measurement");
- hestOptAdd(&hopt, "lti", "bool", airTypeBool, 1, 1, &liveThresholdOnInit, "true",
- "impose liveThresh on initialization");
- hestOptAdd(&hopt, "por", "bool", airTypeBool, 1, 1, &permuteOnRebin, "true",
- "permute points during rebinning");
- hestOptAdd(&hopt, "npcwza", "bool", airTypeBool, 1, 1, &noPopCntlWithZeroAlpha,
- "false", "no pop cntl with zero alpha");
- hestOptAdd(&hopt, "ubfgl", "bool", airTypeBool, 1, 1, &useBetaForGammaLearn, "false",
- "use beta for gamma learning");
- hestOptAdd(&hopt, "ratb", "bool", airTypeBool, 1, 1, &restrictiveAddToBins, "true",
- "be choosy when adding points to bins to avoid overlap");
- hestOptAdd(&hopt, "svec", "vec", airTypeDouble, 3, 3, scaleVec, "0 0 0",
- "if non-zero (length), vector to use for displaying scale "
- "in 3-space");
- hestOptAdd(&hopt, "gssr", "rad", airTypeDouble, 1, 1, &glyphScaleRad, "0.0",
- "if non-zero (length), scaling of scale to cylindrical tensors");
- hestOptAdd(&hopt, "v", "verbosity", airTypeInt, 1, 1, &verbose, "1",
- "verbosity level");
- hestOptAdd(&hopt, "vol", "vol0 vol1", airTypeOther, 1, -1, &vspec, NULL,
- "input volumes, in format <filename>:<kind>:<volname>", &vspecNum, NULL,
- meetHestPullVol);
- hestOptAdd(&hopt, "info", "info0 info1", airTypeOther, 1, -1, &idef, NULL,
- "info definitions, in format "
- "<info>[-c]:<volname>:<item>[:<zero>:<scale>]",
- &idefNum, NULL, meetHestPullInfo);
+ hestOptAdd_1_String(&hopt, "sscp", "path", &cachePathSS, "./",
+ "path (without trailing /) for where to read/write "
+ "pre-blurred volumes for scale-space");
+ kssOpi = hestOptAdd_1_Other(&hopt, "kssb", "kernel", &kSSblur, "dgauss:1,5",
+ "default blurring kernel, to sample scale space",
+ nrrdHestKernelSpec);
+ bspOpi = hestOptAdd_1_Other(&hopt, "bsp", "boundary", &bspec, "wrap",
+ "default boundary behavior of scale-space blurring",
+ nrrdHestBoundarySpec);
+ hestOptAdd_1_Other(&hopt, "kssr", "kernel", &kSSrecon, "hermite",
+ "kernel for reconstructing from scale space samples",
+ nrrdHestKernelSpec);
+ hestOptAdd_1_UInt(&hopt, "nss", "# scl smpls", &samplesAlongScaleNum, "1",
+ "if using \"-ppv\", number of samples along scale axis "
+ "for each spatial position");
- hestOptAdd(&hopt, "k00", "kern00", airTypeOther, 1, 1, &k00, "cubic:1,0",
- "kernel for gageKernel00", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k11", "kern11", airTypeOther, 1, 1, &k11, "cubicd:1,0",
- "kernel for gageKernel11", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k22", "kern22", airTypeOther, 1, 1, &k22, "cubicdd:1,0",
- "kernel for gageKernel22", NULL, NULL, nrrdHestKernelSpec);
+ hestOptAdd_1_UInt(&hopt, "np", "# points", &pointNumInitial, "1000",
+ "number of points to start in system");
+ hestOptAdd_Flag(&hopt, "halton", &useHalton,
+ "use Halton sequence initialization instead of "
+ "uniform random");
+ /* really signed; see pull.h */
+ hestOptAdd_1_Int(&hopt, "ppv", "# pnts/vox", &pointPerVoxel, "0",
+ "number of points per voxel to start in simulation "
+ "(need to have a seed thresh vol, overrides \"-np\")");
+ hestOptAdd_2_UInt(&hopt, "ppvzr", "z range", ppvZRange, "1 0",
+ "range of Z slices (1st num < 2nd num) to do ppv in, or, "
+ "\"1 0\" for whole volume");
+ hestOptAdd_1_Double(&hopt, "jit", "jitter", &jitter, "0",
+ "amount of jittering to do with ppv");
+ hestOptAdd_1_Other(&hopt, "pi", "npos", &nPosIn, "",
+ "4-by-N array of positions to start at (overrides \"-np\")",
+ nrrdHestNrrd);
+ hestOptAdd_1_Double(&hopt, "step", "step", &stepInitial, "1",
+ "initial step size for gradient descent");
+ hestOptAdd_1_Double(&hopt, "csm", "step", &constraintStepMin, "0.0001",
+ "convergence criterion for constraint satisfaction");
+ hestOptAdd_1_UInt(&hopt, "snap", "# iters", &snap, "0",
+ "if non-zero, # iters between saved snapshots");
+ hestOptAdd_1_UInt(&hopt, "maxi", "# iters", &iterMax, "0",
+ "if non-zero, max # iterations to run whole system");
+ hestOptAdd_1_UInt(&hopt, "stim", "# iters", &stuckIterMax, "5",
+ "if non-zero, max # iterations to allow a particle "
+ " to be stuck before nixing");
+ hestOptAdd_1_UInt(&hopt, "maxci", "# iters", &constraintIterMax, "15",
+ "if non-zero, max # iterations for contraint enforcement");
+ hestOptAdd_1_Double(&hopt, "irad", "scale", &radiusSpace, "1",
+ "particle radius in spatial domain");
+ hestOptAdd_1_Double(&hopt, "srad", "scale", &radiusScale, "1",
+ "particle radius in scale domain");
+ hestOptAdd_1_Double(&hopt, "bws", "bin width", &binWidthSpace, "1.001",
+ "spatial bin width as multiple of spatial radius");
+ hestOptAdd_1_Double(&hopt, "alpha", "alpha", &alpha, "0.5",
+ "blend between particle-image (alpha=0) and "
+ "inter-particle (alpha=1) energies");
+ hestOptAdd_1_Double(&hopt, "beta", "beta", &beta, "1.0",
+ "when using Phi2 energy, blend between pure "
+ "space repulsion (beta=0) and "
+ "scale attraction (beta=1)");
+ hestOptAdd_1_Double(&hopt, "gamma", "gamma", &_gamma, "1.0",
+ "scaling factor on energy from strength");
+ hestOptAdd_1_Double(&hopt, "wall", "k", &wall, "0.0", "spring constant on walls");
+ hestOptAdd_1_Double(&hopt, "eip", "k", &energyIncreasePermit, "0.0",
+ "amount by which its okay for *per-particle* energy to increase "
+ "during gradient descent process");
+ hestOptAdd_1_Double(&hopt, "ess", "scl", &backStepScale, "0.5",
+ "when energy goes up instead of down, scale step "
+ "size by this");
+ hestOptAdd_1_Double(&hopt, "oss", "scl", &opporStepScale, "1.0",
+ "opportunistic scaling (hopefully up, >1) of step size "
+ "on every iteration");
+ hestOptAdd_1_Double(&hopt, "edmin", "frac", &energyDecreaseMin, "0.0001",
+ "convergence threshold: stop when fractional improvement "
+ "(decrease) in energy dips below this");
+ hestOptAdd_1_Double(&hopt, "edpcmin", "frac", &energyDecreasePopCntlMin, "0.01",
+ "population control is triggered when energy improvement "
+ "goes below this threshold");
+ hestOptAdd_1_Double(&hopt, "fnnm", "frac", &fracNeighNixedMax, "0.25",
+ "don't nix if this fraction (or more) of neighbors "
+ "have been nixed");
+ hestOptAdd_1_UInt(&hopt, "pcp", "period", &popCntlPeriod, "20",
+ "# iters to wait between attempts at population control");
+ hestOptAdd_1_UInt(&hopt, "iad", "# iters", &addDescent, "10",
+ "# iters to run descent on tentative new points during PC");
+ hestOptAdd_1_UInt(&hopt, "icb", "# iters", &iterCallback, "1",
+ "periodicity of calling rendering callback");
- hestOptAdd(&hopt, "sscp", "path", airTypeString, 1, 1, &cachePathSS, "./",
- "path (without trailing /) for where to read/write "
- "pre-blurred volumes for scale-space");
- kssOpi = hestOptAdd(&hopt, "kssb", "kernel", airTypeOther, 1, 1, &kSSblur,
- "dgauss:1,5", "default blurring kernel, to sample scale space",
- NULL, NULL, nrrdHestKernelSpec);
- bspOpi = hestOptAdd(&hopt, "bsp", "boundary", airTypeOther, 1, 1, &bspec, "wrap",
- "default boundary behavior of scale-space blurring", NULL, NULL,
- nrrdHestBoundarySpec);
- hestOptAdd(&hopt, "kssr", "kernel", airTypeOther, 1, 1, &kSSrecon, "hermite",
- "kernel for reconstructing from scale space samples", NULL, NULL,
- nrrdHestKernelSpec);
- hestOptAdd(&hopt, "nss", "# scl smpls", airTypeUInt, 1, 1, &samplesAlongScaleNum, "1",
- "if using \"-ppv\", number of samples along scale axis "
- "for each spatial position");
+ hestOptAdd_1_Bool(&hopt, "ac3c", "ac3c", &allowCodimension3Constraints, "false",
+ "allow codimensions 3 constraints");
+ hestOptAdd_1_Bool(&hopt, "sit", "sit", &scaleIsTau, "false", "scale is tau");
+ hestOptAdd_1_UInt(&hopt, "rng", "seed", &rngSeed, "42", "base seed value for RNGs");
+ hestOptAdd_1_UInt(&hopt, "pbm", "mod", &progressBinMod, "50", "progress bin mod");
+ hestOptAdd_1_UInt(&hopt, "eiphl", "hl", &eipHalfLife, "0",
+ "half-life of energyIncreasePermute (\"-eip\")");
+ hestOptAdd_1_UInt(&hopt, "nt", "# threads", &threadNum, "1",
+ (airThreadCapable
+ ? "number of threads hoover should use"
+ : "if threads where enabled in this Teem build, this is how "
+ "you would control the number of threads to use"));
+ hestOptAdd_1_Double(&hopt, "nprob", "prob", &neighborTrueProb, "1.0",
+ "do full neighbor discovery with this probability");
+ hestOptAdd_1_Double(&hopt, "pprob", "prob", &probeProb, "1.0",
+ "probe local image values with this probability");
- hestOptAdd(&hopt, "np", "# points", airTypeUInt, 1, 1, &pointNumInitial, "1000",
- "number of points to start in system");
- hestOptAdd(&hopt, "halton", NULL, airTypeInt, 0, 0, &useHalton, NULL,
- "use Halton sequence initialization instead of "
- "uniform random");
- hestOptAdd(&hopt, "ppv", "# pnts/vox", airTypeInt, 1, 1, &pointPerVoxel, "0",
- "number of points per voxel to start in simulation "
- "(need to have a seed thresh vol, overrides \"-np\")");
- hestOptAdd(&hopt, "ppvzr", "z range", airTypeUInt, 2, 2, ppvZRange, "1 0",
- "range of Z slices (1st num < 2nd num) to do ppv in, or, "
- "\"1 0\" for whole volume");
- hestOptAdd(&hopt, "jit", "jitter", airTypeDouble, 1, 1, &jitter, "0",
- "amount of jittering to do with ppv");
- hestOptAdd(&hopt, "pi", "npos", airTypeOther, 1, 1, &nPosIn, "",
- "4-by-N array of positions to start at (overrides \"-np\")", NULL, NULL,
- nrrdHestNrrd);
- hestOptAdd(&hopt, "step", "step", airTypeDouble, 1, 1, &stepInitial, "1",
- "initial step size for gradient descent");
- hestOptAdd(&hopt, "csm", "step", airTypeDouble, 1, 1, &constraintStepMin, "0.0001",
- "convergence criterion for constraint satisfaction");
- hestOptAdd(&hopt, "snap", "# iters", airTypeUInt, 1, 1, &snap, "0",
- "if non-zero, # iters between saved snapshots");
- hestOptAdd(&hopt, "maxi", "# iters", airTypeUInt, 1, 1, &iterMax, "0",
- "if non-zero, max # iterations to run whole system");
- hestOptAdd(&hopt, "stim", "# iters", airTypeUInt, 1, 1, &stuckIterMax, "5",
- "if non-zero, max # iterations to allow a particle "
- " to be stuck before nixing");
- hestOptAdd(&hopt, "maxci", "# iters", airTypeUInt, 1, 1, &constraintIterMax, "15",
- "if non-zero, max # iterations for contraint enforcement");
- hestOptAdd(&hopt, "irad", "scale", airTypeDouble, 1, 1, &radiusSpace, "1",
- "particle radius in spatial domain");
- hestOptAdd(&hopt, "srad", "scale", airTypeDouble, 1, 1, &radiusScale, "1",
- "particle radius in scale domain");
- hestOptAdd(&hopt, "bws", "bin width", airTypeDouble, 1, 1, &binWidthSpace, "1.001",
- "spatial bin width as multiple of spatial radius");
- hestOptAdd(&hopt, "alpha", "alpha", airTypeDouble, 1, 1, &alpha, "0.5",
- "blend between particle-image (alpha=0) and "
- "inter-particle (alpha=1) energies");
- hestOptAdd(&hopt, "beta", "beta", airTypeDouble, 1, 1, &beta, "1.0",
- "when using Phi2 energy, blend between pure "
- "space repulsion (beta=0) and "
- "scale attraction (beta=1)");
- hestOptAdd(&hopt, "gamma", "gamma", airTypeDouble, 1, 1, &_gamma, "1.0",
- "scaling factor on energy from strength");
- hestOptAdd(&hopt, "wall", "k", airTypeDouble, 1, 1, &wall, "0.0",
- "spring constant on walls");
- hestOptAdd(&hopt, "eip", "k", airTypeDouble, 1, 1, &energyIncreasePermit, "0.0",
- "amount by which its okay for *per-particle* energy to increase "
- "during gradient descent process");
- hestOptAdd(&hopt, "ess", "scl", airTypeDouble, 1, 1, &backStepScale, "0.5",
- "when energy goes up instead of down, scale step "
- "size by this");
- hestOptAdd(&hopt, "oss", "scl", airTypeDouble, 1, 1, &opporStepScale, "1.0",
- "opportunistic scaling (hopefully up, >1) of step size "
- "on every iteration");
- hestOptAdd(&hopt, "edmin", "frac", airTypeDouble, 1, 1, &energyDecreaseMin, "0.0001",
- "convergence threshold: stop when fractional improvement "
- "(decrease) in energy dips below this");
- hestOptAdd(&hopt, "edpcmin", "frac", airTypeDouble, 1, 1, &energyDecreasePopCntlMin,
- "0.01",
- "population control is triggered when energy improvement "
- "goes below this threshold");
- hestOptAdd(&hopt, "fnnm", "frac", airTypeDouble, 1, 1, &fracNeighNixedMax, "0.25",
- "don't nix if this fraction (or more) of neighbors "
- "have been nixed");
- hestOptAdd(&hopt, "pcp", "period", airTypeUInt, 1, 1, &popCntlPeriod, "20",
- "# iters to wait between attempts at population control");
- hestOptAdd(&hopt, "iad", "# iters", airTypeUInt, 1, 1, &addDescent, "10",
- "# iters to run descent on tentative new points during PC");
- hestOptAdd(&hopt, "icb", "# iters", airTypeUInt, 1, 1, &iterCallback, "1",
- "periodicity of calling rendering callback");
+ hestOptAdd_1_String(&hopt, "addlog", "fname", &addLogS, "",
+ "name of file in which to log all particle additions");
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-",
+ "filename for saving computed positions");
+ hestOptAdd_1_String(&hopt, "eob", "base", &extraOutBaseS, "",
+ "save extra info (besides position), and use this string as "
+ "the base of the filenames. Not using this means the extra "
+ "info is not saved.");
- hestOptAdd(&hopt, "ac3c", "ac3c", airTypeBool, 1, 1, &allowCodimension3Constraints,
- "false", "allow codimensions 3 constraints");
- hestOptAdd(&hopt, "sit", "sit", airTypeBool, 1, 1, &scaleIsTau, "false",
- "scale is tau");
- hestOptAdd(&hopt, "rng", "seed", airTypeUInt, 1, 1, &rngSeed, "42",
- "base seed value for RNGs");
- hestOptAdd(&hopt, "pbm", "mod", airTypeUInt, 1, 1, &progressBinMod, "50",
- "progress bin mod");
- hestOptAdd(&hopt, "eiphl", "hl", airTypeUInt, 1, 1, &eipHalfLife, "0",
- "half-life of energyIncreasePermute (\"-eip\")");
- hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1, &threadNum, "1",
- (airThreadCapable
- ? "number of threads hoover should use"
- : "if threads where enabled in this Teem build, this is how "
- "you would control the number of threads to use"));
- hestOptAdd(&hopt, "nprob", "prob", airTypeDouble, 1, 1, &neighborTrueProb, "1.0",
- "do full neighbor discovery with this probability");
- hestOptAdd(&hopt, "pprob", "prob", airTypeDouble, 1, 1, &probeProb, "1.0",
- "probe local image values with this probability");
-
- hestOptAdd(&hopt, "addlog", "fname", airTypeString, 1, 1, &addLogS, "",
- "name of file in which to log all particle additions");
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "filename for saving computed positions");
- hestOptAdd(&hopt, "eob", "base", airTypeString, 1, 1, &extraOutBaseS, "",
- "save extra info (besides position), and use this string as "
- "the base of the filenames. Not using this means the extra "
- "info is not saved.");
-
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, info, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
-#ifdef DEFT
- if (const char *envS = getenv("DEFT_HOME")) {
- strcpy(Deft::homeDir, envS);
- strcat(Deft::homeDir, "/");
- } else {
- fprintf(stderr,
- "%s: WARNING: \"DEFT_HOME\" environment variable "
- "not set; assuming \".\"\n",
- me);
- strcpy(Deft::homeDir, "./");
- }
-#endif
/*
airEnumPrint(stderr, gageScl);
exit(0);
@@ -1157,495 +391,6 @@
* all lines: +1 evec0 evec1 -1
*/
-#ifdef DEFT
- ssrange[0] = FLT_MAX;
- ssrange[1] = -FLT_MAX;
- for (vsi = 0; vsi < vspecNum; vsi++) {
- meetPullVol *vol;
- vol = vspec[vsi];
- if (vol->numSS) {
- ssrange[0] = AIR_MIN(ssrange[0], vol->rangeSS[0]);
- ssrange[1] = AIR_MAX(ssrange[1], vol->rangeSS[1]);
- }
- }
- if (pctx->flag.scaleIsTau) {
- ssrange[0] = gageTauOfSig(ssrange[0]);
- ssrange[1] = gageTauOfSig(ssrange[1]);
- }
- /* -------------------------------------------------- */
- /* initialize bag and its UI */
- bag.pctx = pctx;
- bag.nPosOut = nrrdNew();
- bag.nTenOut = nrrdNew();
- bag.nFrcOut = nrrdNew();
- bag.nposOld = nrrdNew();
- bag.nposNew = nrrdNew();
- bag.nten = nrrdNew();
- bag.ntmp = nrrdNew();
- bag.nenr = nrrdNew();
- bag.nscl = nrrdNew();
- bag.nidcc = nrrdNew();
- bag.ncovar = nrrdNew();
-# if PULL_TANCOVAR
- bag.ntcovar = nrrdNew();
-# endif
- bag.nstab = nrrdNew();
- bag.nintern = nrrdNew();
- if (pctx->ispec[pullInfoStrength]) {
- printf("!%s: trouble creating strength nrrd\n", me);
- bag.nstrn = nrrdNew();
- } else {
- bag.nstrn = NULL;
- }
- if (pctx->ispec[pullInfoQuality]) {
- printf("!%s: trouble creating quality nrrd\n", me);
- bag.nqual = nrrdNew();
- } else {
- bag.nqual = NULL;
- }
- bag.nstuck = nrrdNew();
- bag.nfrcOld = nrrdNew();
- bag.nfrcNew = nrrdNew();
- bag.nrgb = nrrdNew();
- bag.nccrgb = nrrdNew();
- bag.ncmapOut = nrrdNew();
- bag.nblur = nrrdNew();
- bag.norig = vspec[0]->nin;
- nrrdCopy(bag.nblur, bag.norig);
- bag.rsmc = nrrdResampleContextNew();
- E = 0;
- if (!E) E |= nrrdResampleDefaultCenterSet(bag.rsmc, nrrdDefaultCenter);
- if (!E) E |= nrrdResampleInputSet(bag.rsmc, bag.norig);
- for (unsigned int axi = 0; axi < 3; axi++) {
- if (!E) E |= nrrdResampleSamplesSet(bag.rsmc, axi, bag.norig->axis[axi].size);
- if (!E) E |= nrrdResampleRangeFullSet(bag.rsmc, axi);
- }
- if (!E) E |= nrrdResampleBoundarySet(bag.rsmc, nrrdBoundaryBleed);
- if (!E) E |= nrrdResampleTypeOutSet(bag.rsmc, nrrdTypeDefault);
- if (!E) E |= nrrdResampleRenormalizeSet(bag.rsmc, AIR_TRUE);
- if (E) {
- airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
- fprintf(stderr, "%s: trouble setting up resampler:\n%s", me, err);
- airMopError(mop);
- return 1;
- }
- /* bag.ncval is just a pointer to other nrrds */
- bag.cvalRange = nrrdRangeNew(AIR_NAN, AIR_NAN);
- ELL_3V_COPY(bag.scaleVec, scaleVec);
- bag.glyphScaleRad = glyphScaleRad;
-
- bag.scene = new Deft::Scene();
- bag.scene->bgColor(bg[0], bg[1], bg[2]);
-
- int winy = 10;
- int incy;
- fltk::Window *win = new fltk::Window(400, 600, "pull UI");
- win->begin();
- fltk::Button *stepButton = new fltk::Button(10, winy, 50, incy = 20, "step");
- stepButton->callback((fltk::Callback *)step_cb, &bag);
-
- bag.verbose = new fltk::ValueInput(100, winy, 30, 20, "verb");
- bag.verbose->value(pctx->verbose);
- bag.verbose->callback((fltk::Callback *)verbose_cb, &bag);
-
- bag.iters = new fltk::IntInput(200, winy, 50, 20, "# iters");
- bag.iters->value(1);
-
- if (ssrange[1] > ssrange[0]) {
- fltk::Button *gamButton = new fltk::Button(260, winy, 50, 20, "gamma");
- gamButton->callback((fltk::Callback *)gammaSet_cb, &bag);
- }
- fltk::Button *ccButton = new fltk::Button(360, winy, 30, 20, "CC");
- ccButton->callback((fltk::Callback *)cc_cb, &bag);
-
- winy += incy + 5;
- fltk::Button *saveButton = new fltk::Button(10, winy, 50, 20, "save");
- saveButton->callback((fltk::Callback *)save_cb, &bag);
-
- bag.scaleVecInput[0] = new fltk::FloatInput(120, winy, 35, 20, "scaleVec");
- bag.scaleVecInput[1] = new fltk::FloatInput(160, winy, 35, 20, "");
- bag.scaleVecInput[2] = new fltk::FloatInput(200, winy, 35, 20, "");
- bag.scaleVecInput[0]->value(scaleVec[0]);
- bag.scaleVecInput[1]->value(scaleVec[1]);
- bag.scaleVecInput[2]->value(scaleVec[2]);
- bag.scaleVecInput[0]->callback((fltk::Callback *)scaleGlyph_cb, &bag);
- bag.scaleVecInput[1]->callback((fltk::Callback *)scaleGlyph_cb, &bag);
- bag.scaleVecInput[2]->callback((fltk::Callback *)scaleGlyph_cb, &bag);
-
- bag.glyphScaleRadInput = new fltk::ValueInput(300, winy, 45, 20, "gssr");
- bag.glyphScaleRadInput->range(0.0, 100.0);
- bag.glyphScaleRadInput->step(0.1);
- bag.glyphScaleRadInput->linesize(0.1);
- bag.glyphScaleRadInput->value(glyphScaleRad);
- bag.glyphScaleRadInput->callback((fltk::Callback *)scaleGlyph_cb, &bag);
-
- winy += incy;
- bag.alpha = new Deft::Slider(0, winy, win->w(), incy = 55, "alpha");
- bag.alpha->align(fltk::ALIGN_LEFT);
- bag.alpha->range(0, 1);
- bag.alpha->value(pctx->sysParm.alpha);
- bag.alpha->fastUpdate(1);
- bag.alpha->callback((fltk::Callback *)alpha_cb, &bag);
-
- if (pullInterTypeAdditive == pctx->interType) {
- winy += incy;
- bag.beta = new Deft::Slider(0, winy, win->w(), incy = 55, "beta");
- bag.beta->align(fltk::ALIGN_LEFT);
- bag.beta->range(0, 1);
- bag.beta->value(pctx->sysParm.beta);
- bag.beta->fastUpdate(1);
- bag.beta->callback((fltk::Callback *)beta_cb, &bag);
- }
-
- if (pullEnergyCubicWell == pctx->energySpecR->energy
- || pullEnergyBetterCubicWell == pctx->energySpecR->energy) {
- winy += incy;
- bag.cwell = new Deft::Slider(0, winy, win->w(), incy = 55, "well depth");
- bag.cwell->align(fltk::ALIGN_LEFT);
- bag.cwell->range(-0.04, 0);
- bag.cwell->value(bag.pctx->energySpecR->parm[1]);
- bag.cwell->fastUpdate(1);
- bag.cwell->callback((fltk::Callback *)cwell_cb, &bag);
- /* remember eip as fraction of well depth */
- bag.energyIncreasePermitFrac = energyIncreasePermit / bag.pctx->energySpecR->parm[1];
- } else {
- bag.energyIncreasePermitFrac = AIR_NAN;
- }
-
- winy += incy;
- bag.gamma = new Deft::Slider(0, winy, win->w(), incy = 55, "gamma");
- bag.gamma->align(fltk::ALIGN_LEFT);
- bag.gamma->range(0, 2 * pctx->sysParm.gamma);
- bag.gamma->value(pctx->sysParm.gamma);
- bag.gamma->fastUpdate(1);
- bag.gamma->callback((fltk::Callback *)gamma_cb, &bag);
-
- winy += incy;
- bag.ccSelect = new Deft::Slider(0, winy, win->w(), incy = 55, "CC Select");
- bag.ccSelect->align(fltk::ALIGN_LEFT);
- bag.ccSelect->range(0, 0);
- bag.ccSelect->step(1);
- bag.ccSelect->value(0);
- bag.ccSelect->fastUpdate(1);
- bag.ccSelect->callback((fltk::Callback *)ccSelect_cb, &bag);
-
- bag.ccSingle = new fltk::CheckButton(130, winy + 4, 50, 20, "Single");
- bag.ccSingle->value(0);
- bag.ccSingle->callback((fltk::Callback *)ccSelect_cb, &bag);
-
- winy += incy;
- bag.rho = new Deft::Slider(0, winy, win->w(), incy = 55, "rho");
- bag.rho->align(fltk::ALIGN_LEFT);
- bag.rho->range(0, 1.0);
- bag.rho->value(0.5);
- bag.rho->fastUpdate(1);
- bag.rho->callback((fltk::Callback *)cc_cb, &bag);
-
- if (ssrange[1] > ssrange[0]) {
- winy += incy;
- bag.sclMean = new Deft::Slider(0, winy, win->w(), incy = 55, "scale mean");
- bag.sclMean->align(fltk::ALIGN_LEFT);
- bag.sclMean->range(ssrange[0], ssrange[1]);
- bag.sclMean->value((ssrange[0] + ssrange[1]) / 2);
- bag.sclMean->fastUpdate(1);
- bag.sclMean->callback((fltk::Callback *)scale_cb, &bag);
-
- fltk::Button *reblurButton = new fltk::Button(130, winy + 4, 50, 20, "reblur");
- reblurButton->callback((fltk::Callback *)reblur_cb, &bag);
-
- winy += incy;
- bag.sclWind = new Deft::Slider(0, winy, win->w(), incy = 55, "scale window");
- bag.sclWind->align(fltk::ALIGN_LEFT);
- bag.sclWind->range(0, ssrange[1] - ssrange[0]);
- bag.sclWind->value(ssrange[1] - ssrange[0]);
- bag.sclWind->fastUpdate(1);
- bag.sclWind->callback((fltk::Callback *)scale_cb, &bag);
- scale_cb(NULL, &bag);
- } else {
- bag.sclMin = bag.sclMax = 0;
- }
-
- if (pctx->ispec[pullInfoStrength]) {
- winy += incy;
- bag.strength = new Deft::Slider(0, winy, win->w(), incy = 55, "strength");
- bag.strength->align(fltk::ALIGN_LEFT);
- bag.strength->range(0, 1);
- bag.strength->callback((fltk::Callback *)strength_cb, &bag);
- bag.strength->fastUpdate(1);
- bag.strength->value(0);
- } else {
- bag.strnMin = 0;
- }
- if (pctx->ispec[pullInfoQuality]) {
- winy += incy;
- bag.quality = new Deft::Slider(0, winy, win->w(), incy = 55, "quality");
- bag.quality->align(fltk::ALIGN_LEFT);
- bag.quality->range(-0.1, 1);
- bag.quality->callback((fltk::Callback *)quality_cb, &bag);
- bag.quality->fastUpdate(1);
- bag.quality->value(-0.1);
- } else {
- bag.qualMin = 0;
- }
-
- /*
- winy += incy;
- bag.height = new Deft::Slider(0, winy, win->w(), incy=55, "height");
- bag.height->align(fltk::ALIGN_LEFT);
- bag.height->range(0, 10);
- bag.height->value(10);
- bag.height->fastUpdate(1);
- bag.height->callback((fltk::Callback*)strength_cb, &bag);
- */
-
- win->end();
- win->show();
-
- /* -------------------------------------------------- */
- bag.viewer = new Deft::Viewer(bag.scene, imgSize[0], imgSize[1]);
- if (camkeep) {
- bag.viewer->camera(fr[0], fr[1], fr[2], at[0], at[1], at[2], up[0], up[1], up[2],
- fovy, neer, faar);
- }
- bag.viewer->resizable(bag.viewer);
- bag.viewer->end();
- const char *fakeArgv[2] = {"Deft_pull", NULL};
- bag.viewer->show(1, (char **)fakeArgv);
- if (ortho) {
- /* total hack */
- bag.viewer->keyboard('p', 0, 0);
- }
- /* bag.viewer->helpPrint(); */
- Deft::ViewerUI *viewerUI = new Deft::ViewerUI(bag.viewer);
- viewerUI->show();
- fltk::flush();
-
- /* -------------------------------------------------- */
- if (gageKindScl == vspec[0]->kind) {
- bag.contour = new Deft::Contour();
- bag.contour->volumeSet(bag.nblur);
- bag.contour->twoSided(true);
- bag.scene->objectAdd(bag.contour);
- } else {
- bag.contour = NULL;
- }
-
- /* -------------------------------------------------- */
- Deft::TensorGlyph *glyph = new Deft::TensorGlyph();
- glyph->dynamic(true);
- glyph->twoSided(true);
- glyph->anisoType(aniso);
- glyph->anisoThreshMin(anisoThreshMin);
- glyph->anisoThresh(anisoThresh);
- glyph->glyphType(glyphType);
- glyph->superquadSharpness(sqdSharp);
- glyph->glyphResolution(glyphFacetRes);
- if (tenGlyphTypeBetterquad) {
- glyph->barycentricResolution(baryRes);
- } else {
- glyph->barycentricResolution(20);
- }
- glyph->glyphScale(glyphScale);
- glyph->glyphHaloWidth(glyphHaloWidth);
- glyph->haloTraceBound(haloTraceBound);
- glyph->glyphNormPow(glyphNormPow);
- glyph->glyphEvalPow(glyphEvalPow);
- glyph->rgbEvecParmSet(tenAniso_Cl2, 0, 0.7, 1.0, 2.3, 1.0);
- glyph->rgbEvecParmSet(tenAniso_Cl2, 0, 0, 1.0, 1, 0.0);
- glyph->maskThresh(0.5);
- /*
- void rgbParmSet(int aniso, unsigned int evec,
- double maxSat, double isoGray,
- double gamma, do...
[truncated message content] |
