int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
int size[3];
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "s", "sx sy sz", airTypeInt, 3, 3, size, "128 128 128",
"dimensions of output volume");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, tmplInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
airMopOkay(mop);
exit(0);
}
int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
Nrrd *nin, *_nin;
double *in, sym[21], eval[6], evec[36];
unsigned int rr, cc, ii, jj;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, NULL, "matrix", airTypeOther, 1, 1, &_nin, NULL,
"6x6 matrix", NULL, NULL, nrrdHestNrrd);
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, es6Info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nin = nrrdNew();
airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
if (!(2 == _nin->dim
&& 6 == _nin->axis[0].size
&& 6 == _nin->axis[1].size)) {
fprintf(stderr, "%s: didn't get 2-D 6x6 matrix (got %u-D %ux%u)\n", me,
_nin->dim,
AIR_CAST(unsigned int, _nin->axis[0].size),
AIR_CAST(unsigned int, _nin->axis[1].size));
airMopError(mop); return 1;
}
void
hestInfo(FILE *file, const char *argv0, const char *info, hestParm *_parm) {
hestParm *parm;
parm = !_parm ? hestParmNew() : _parm;
if (info) {
fprintf(file, "\n%s: ", argv0);
_hestPrintStr(file, 0, strlen(argv0) + 2, parm->columns, info, AIR_FALSE);
}
parm = !_parm ? hestParmFree(parm) : NULL;
}
int
main(int argc, char *argv[]) {
char *me, *outS, *err;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
Nrrd *_ninA, *_ninB, *ninA, *ninB, *nmul;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, NULL, "matrix", airTypeOther, 1, 1, &_ninA, NULL,
"first matrix",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, NULL, "matrix", airTypeOther, 1, 1, &_ninB, NULL,
"first matrix",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write output nrrd to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, mulInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
ninA = nrrdNew();
airMopAdd(mop, ninA, (airMopper)nrrdNuke, airMopAlways);
ninB = nrrdNew();
airMopAdd(mop, ninB, (airMopper)nrrdNuke, airMopAlways);
nmul = nrrdNew();
airMopAdd(mop, nmul, (airMopper)nrrdNuke, airMopAlways);
nrrdConvert(ninA, _ninA, nrrdTypeDouble);
nrrdConvert(ninB, _ninB, nrrdTypeDouble);
if (ell_Nm_mul(nmul, ninA, ninB)) {
airMopAdd(mop, err = biffGetDone(ELL), airFree, airMopAlways);
fprintf(stderr, "%s: problem inverting:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (nrrdSave(outS, nmul, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: problem saving output:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, const char **argv) {
const char *me;
airArray *mop;
hestParm *hparm;
unsigned int uci;
FILE *out;
int ret;
AIR_UNUSED(argc);
out = stdout;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
/* This just generates all the usage information for unu itself, and then
for all the unu sub-commands. The purpose is to exercise hest's
generation of usage info for all the options, and to make sure (by human
inspection now, later by something automated) that the use of stderr vs
stdout, and return values, is consistent across all commands */
fprintf(out, "%s: ################### BEGIN unu\n", me);
unrrduUsageUnu("unu", hparm);
fprintf(out, "%s: ################### END unu\n", me);
uci = 0;
do {
fprintf(out, "%s: ################### BEGIN unu %s\n",
me, unrrduCmdList[uci]->name);
ret = unrrduCmdList[uci]->main(0, NULL, unrrduCmdList[uci]->name, hparm);
fprintf(out, "%s: ################### END unu %s (ret=%d)\n",
me, unrrduCmdList[uci]->name, ret);
uci++;
} while (unrrduCmdList[uci]);
airMopOkay(mop);
return 0;
}
/*
******** hestMinNumArgs
**
** The idea is that this helps quickly determine if the options given
** on the command line are insufficient, in order to produce general
** usage information instead of some specific parse error.
**
** Because hest is strictly agnostic with respect to how many command-line
** arguments actually constitute the command itself ("rmdir": one argument,
** "cvs checkout": two arguments), it only concerns itself with the
** command-line arguments following the command.
**
** Thus, hestMinMinArgs() returns the minimum number of command-line
** arguments (following the command) that could be valid. If your
** command is only one argument (like "rmdir"), then you might use
** the true argc passed by the OS to main() as such:
**
** if (argc-1 < hestMinNumArgs(opt)) {
** ... usage ...
** }
**
** But if your command is two arguments (like "cvs checkout"):
**
** if (argc-2 < hestMinNumArgs(opt)) {
** ... usage ...
** }
**
** HOWEVER! don't forget the response files can complicate all this:
** in one argument a response file can provide information for any
** number of arguments, and the argc itself is kind of meaningless.
** The code examples above only really apply when
** hparm->respFileEnable is false. For example, in unrrdu (private.h)
** we find:
**
** if ( (hparm->respFileEnable && !argc) ||
** (!hparm->respFileEnable && argc < hestMinNumArgs(opt)) ) {
** ... usage ...
** }
**
*/
int
hestMinNumArgs(hestOpt *opt) {
hestParm *parm;
int i, count, numOpts;
parm = hestParmNew();
if (_hestPanic(opt, NULL, parm)) {
parm = hestParmFree(parm);
return _hestMax(-1);
}
count = 0;
numOpts = _hestNumOpts(opt);
for (i=0; i<numOpts; i++) {
if (!opt[i].dflt) {
count += opt[i].min;
if (!(0 == opt[i].min && 0 == opt[i].max)) {
count += !!opt[i].flag;
}
}
}
parm = hestParmFree(parm);
return count;
}
int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err;
Nrrd *nhist;
double thresh, expo;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "i", "nhist", airTypeOther, 1, 1, &nhist, NULL,
"input histogram", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "e", "expo", airTypeDouble, 1, 1, &expo, "2.0",
"exponent to use for variance calculation");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, otsuInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (nrrdHistoThresholdOtsu(&thresh, nhist, expo)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
fprintf(stderr, "%s: threshold = %g\n", me, thresh);
airMopOkay(mop);
exit(0);
}
void
hestUsage(FILE *f, hestOpt *opt, const char *argv0, hestParm *_parm) {
int i, numOpts;
char buff[2*AIR_STRLEN_HUGE], tmpS[AIR_STRLEN_HUGE];
hestParm *parm;
parm = !_parm ? hestParmNew() : _parm;
if (_hestPanic(opt, NULL, parm)) {
/* we can't continue; the opt array is botched */
parm = !_parm ? hestParmFree(parm) : NULL;
return;
}
numOpts = _hestNumOpts(opt);
fprintf(f, "\n");
strcpy(buff, "Usage: ");
strcat(buff, argv0 ? argv0 : "");
if (parm && parm->respFileEnable) {
sprintf(tmpS, " [%cfile\t...]", parm->respFileFlag);
strcat(buff, tmpS);
}
for (i=0; i<numOpts; i++) {
strcat(buff, " ");
if (1 == opt[i].kind || (opt[i].flag && opt[i].dflt))
strcat(buff, "[");
_hestSetBuff(buff, opt + i, parm, AIR_TRUE, AIR_TRUE);
if (1 == opt[i].kind || (opt[i].flag && opt[i].dflt))
strcat(buff, "]");
}
_hestPrintStr(f, strlen("Usage: "), 0, parm->columns, buff, AIR_TRUE);
parm = !_parm ? hestParmFree(parm) : NULL;
return;
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
int fidx, aidx, num, frames;
double psc, width[2], arrowWidth, lineWidth, angle, seglen,
x0, y0, x1, y1, cc, ss;
wheelPS wps;
char filename[AIR_STRLEN_MED];
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "w", "arrowWidth lineWidth", airTypeDouble, 2, 2, width,
"1.0 0.2", "widths");
hestOptAdd(&hopt, "n", "number", airTypeInt, 1, 1, &num, "10",
"number of arrows");
hestOptAdd(&hopt, "f", "frames", airTypeInt, 1, 1, &frames, "10",
"number of frames");
hestOptAdd(&hopt, "psc", "scale", airTypeDouble, 1, 1, &psc, "200",
"scaling from world space to PostScript points");
hestOptAdd(&hopt, "o", "prefix", airTypeString, 1, 1, &outS, NULL,
"prefix of file names");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, interInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
for (fidx=0; fidx<frames; fidx++) {
sprintf(filename, "%s%03d.eps", outS, fidx);
if (!(wps.file = airFopen(filename, stdout, "wb"))) {
fprintf(stderr, "%s: couldn't open output file\n", me);
airMopError(mop);
return 1;
}
lineWidth = width[0];
arrowWidth = width[1];
wps.psc = psc;
ELL_4V_SET(wps.bbox, -0.45, -0.85, 1.1, 0.85);
wheelPreamble(&wps);
fprintf(wps.file, "0 setlinecap\n");
wheelGray(&wps, 0.4);
wheelWidth(&wps, lineWidth);
x0 = 0;
y0 = 0;
seglen = 1.0/num;
angle = AIR_AFFINE(0, fidx, frames, 0, 2*AIR_PI);
for (aidx=1; aidx<=num; aidx++) {
cc = cos(angle*aidx)*seglen;
ss = sin(angle*aidx)*seglen;
x1 = x0 + 0.90*cc;
y1 = y0 + 0.90*ss;
wheelArrow(&wps, x0, y0, x1, y1, arrowWidth, arrowWidth*0.4);
x0 += cc;
y0 += ss;
}
wheelGray(&wps, 0.0);
wheelArrow(&wps, 0, 0, x0, y0, arrowWidth, arrowWidth*0.4);
wheelEpilog(&wps);
airFclose(wps.file);
}
airMopOkay(mop);
exit(0);
}
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
main(int argc, char *argv[]) {
char *me, *errS, *outS;
hestOpt *hopt=NULL;
hestParm *hparm;
airArray *mop;
Nrrd *nin, *nout;
NrrdKernelSpec *ksp;
mossSampler *msp;
double mat[6], **matList, *origInfo, origMat[6], origInvMat[6], ox, oy,
min[2], max[2];
int d, bound, ax0, size[2];
unsigned int matListLen, _bkgLen, i, avgNum;
float *bkg, *_bkg, scale[4];
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_FALSE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->respFileEnable = AIR_TRUE;
hestOptAdd(&hopt, "i", "image", airTypeOther, 1, 1, &nin, "-",
"input image", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "0", "origin", airTypeOther, 1, 1, &origInfo, "p:0,0",
"where to location (0,0) prior to applying transforms.\n "
"\b\bo \"u:<float>,<float>\" locate origin in a unit box "
"[0,1]x[0,1] which covers the original image\n "
"\b\bo \"p:<float>,<float>\" locate origin at a particular "
"pixel location, in the index space of the image",
NULL, NULL, mossHestOrigin);
hestOptAdd(&hopt, "t", "xform0", airTypeOther, 1, -1, &matList, NULL,
"transform(s) to apply to image. Transforms "
"are applied in the order in which they appear.\n "
"\b\bo \"identity\": no geometric transform, just resampling\n "
"\b\bo \"translate:x,y\": shift image by vector (x,y), as "
"measured in pixels\n "
"\b\bo \"rotate:ang\": rotate CCW by ang degrees\n "
"\b\bo \"scale:xs,ys\": scale by xs in X, and ys in Y\n "
"\b\bo \"shear:fix,amnt\": shear by amnt, keeping fixed "
"the pixels along a direction <fix> degrees from the X axis\n "
"\b\bo \"flip:ang\": flip along axis an angle <ang> degrees from "
"the X axis\n "
"\b\bo \"a,b,tx,c,d,ty\": specify the transform explicitly "
"in row-major order (opposite of PostScript) ",
&matListLen, NULL, mossHestTransform);
hestOptAdd(&hopt, "k", "kernel", airTypeOther, 1, 1, &ksp,
"cubic:0,0.5", "reconstruction kernel",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "min", "xMin yMin", airTypeDouble, 2, 2, min, "nan nan",
"lower bounding corner of output image. Default (by not "
"using this option) is the lower corner of input image. ");
hestOptAdd(&hopt, "max", "xMax yMax", airTypeDouble, 2, 2, max, "nan nan",
"upper bounding corner of output image. Default (by not "
"using this option) is the upper corner of input image. ");
hestOptAdd(&hopt, "b", "boundary", airTypeEnum, 1, 1, &bound, "bleed",
"what to do when sampling outside original image.\n "
"\b\bo \"bleed\": copy values at image border outward\n "
"\b\bo \"wrap\": do wrap-around on image locations\n "
"\b\bo \"pad\": use a given background value (via \"-bg\")",
NULL, nrrdBoundary);
hestOptAdd(&hopt, "bg", "bg0 bg1", airTypeFloat, 1, -1, &_bkg, "nan",
"background color to use with boundary behavior \"pad\". "
"Defaults to all zeroes.",
&_bkgLen);
hestOptAdd(&hopt, "s", "xSize ySize", airTypeOther, 2, 2, scale, "x1 x1",
"For each axis, information about how many samples in output:\n "
"\b\bo \"x<float>\": number of output samples is some scaling of "
" the number input of samples; multiplied by <float>\n "
"\b\bo \"<int>\": specify exact number of samples",
NULL, NULL, &unrrduHestScaleCB);
hestOptAdd(&hopt, "a", "avg #", airTypeUInt, 1, 1, &avgNum, "0",
"number of averages (if there there is only one "
"rotation)");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write output nrrd to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, ilkInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
msp = mossSamplerNew();
airMopAdd(mop, msp, (airMopper)mossSamplerNix, airMopAlways);
msp->boundary = bound;
if (mossSamplerKernelSet(msp, ksp->kernel, ksp->parm)) {
fprintf(stderr, "%s: trouble with sampler:\n%s\n",
me, errS = biffGetDone(MOSS)); free(errS);
airMopError(mop); return 1;
}
if (nrrdBoundaryPad == bound) {
if (_bkgLen != MOSS_NCOL(nin)) {
fprintf(stderr, "%s: got %d background colors, image has "
_AIR_SIZE_T_CNV " colors\n",
me, _bkgLen, MOSS_NCOL(nin));
airMopError(mop); return 1;
} else {
bkg = _bkg;
}
} else {
/* maybe warn user if they gave a background that won't be used? */
/* No- because hest is stupid, and right now we always parse the
single (default) "nan" for this argument! */
bkg = NULL;
}
ax0 = MOSS_AXIS0(nin);
if (!( AIR_EXISTS(nin->axis[ax0+0].min)
&& AIR_EXISTS(nin->axis[ax0+0].max))) {
nrrdAxisInfoMinMaxSet(nin, ax0+0, mossDefCenter);
}
if (!( AIR_EXISTS(nin->axis[ax0+1].min)
&& AIR_EXISTS(nin->axis[ax0+1].max))) {
nrrdAxisInfoMinMaxSet(nin, ax0+1, mossDefCenter);
}
min[0] = AIR_EXISTS(min[0]) ? min[0] : nin->axis[ax0+0].min;
max[0] = AIR_EXISTS(max[0]) ? max[0] : nin->axis[ax0+0].max;
min[1] = AIR_EXISTS(min[1]) ? min[1] : nin->axis[ax0+1].min;
max[1] = AIR_EXISTS(max[1]) ? max[1] : nin->axis[ax0+1].max;
for (d=0; d<2; d++) {
switch((int)scale[0 + 2*d]) {
case 0:
/* same number of samples as input */
size[d] = nin->axis[ax0+d].size;
break;
case 1:
/* scaling of input # samples */
size[d] = (int)(scale[1 + 2*d]*nin->axis[ax0+d].size);
break;
case 2:
/* explicit # of samples */
size[d] = (int)(scale[1 + 2*d]);
break;
}
}
/* find origin-based pre- and post- translate */
if (0 == origInfo[0]) {
/* absolute pixel position */
mossMatTranslateSet(origMat, -origInfo[1], -origInfo[2]);
} else {
/* in unit box [0,1]x[0,1] */
ox = AIR_AFFINE(0.0, origInfo[1], 1.0,
nin->axis[ax0+0].min, nin->axis[ax0+0].max);
oy = AIR_AFFINE(0.0, origInfo[2], 1.0,
nin->axis[ax0+1].min, nin->axis[ax0+1].max);
mossMatTranslateSet(origMat, -ox, -oy);
}
mossMatInvert(origInvMat, origMat);
/* form complete transform */
mossMatIdentitySet(mat);
mossMatLeftMultiply(mat, origMat);
for (i=0; i<matListLen; i++) {
mossMatLeftMultiply(mat, matList[i]);
}
mossMatLeftMultiply(mat, origInvMat);
if (!AIR_EXISTS(nin->axis[ax0+0].min) || !AIR_EXISTS(nin->axis[ax0+0].max)) {
nrrdAxisInfoMinMaxSet(nin, ax0+0, mossDefCenter);
}
if (!AIR_EXISTS(nin->axis[ax0+1].min) || !AIR_EXISTS(nin->axis[ax0+1].max)) {
nrrdAxisInfoMinMaxSet(nin, ax0+1, mossDefCenter);
}
if (avgNum > 1) {
unsigned int ai;
double angleMax, angle, mrot[6];
Nrrd *ntmp, *nacc;
NrrdIter *itA, *itB;
int E;
ntmp = nrrdNew();
airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
nacc = nrrdNew();
airMopAdd(mop, nacc, (airMopper)nrrdNuke, airMopAlways);
itA = nrrdIterNew();
airMopAdd(mop, itA, (airMopper)nrrdIterNix, airMopAlways);
itB = nrrdIterNew();
airMopAdd(mop, itB, (airMopper)nrrdIterNix, airMopAlways);
E = 0;
angleMax = atan2(mat[3], mat[0]);
fprintf(stderr, "%s: %u angles ", me, avgNum);
for (ai=0; ai<avgNum; ai++) {
fprintf(stderr, "."); fflush(stderr);
angle = (180/AIR_PI)*AIR_AFFINE(0, ai, avgNum-1, angleMax, -angleMax);
mossMatIdentitySet(mat);
mossMatLeftMultiply(mat, origMat);
mossMatRotateSet(mrot, angle);
mossMatLeftMultiply(mat, mrot);
mossMatLeftMultiply(mat, origInvMat);
if (mossLinearTransform(ntmp, nin, bkg,
mat, msp,
min[0], max[0], min[1], max[1],
size[0], size[1])) {
fprintf(stderr, "%s: problem doing transform:\n%s\n",
me, errS = biffGetDone(MOSS)); free(errS);
airMopError(mop); return 1;
}
if (!ai) {
if (!E) E |= nrrdCopy(nacc, ntmp);
} else {
if (!E) E |= nrrdArithBinaryOp(nacc, nrrdBinaryOpAdd, nacc, ntmp);
}
if (E) {
break;
}
}
fprintf(stderr, "\n");
nrrdIterSetNrrd(itA, nacc);
nrrdIterSetValue(itB, avgNum);
if (!E) E |= nrrdArithIterBinaryOp(nout, nrrdBinaryOpDivide,
itA, itB);
if (E) {
fprintf(stderr, "%s: problem making output:\n%s\n",
me, errS = biffGetDone(NRRD)); free(errS);
airMopError(mop); return 1;
}
} else {
if (mossLinearTransform(nout, nin, bkg,
mat, msp,
min[0], max[0], min[1], max[1],
size[0], size[1])) {
fprintf(stderr, "%s: problem doing transform:\n%s\n",
me, errS = biffGetDone(MOSS)); free(errS);
airMopError(mop); return 1;
}
}
if (nrrdSave(outS, nout, NULL)) {
fprintf(stderr, "%s: problem saving output:\n%s\n",
me, errS = biffGetDone(NRRD)); free(errS);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, char **argv) {
int i, ret;
char *me, *argv0 = NULL, *err;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* if user hasn't tried to set nrrdStateKindNoop by an environment
variable, we set it to false, since its probably what people expect */
if (!getenv("NRRD_STATE_KIND_NOOP")) {
nrrdStateKindNoop = AIR_FALSE;
}
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for how Teem was built here.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_TRUE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->columns = unrrduDefNumColumns;
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
unrrduUsage("unu", hparm);
airMopError(mop);
exit(1);
}
/* else, we should see if they're asking for a command we know about */
for (i=0; unrrduCmdList[i]; i++) {
if (!strcmp(argv[1], unrrduCmdList[i]->name))
break;
}
/* unrrduCmdList[] is NULL-terminated */
if (unrrduCmdList[i]) {
/* yes, we have that command */
/* initialize variables used by the various commands */
argv0 = (char *)calloc(strlen(UNU) + strlen(argv[1]) + 2, sizeof(char));
airMopMem(mop, &argv0, airMopAlways);
sprintf(argv0, "%s %s", UNU, argv[1]);
/* run the individual unu program, saving its exit status */
ret = unrrduCmdList[i]->main(argc-2, argv+2, argv0, hparm);
} else {
fprintf(stderr, "%s: unrecognized command: \"%s\"; type \"%s\" for "
"complete list\n", me, argv[1], me);
ret = 1;
}
airMopDone(mop, ret);
return ret;
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, done[13];
Nrrd *nin, *nblur, *nout;
NrrdKernelSpec *kb0, *kb1, *k00, *k11, *k22;
NrrdResampleContext *rsmc;
int E;
unsigned int sx, sy, sz, xi, yi, zi, ai;
gageContext *ctx;
gagePerVolume *pvl;
const double *gvec, *gmag, *evec0, *eval;
double (*ins)(void *v, size_t I, double d);
double (*lup)(const void *v, size_t I);
double dotmax, dotpow, gmmax, evalshift, gmpow, _dotmax, _gmmax, scl, clamp;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "kb0", "kernel", airTypeOther, 1, 1, &kb0,
"guass:3,5", "kernel to use for pre-process blurring",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "kb1", "kernel", airTypeOther, 1, 1, &kb1,
"cubic:1.5,1,0", "kernel to use for pos-process blurring",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &k00,
"cubic:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &k11,
"cubicd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "dotmax", "dot", airTypeDouble, 1, 1, &dotmax, "5",
"max effective value of dot(gvec, evec0)");
hestOptAdd(&hopt, "evs", "shift", airTypeDouble, 1, 1, &evalshift, "0",
"negative shift to avoid changing mostly flat regions");
hestOptAdd(&hopt, "clamp", "clamp", airTypeDouble, 1, 1, &clamp, "nan",
"if it exists, data value can't be forced below this");
hestOptAdd(&hopt, "dotpow", "pow", airTypeDouble, 1, 1, &dotpow, "1",
"exponent for dot");
hestOptAdd(&hopt, "gmmax", "dot", airTypeDouble, 1, 1, &gmmax, "2",
"max effective value of gmag");
hestOptAdd(&hopt, "gmpow", "pow", airTypeDouble, 1, 1, &gmpow, "1",
"exponent for gmag");
hestOptAdd(&hopt, "scl", "scale", airTypeDouble, 1, 1, &scl, "0.1",
"how much to scale hack to decrease input value");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"fixed volume output");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, vhInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!( 3 == nin->dim
&& nrrdTypeBlock != nin->type )) {
fprintf(stderr, "%s: need a 3-D scalar nrrd (not %u-D %s)", me,
nin->dim, airEnumStr(nrrdType, nin->type));
airMopError(mop); return 1;
}
nblur = nrrdNew();
airMopAdd(mop, nblur, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nblur, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
fprintf(stderr, "%s: pre-blurring ... ", me);
fflush(stderr);
rsmc = nrrdResampleContextNew();
airMopAdd(mop, rsmc, (airMopper)nrrdResampleContextNix, airMopAlways);
E = AIR_FALSE;
if (!E) E |= nrrdResampleDefaultCenterSet(rsmc, nrrdCenterCell);
if (!E) E |= nrrdResampleNrrdSet(rsmc, nin);
for (ai=0; ai<3; ai++) {
if (!E) E |= nrrdResampleKernelSet(rsmc, ai, kb0->kernel, kb0->parm);
if (!E) E |= nrrdResampleSamplesSet(rsmc, ai, nin->axis[ai].size);
if (!E) E |= nrrdResampleRangeFullSet(rsmc, ai);
}
if (!E) E |= nrrdResampleBoundarySet(rsmc, nrrdBoundaryBleed);
if (!E) E |= nrrdResampleTypeOutSet(rsmc, nrrdTypeDefault);
if (!E) E |= nrrdResampleRenormalizeSet(rsmc, AIR_TRUE);
if (!E) E |= nrrdResampleExecute(rsmc, nblur);
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
fprintf(stderr, "done.\n");
ctx = gageContextNew();
airMopAdd(mop, ctx, (airMopper)gageContextNix, airMopAlways);
gageParmSet(ctx, gageParmRenormalize, AIR_TRUE);
gageParmSet(ctx, gageParmCheckIntegrals, AIR_TRUE);
E = 0;
if (!E) E |= !(pvl = gagePerVolumeNew(ctx, nblur, gageKindScl));
if (!E) E |= gagePerVolumeAttach(ctx, pvl);
if (!E) E |= gageKernelSet(ctx, gageKernel00, k00->kernel, k00->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel11, k11->kernel, k11->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel22, k22->kernel, k22->parm);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradVec);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradMag);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclHessEvec0);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclHessEval);
if (!E) E |= gageUpdate(ctx);
if (E) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
gvec = gageAnswerPointer(ctx, pvl, gageSclGradVec);
gmag = gageAnswerPointer(ctx, pvl, gageSclGradMag);
evec0 = gageAnswerPointer(ctx, pvl, gageSclHessEvec0);
eval = gageAnswerPointer(ctx, pvl, gageSclHessEval);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
if (!(nout->type == nin->type && nblur->type == nin->type)) {
fprintf(stderr, "%s: whoa, types (%s %s %s) not all equal\n", me,
airEnumStr(nrrdType, nin->type),
airEnumStr(nrrdType, nblur->type),
airEnumStr(nrrdType, nout->type));
}
ins = nrrdDInsert[nout->type];
lup = nrrdDLookup[nout->type];
sx = nin->axis[0].size;
sy = nin->axis[1].size;
sz = nin->axis[2].size;
gageProbe(ctx, 0, 0, 0);
_dotmax = ELL_3V_DOT(gvec, evec0);
_gmmax = *gmag;
fprintf(stderr, "%s: hacking ", me);
fflush(stderr);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
fflush(stderr);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
size_t si;
double dot, evl, gm, shift, in, out, mode;
gageProbe(ctx, xi, yi, zi);
si = xi + sx*(yi + sy*zi);
dot = ELL_3V_DOT(gvec, evec0);
_dotmax = AIR_MAX(_dotmax, dot);
dot = AIR_ABS(dot);
dot = 1 - AIR_MIN(dot, dotmax)/dotmax;
dot = pow(dot, dotpow);
evl = AIR_MAX(0, eval[0] - evalshift);
mode = airMode3_d(eval);
evl *= AIR_AFFINE(-1, mode, 1, 0, 1);
_gmmax = AIR_MAX(_gmmax, *gmag);
gm = 1 - AIR_MIN(*gmag, gmmax)/gmmax;
gm = pow(gm, gmpow);
shift = scl*gm*evl*dot;
if (AIR_EXISTS(clamp)) {
in = lup(nin->data, si);
out = in - shift;
out = AIR_MAX(out, clamp);
shift = AIR_MAX(0, in - out);
}
ins(nout->data, si, shift);
}
}
}
fprintf(stderr, "\n");
fprintf(stderr, "%s: max dot seen: %g\n", me, _dotmax);
fprintf(stderr, "%s: max gm seen: %g\n", me, _gmmax);
fprintf(stderr, "%s: post-blurring ... ", me);
fflush(stderr);
E = AIR_FALSE;
if (!E) E |= nrrdResampleNrrdSet(rsmc, nout);
for (ai=0; ai<3; ai++) {
if (!E) E |= nrrdResampleKernelSet(rsmc, ai, kb1->kernel, kb1->parm);
if (!E) E |= nrrdResampleSamplesSet(rsmc, ai, nout->axis[ai].size);
if (!E) E |= nrrdResampleRangeFullSet(rsmc, ai);
}
if (!E) E |= nrrdResampleExecute(rsmc, nblur);
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
fprintf(stderr, "done.\n");
for (zi=0; zi<sz; zi++) {
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
size_t si;
double in, shift;
si = xi + sx*(yi + sy*zi);
in = lup(nin->data, si);
shift = lup(nblur->data, si);
ins(nout->data, si, in - shift);
}
}
}
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, char **argv) {
int i, ret;
char *me, *argv0 = NULL, *err;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for Teem.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_FALSE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->cleverPluralizeOtherY = AIR_TRUE;
hparm->columns = 78;
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
baneGkmsUsage(GKMS, hparm);
airMopError(mop);
exit(1);
}
/* else, we should see if they're asking for a command we know about */
/* baneGkmsCmdList[] is NULL-terminated */
for (i=0; baneGkmsCmdList[i]; i++) {
if (!strcmp(argv[1], baneGkmsCmdList[i]->name))
break;
}
if (baneGkmsCmdList[i]) {
/* yes, we have that command */
/* initialize variables used by the various commands */
argv0 = AIR_CAST(char*, malloc(strlen(GKMS) + strlen(argv[1]) + 2));
airMopMem(mop, &argv0, airMopAlways);
sprintf(argv0, "%s %s", GKMS, argv[1]);
/* run the individual unu program, saving its exit status */
ret = baneGkmsCmdList[i]->main(argc-2, argv+2, argv0, hparm);
if (1 == ret) {
airMopAdd(mop, err=biffGetDone(BANE), airFree, airMopAlways);
fprintf(stderr, "%s: error:\n%s", argv0, err);
} else if (2 == ret) {
/* gkms command has already handled printing error messages */
ret = 1;
}
} else {
int
main(int argc, char *argv[]) {
gageKind *kind;
char *me, *outS, *err;
hestParm *hparm;
hestOpt *hopt = NULL;
NrrdKernelSpec *ksp;
int otype;
unsigned int maxIter;
double epsilon, lastDiff, step;
Nrrd *nin, *nout;
airArray *mop;
mop = airMopNew();
me = argv[0];
hparm = hestParmNew();
airMopAdd(mop, hparm, AIR_CAST(airMopper, hestParmFree), airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
"\"kind\" of volume (\"scalar\", \"vector\", "
"\"tensor\", or \"dwi\")",
NULL, NULL, &probeKindHestCB);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &ksp, NULL,
"convolution kernel",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "mi", "max # iters", airTypeUInt, 1, 1, &maxIter, "100",
"maximum number of iterations with which to compute the "
"deconvolution");
hestOptAdd(&hopt, "e", "epsilon", airTypeDouble, 1, 1, &epsilon, "0.000001",
"convergence threshold");
hestOptAdd(&hopt, "s", "step", airTypeDouble, 1, 1, &step, "1.0",
"scaling of value update");
hestOptAdd(&hopt, "t", "type", airTypeOther, 1, 1, &otype, "default",
"type to save output as. By default (not using this option), "
"the output type is the same as the input type",
NULL, NULL, &unrrduHestMaybeTypeCB);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output volume");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, deconvInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestOptFree), airMopAlways);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestParseFree), airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, AIR_CAST(airMopper, nrrdNuke), airMopAlways);
if (gageDeconvolve(nout, &lastDiff,
nin, kind,
ksp, otype,
maxIter, AIR_TRUE,
step, epsilon, 1)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop);
return 1;
}
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble saving output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err;
Nrrd *nin, *nhist;
double vmin, vmax, rmax, val, cent[2], rad;
int bins[2], sx, sy, xi, yi, ridx, hidx, rbins, hbins;
NrrdRange *range;
double (*lup)(const void *v, size_t I), *hist;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input image", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "rbins hbins", airTypeInt, 2, 2, bins, NULL,
"# of histogram bins: radial and value");
hestOptAdd(&hopt, "min", "value", airTypeDouble, 1, 1, &vmin, "nan",
"Value at low end of histogram. Defaults to lowest value "
"found in input nrrd.");
hestOptAdd(&hopt, "max", "value", airTypeDouble, 1, 1, &vmax, "nan",
"Value at high end of histogram. Defaults to highest value "
"found in input nrrd.");
hestOptAdd(&hopt, "rmax", "max radius", airTypeDouble, 1, 1, &rmax, "nan",
"largest radius to include in histogram");
hestOptAdd(&hopt, "c", "center x, y", airTypeDouble, 2, 2, cent, NULL,
"The center point around which to build radial histogram");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write histogram to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, histradInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (2 != nin->dim) {
fprintf(stderr, "%s: need 2-D input (not %d-D)\n", me, nin->dim);
airMopError(mop); return 1;
}
rbins = bins[0];
hbins = bins[1];
nhist = nrrdNew();
airMopAdd(mop, nhist, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nhist, nrrdTypeDouble, 2,
AIR_CAST(size_t, rbins),
AIR_CAST(size_t, hbins))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate histogram:\n%s", me, err);
airMopError(mop); return 1;
}
if (!( AIR_EXISTS(vmin) && AIR_EXISTS(vmax) )) {
range = nrrdRangeNewSet(nin, nrrdStateBlind8BitRange);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
vmin = AIR_EXISTS(vmin) ? vmin : range->min;
vmax = AIR_EXISTS(vmax) ? vmax : range->max;
}
#define DIST(x0, y0, x1, y1) (sqrt((x0-x1)*(x0-x1) + (y0-y1)*(y0-y1)))
sx = nin->axis[0].size;
sy = nin->axis[1].size;
if (!AIR_EXISTS(rmax)) {
rmax = 0;
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], 0, 0));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], sx-1, 0));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], 0, sy-1));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], sx-1, sy-1));
}
lup = nrrdDLookup[nin->type];
hist = (double*)(nhist->data);
for (xi=0; xi<sx; xi++) {
for (yi=0; yi<sy; yi++) {
rad = DIST(cent[0], cent[1], xi, yi);
if (!AIR_IN_OP(0, rad, rmax)) {
continue;
}
val = lup(nin->data, xi + sx*yi);
if (!AIR_IN_OP(vmin, val, vmax)) {
continue;
}
ridx = airIndex(0, rad, rmax, rbins);
hidx = airIndex(vmin, val, vmax, hbins);
hist[ridx + rbins*hidx] += 1;
}
}
nhist->axis[0].min = 0;
nhist->axis[0].max = rmax;
nhist->axis[1].min = vmin;
nhist->axis[1].max = vmax;
if (nrrdSave(outS, nhist, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
double tval[6], ABC[3], geom[3], rnth[3], RA, norm, mu2, tmpr=0, tmpa=0,
xroot[3], yroot[3], bbox[4], htick, htth, psc;
wheelPS wps;
int correct, labels, drawRA;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "t", "a b c d e f", airTypeDouble, 6, 6, tval,
"nan nan nan nan nan nan nan",
"six values of symmetric tensors");
hestOptAdd(&hopt, "ABC", "A B C", airTypeDouble, 3, 3, ABC, "nan nan nan",
"directly give coefficients of cubic polynomial "
"(and override info from \"-t\")");
hestOptAdd(&hopt, "g", "c rad th", airTypeDouble, 3, 3, geom, "nan nan nan",
"directly give center, radius, and angle (in degrees) of wheel "
"(and override info from \"-t\" and \"-ABC\"");
hestOptAdd(&hopt, "p", "RA norm th", airTypeDouble, 3, 3, rnth,
"nan nan nan",
"directly give RA, norm, and angle (in degrees) of tensor "
"(and override info from \"-t\", \"-ABC\", and \"-geom\"");
hestOptAdd(&hopt, "correct", NULL, airTypeInt, 0, 0, &correct, NULL,
"when using \"-g\", be honest about what the estimated "
"acos(sqrt(2)*skew)/3 is going to be");
hestOptAdd(&hopt, "labels", NULL, airTypeInt, 0, 0, &labels, NULL,
"put little labels on things; fix with psfrag in LaTeX");
hestOptAdd(&hopt, "RA", NULL, airTypeInt, 0, 0, &drawRA, NULL,
"draw extra geometry associated with RA");
hestOptAdd(&hopt, "htick", "pos", airTypeDouble, 1, 1, &htick, "nan",
"location of single tick mark on horizontal axis");
hestOptAdd(&hopt, "htth", "thick", airTypeDouble, 1, 1, &htth, "3",
"thickness of horizontal tick");
hestOptAdd(&hopt, "bb", "bbox", airTypeDouble, 4, 4, bbox,
"nan nan nan nan", "bounding box, in world space around the "
"region of the graph that should be drawn to EPS");
hestOptAdd(&hopt, "ysc", "scale", airTypeDouble, 1, 1, &(wps.yscale), "0.5",
"scaling on Y axis for drawing graph of characteristic "
"polynomial, or \"0\" to turn this off.");
hestOptAdd(&hopt, "psc", "scale", airTypeDouble, 1, 1, &psc, "100",
"scaling from world space to PostScript points");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write EPS output to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, wheelInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!(wps.file = airFopen(outS, stdout, "wb"))) {
fprintf(stderr, "%s: couldn't open output file\n", me);
airMopError(mop); return 1;
}
airMopAdd(mop, wps.file, (airMopper)airFclose, airMopAlways);
if (AIR_EXISTS(rnth[0])) {
RA = rnth[0];
norm = rnth[1];
mu2 = (norm*norm/3)*(2*RA*RA/(1 + 2*RA*RA));
geom[0] = sqrt(mu2)/(sqrt(2)*RA);
geom[1] = sqrt(2*mu2);
geom[2] = rnth[2];
wheelGeomToRoot(xroot, yroot, geom);
wheelGeomToABC(ABC, geom[0], geom[1], geom[2]);
} else if (AIR_EXISTS(geom[0])) {
wheelGeomToRoot(xroot, yroot, geom);
if (correct) {
tval[0] = xroot[0];
tval[1] = tval[2] = 0;
tval[3] = xroot[1];
tval[4] = 0;
tval[5] = xroot[2];
wheelTenToGeom(geom,
tval[0], tval[1], tval[2], tval[3], tval[4], tval[5]);
wheelGeomToRoot(xroot, yroot, geom);
}
wheelGeomToABC(ABC, geom[0], geom[1], geom[2]);
wheelGeomToRNTH(rnth, geom[0], geom[1], geom[2]);
} else if (AIR_EXISTS(ABC[0])) {
wheelABCToGeom(geom, ABC[0], ABC[1], ABC[2]);
wheelGeomToRNTH(rnth, geom[0], geom[1], geom[2]);
wheelGeomToRoot(xroot, yroot, geom);
} else {
wheelTenToGeom(geom, tval[0], tval[1], tval[2], tval[3], tval[4], tval[5]);
wheelGeomToRoot(xroot, yroot, geom);
wheelGeomToRNTH(rnth, geom[0], geom[1], geom[2]);
wheelGeomToABC(ABC, geom[0], geom[1], geom[2]);
}
fprintf(stderr, "%s: RNTH: %g %g %g\n", me, rnth[0], rnth[1], rnth[2]);
fprintf(stderr, "%s: ABC: %g %g %g\n", me, ABC[0], ABC[1], ABC[2]);
fprintf(stderr, "%s: xroot: %g %g %g\n",
me, xroot[0], xroot[1], xroot[2]);
fprintf(stderr, "%s: geom: %g %g %g\n", me, geom[0], geom[1], geom[2]);
if (!AIR_EXISTS(bbox[0])) {
bbox[0] = geom[0] - 1.2*geom[1];
bbox[1] = - 1.2*geom[1];
bbox[2] = geom[0] + 1.2*geom[1];
bbox[3] = + 1.2*geom[1];
fprintf(stderr, "%s: bbox %g %g %g %g\n", me,
bbox[0], bbox[1], bbox[2], bbox[3]);
}
wps.psc = psc;
ELL_4V_COPY(wps.bbox, bbox);
wheelPreamble(&wps);
/* graph */
if (wps.yscale) {
wheelWidth(&wps, 4);
wheelGray(&wps, 0.5);
wheelGraph(&wps, xroot[0], xroot[1], xroot[2]);
}
/* axis */
wheelWidth(&wps, 2);
wheelGray(&wps, 0.0);
wheelLine(&wps, bbox[0], 0, bbox[2], 0);
/* circle */
wheelWidth(&wps, 3);
wheelCircle(&wps, geom[0], 0, geom[1]);
/* spokes */
wheelWidth(&wps, 4);
wheelLine(&wps, geom[0], 0, xroot[0], yroot[0]);
wheelLine(&wps, geom[0], 0, xroot[1], yroot[1]);
wheelLine(&wps, geom[0], 0, xroot[2], yroot[2]);
/* dots at spoke ends */
wheelDot(&wps, xroot[0], yroot[0], 0.025*geom[1]);
wheelDot(&wps, xroot[1], yroot[1], 0.025*geom[1]);
wheelDot(&wps, xroot[2], yroot[2], 0.025*geom[1]);
/* lines from dots to roots */
wheelWidth(&wps, 2);
fprintf(wps.file, "gsave\n");
fprintf(wps.file, "[2 4] 0 setdash\n");
wheelLine(&wps, xroot[0], 0, xroot[0], yroot[0]);
wheelLine(&wps, xroot[1], 0, xroot[1], yroot[1]);
wheelLine(&wps, xroot[2], 0, xroot[2], yroot[2]);
fprintf(wps.file, "grestore\n");
/* tickmarks */
wheelWidth(&wps, 6);
wheelLine(&wps, xroot[0], -0.02*geom[1], xroot[0], 0.02*geom[1]);
wheelLine(&wps, xroot[1], -0.02*geom[1], xroot[1], 0.02*geom[1]);
wheelLine(&wps, xroot[2], -0.02*geom[1], xroot[2], 0.02*geom[1]);
if (AIR_EXISTS(htick)) {
wheelWidth(&wps, htth);
wheelLine(&wps, htick, -0.04, htick, 0.04);
}
/* RA angle */
if (drawRA) {
wheelWidth(&wps, 3);
wheelLine(&wps, 0.0, 0.0, geom[0], geom[1]);
wheelWidth(&wps, 2);
fprintf(wps.file, "gsave\n");
fprintf(wps.file, "[2 4] 0 setdash\n");
wheelLine(&wps, geom[0], geom[1], geom[0], 0);
fprintf(wps.file, "grestore\n");
}
/* labels, if wanted */
if (labels) {
fprintf(wps.file, "/Helvetica findfont 20 scalefont setfont\n");
wheelLabel(&wps, geom[0], 0, "center");
wheelLine(&wps, geom[0], -0.02*geom[1], geom[0], 0.02*geom[1]);
wheelLabel(&wps, (geom[0] + xroot[0])/1.8, yroot[0]/1.8, "radius");
wheelWidth(&wps, 2);
wheelArc(&wps, geom[0], 0, geom[1]/2, 0, geom[2]);
wheelLabel(&wps, geom[0] + geom[1]*cos(AIR_PI*geom[2]/180/2)/2.5,
geom[1]*sin(AIR_PI*geom[2]/180/2)/2.5, "theta");
if (drawRA) {
tmpr = sqrt(geom[0]*geom[0] + geom[1]*geom[1]);
tmpa = atan(2.0*rnth[0]);
wheelWidth(&wps, 2);
wheelArc(&wps, 0, 0, 0.2*tmpr, 0, 180*tmpa/AIR_PI);
wheelLabel(&wps, 0.2*tmpr*cos(tmpa/2), 0.2*tmpr*sin(tmpa/2), "phi");
}
wheelLabel(&wps, xroot[0], yroot[0], "spoke0");
wheelLabel(&wps, xroot[1], yroot[1], "spoke-");
wheelLabel(&wps, xroot[2], yroot[2], "spoke+");
wheelLabel(&wps, xroot[0], 0, "root0");
wheelLabel(&wps, xroot[1], 0, "root-");
wheelLabel(&wps, xroot[2], 0, "root+");
}
wheelEpilog(&wps);
airMopOkay(mop);
exit(0);
}
int
main(int argc, const char *argv[]) {
hestOpt *hopt=NULL;
hestParm *hparm;
Nrrd *nlight, *nmap, *ndebug;
const char *me;
char *outS, *errS, *debugS;
airArray *mop;
float amb[3], *linfo, *debug, *map, vscl;
unsigned li, ui, vi;
int qn, bits, method, doerr;
limnLight *light;
limnCamera *cam;
double u, v, r, w, V2W[9], diff, WW[3], VV[3];
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
cam = limnCameraNew();
airMopAdd(mop, cam, (airMopper)limnCameraNix, airMopAlways);
hestOptAdd(&hopt, "i", "nlight", airTypeOther, 1, 1, &nlight, NULL,
"input nrrd containing light information",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "# bits", airTypeInt, 1, 1, &bits, "16",
"number of bits to use for normal quantization, "
"between 8 and 16 inclusive. ");
hestOptAdd(&hopt, "amb", "ambient RGB", airTypeFloat, 3, 3, amb, "0 0 0",
"ambient light color");
hestOptAdd(&hopt, "fr", "from point", airTypeDouble, 3, 3, cam->from,"1 0 0",
"position of camera, used to determine view vector");
hestOptAdd(&hopt, "at", "at point", airTypeDouble, 3, 3, cam->at, "0 0 0",
"camera look-at point, used to determine view vector");
hestOptAdd(&hopt, "up", "up vector", airTypeDouble, 3, 3, cam->up, "0 0 1",
"camera pseudo-up vector, used to determine view coordinates");
hestOptAdd(&hopt, "rh", NULL, airTypeInt, 0, 0, &(cam->rightHanded), NULL,
"use a right-handed UVN frame (V points down)");
hestOptAdd(&hopt, "vs", "view-dir scaling", airTypeFloat, 1, 1, &vscl, "1",
"scaling along view-direction of location of "
"view-space lights");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, NULL,
"file to write output envmap to");
hestOptAdd(&hopt, "d", "filename", airTypeString, 1, 1, &debugS, "",
"Use this option to save out (to the given filename) a rendering "
"of the front (on the left) and back (on the right) of a sphere "
"as shaded with the new environment map. U increases "
"right-ward, V increases downward. The back sphere half is "
"rendered as though the front half was removed");
hestOptAdd(&hopt, "err", NULL, airTypeInt, 0, 0, &doerr, NULL,
"If using \"-d\", make the image represent the error between the "
"real and quantized vector");
hestParseOrDie(hopt, argc-1, argv+1, hparm, me, emapInfo,
AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
switch(bits) {
case 16:
method = limnQN16octa;
break;
case 15:
method = limnQN15octa;
break;
case 14:
method = limnQN14octa;
break;
case 13:
method = limnQN13octa;
break;
case 12:
method = limnQN12octa;
break;
case 11:
method = limnQN11octa;
break;
case 10:
method = limnQN10octa;
break;
case 9:
method = limnQN9octa;
break;
case 8:
method = limnQN8octa;
break;
default:
fprintf(stderr, "%s: requested #bits (%d) not in valid range [8,16]\n",
me, bits);
airMopError(mop);
return 1;
}
if (!(nrrdTypeFloat == nlight->type &&
2 == nlight->dim &&
7 == nlight->axis[0].size &&
LIMN_LIGHT_NUM >= nlight->axis[1].size)) {
fprintf(stderr, "%s: nlight isn't valid format for light specification, "
"must be: float type, 2-dimensional, 7\tx\tN size, N <= %d\n",
me, LIMN_LIGHT_NUM);
airMopError(mop);
return 1;
}
cam->neer = -0.000000001;
cam->dist = 0;
cam->faar = 0.0000000001;
cam->atRelative = AIR_TRUE;
if (limnCameraUpdate(cam)) {
airMopAdd(mop, errS = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: problem with camera:\n%s\n", me, errS);
airMopError(mop);
return 1;
}
light = limnLightNew();
airMopAdd(mop, light, (airMopper)limnLightNix, airMopAlways);
limnLightAmbientSet(light, amb[0], amb[1], amb[2]);
for (li=0; li<nlight->axis[1].size; li++) {
int vsp;
float lxyz[3];
linfo = (float *)(nlight->data) + 7*li;
vsp = !!linfo[0];
ELL_3V_COPY(lxyz, linfo + 4);
if (vsp) {
lxyz[2] *= vscl;
}
limnLightSet(light, li, vsp,
linfo[1], linfo[2], linfo[3], lxyz[0], lxyz[1], lxyz[2]);
}
if (limnLightUpdate(light, cam)) {
airMopAdd(mop, errS = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: problem with lights:\n%s\n", me, errS);
airMopError(mop);
return 1;
}
nmap=nrrdNew();
airMopAdd(mop, nmap, (airMopper)nrrdNuke, airMopAlways);
if (limnEnvMapFill(nmap, limnLightDiffuseCB, method, light)) {
airMopAdd(mop, errS = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: problem making environment map:\n%s\n", me, errS);
airMopError(mop);
return 1;
}
map = (float *)nmap->data;
if (nrrdSave(outS, nmap, NULL)) {
fprintf(stderr, "%s: trouble:\n%s", me, errS = biffGetDone(NRRD));
free(errS);
return 1;
}
if (airStrlen(debugS)) {
ELL_34M_EXTRACT(V2W, cam->V2W);
ndebug = nrrdNew();
nrrdMaybeAlloc_va(ndebug, nrrdTypeFloat, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, 1024),
AIR_CAST(size_t, 512));
airMopAdd(mop, ndebug, (airMopper)nrrdNuke, airMopAlways);
debug = (float *)ndebug->data;
for (vi=0; vi<=511; vi++) {
v = AIR_AFFINE(0, vi, 511, -0.999, 0.999);
for (ui=0; ui<=511; ui++) {
u = AIR_AFFINE(0, ui, 511, -0.999, 0.999);
r = sqrt(u*u + v*v);
if (r > 1) {
continue;
}
w = sqrt(1 - r*r);
/* first, the near side of the sphere */
ELL_3V_SET(VV, u, v, -w);
ELL_3MV_MUL(WW, V2W, VV);
qn = limnVtoQN_d[method](WW);
if (doerr) {
limnQNtoV_d[method](VV, qn);
ELL_3V_SUB(WW, WW, VV);
diff = ELL_3V_LEN(WW);
ELL_3V_SET_TT(debug + 3*(ui + 1024*vi), float,
diff, diff, diff);
} else {
ELL_3V_COPY(debug + 3*(ui + 1024*vi), map + 3*qn);
}
/* second, the far side of the sphere */
ELL_3V_SET(VV, u, v, w);
ELL_3MV_MUL(WW, V2W, VV);
qn = limnVtoQN_d[method](WW);
if (doerr) {
limnQNtoV_d[method](VV, qn);
ELL_3V_SUB(WW, WW, VV);
diff = ELL_3V_LEN(WW);
ELL_3V_SET_TT(debug + 3*(ui + 512 + 1024*vi), float,
diff, diff, diff);
} else {
ELL_3V_COPY(debug + 3*(ui + 512 + 1024*vi), map + 3*qn);
}
}
}
int
main(int argc, const char **argv) {
/* stock variables */
char me[] = BKEY;
hestOpt *hopt=NULL;
hestParm *hparm;
airArray *mop;
/* variables specific to this program */
int negskip, progress;
Nrrd *nref, *nin;
size_t *size, ii, nn, tick, pad[2];
unsigned int axi, refCRC, gotCRC, sizeNum;
char *berr, *outS[2], stmp[AIR_STRLEN_SMALL], doneStr[AIR_STRLEN_SMALL];
airRandMTState *rng;
unsigned int seed, *rdata, printbytes;
unsigned char *dataUC;
double time0, time1;
FILE *fout;
/* start-up */
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
/* learn things from hest */
hestOptAdd(&hopt, "seed", "N", airTypeUInt, 1, 1, &seed, "42",
"seed for RNG");
hestOptAdd(&hopt, "s", "sz0", airTypeSize_t, 1, -1, &size, NULL,
"sizes of desired output", &sizeNum);
hestOptAdd(&hopt, "p", "pb pa", airTypeSize_t, 2, 2, pad, "0 0",
"bytes of padding before, and after, the data segment "
"in the written data");
hestOptAdd(&hopt, "ns", "bool", airTypeInt, 0, 0, &negskip, NULL,
"skipping should be relative to end of file");
hestOptAdd(&hopt, "pb", "print", airTypeUInt, 1, 1, &printbytes, "0",
"bytes to print at beginning and end of data, to help "
"debug problems");
hestOptAdd(&hopt, "o", "out.data out.nhdr", airTypeString, 2, 2,
outS, NULL, "output filenames of data and header");
hestParseOrDie(hopt, argc-1, argv+1, hparm, me, tskipInfo,
AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
/* generate reference nrrd data */
nref = nrrdNew();
airMopAdd(mop, nref, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_nva(nref, nrrdTypeUInt, sizeNum, size)) {
airMopAdd(mop, berr=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error allocating data: %s\n", me, berr);
airMopError(mop); return 1;
}
rng = airRandMTStateNew(seed);
airMopAdd(mop, rng, (airMopper)airRandMTStateNix, airMopAlways);
nn = nrrdElementNumber(nref);
rdata = AIR_CAST(unsigned int *, nref->data);
fprintf(stderr, "generating data: . . . "); fflush(stderr);
time0 = airTime();
progress = AIR_FALSE;
tick = nn/100;
for (ii=0; ii<nn; ii++) {
rdata[ii] = airUIrandMT_r(rng);
if (ii && tick && !(ii % tick)) {
time1 = airTime();
if (time1 - time0 > 1.0) {
/* if it took more than a second to do 1% of the thing,
would be good to generate some progress indication */
progress = AIR_TRUE;
}
if (progress) {
fprintf(stderr, "%s", airDoneStr(0, ii, nn, doneStr)); fflush(stderr);
}
}
}
if (progress) {
fprintf(stderr, "%s\n", airDoneStr(0, ii, nn, doneStr)); fflush(stderr);
} else {
fprintf(stderr, "\n");
}
fprintf(stderr, "finding reference (big-endian) CRC: "); fflush(stderr);
refCRC = nrrdCRC32(nref, airEndianBig);
fprintf(stderr, "%u\n", refCRC);
/* write data, with padding */
fprintf(stderr, "saving data . . . "); fflush(stderr);
if (!(fout = fopen(outS[0], "wb" COMMIT))) {
fprintf(stderr, "\n%s: couldn't open %s for writing: %s\n", me,
outS[0], strerror(errno));
airMopError(mop); return 1;
}
airMopAdd(mop, fout, (airMopper)airFclose, airMopAlways);
for (ii=0; ii<pad[0]; ii++) {
if (EOF == fputc(1, fout)) {
fprintf(stderr, "\n%s: error doing pre-padding\n", me);
airMopError(mop); return 1;
}
}
if (nn != fwrite(nref->data, nrrdElementSize(nref), nn, fout)) {
fprintf(stderr, "\n%s: error writing data\n", me);
airMopError(mop); return 1;
}
for (ii=0; ii<pad[1]; ii++) {
if (EOF == fputc(2, fout)) {
fprintf(stderr, "\n%s: error doing post-padding\n", me);
airMopError(mop); return 1;
}
}
if (EOF == fflush(fout)) {
fprintf(stderr, "\n%s: error fflushing data: %s\n", me,
strerror(errno));
}
fprintf(stderr, "\n");
if (printbytes) {
size_t bi, rpb, nn;
char stmp[AIR_STRLEN_SMALL];
nn = nrrdElementSize(nref)*nrrdElementNumber(nref);
rpb = AIR_MIN(printbytes, nn);
dataUC = AIR_CAST(unsigned char *, nref->data);
fprintf(stderr, "CORRECT %s bytes at beginning:\n",
airSprintSize_t(stmp, rpb));
for (bi=0; bi<rpb; bi++) {
fprintf(stderr, "%x ", dataUC[bi]);
}
fprintf(stderr, "...\n");
fprintf(stderr, "CORRECT %s bytes at end:\n",
airSprintSize_t(stmp, rpb));
fprintf(stderr, "...");
for (bi=nn - rpb; bi<nn; bi++) {
fprintf(stderr, " %x", dataUC[bi]);
}
fprintf(stderr, "\n");
}
airMopSingleOkay(mop, fout);
airMopSingleOkay(mop, nref); nref = NULL;
/* write header; for now just writing the header directly */
fprintf(stderr, "writing header . . . \n");
if (!(fout = fopen(outS[1], "w"))) {
fprintf(stderr, "%s: couldn't open %s for writing: %s\n", me,
outS[1], strerror(errno));
airMopError(mop); return 1;
}
airMopAdd(mop, fout, (airMopper)airFclose, airMopAlways);
fprintf(fout, "NRRD0005\n");
fprintf(fout, "type: unsigned int\n");
fprintf(fout, "dimension: %u\n", sizeNum);
fprintf(fout, "sizes:");
for (axi=0; axi<sizeNum; axi++) {
fprintf(fout, " %s", airSprintSize_t(stmp, size[axi]));
}
fprintf(fout, "\n");
fprintf(fout, "endian: %s\n", airEnumStr(airEndian, airMyEndian()));
fprintf(fout, "encoding: %s\n", airEnumStr(nrrdEncodingType,
nrrdEncodingTypeRaw));
if (!negskip) {
if (pad[0]) {
fprintf(fout, "byte skip: %s\n", airSprintSize_t(stmp, pad[0]));
}
} else {
fprintf(fout, "byte skip: -%s\n", airSprintSize_t(stmp, pad[1]+1));
}
fprintf(fout, "data file: %s\n", outS[0]);
airMopSingleOkay(mop, fout);
/* read it in, make sure it checks out */
fprintf(stderr, "reading data . . . \n");
nin = nrrdNew();
airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nin, outS[1], NULL)) {
airMopAdd(mop, berr=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error reading back in: %s\n", me, berr);
airMopError(mop); return 1;
}
if (printbytes) {
size_t bi, rpb, nn;
char stmp[AIR_STRLEN_SMALL];
nn = nrrdElementSize(nin)*nrrdElementNumber(nin);
rpb = AIR_MIN(printbytes, nn);
dataUC = AIR_CAST(unsigned char *, nin->data);
fprintf(stderr, "FOUND %s bytes at beginning:\n",
airSprintSize_t(stmp, rpb));
for (bi=0; bi<rpb; bi++) {
fprintf(stderr, "%x ", dataUC[bi]);
}
fprintf(stderr, "...\n");
fprintf(stderr, "FOUND %s bytes at end:\n",
airSprintSize_t(stmp, rpb));
fprintf(stderr, "...");
for (bi=nn - rpb; bi<nn; bi++) {
fprintf(stderr, " %x", dataUC[bi]);
}
fprintf(stderr, "\n");
}
fprintf(stderr, "finding new CRC . . . \n");
gotCRC = nrrdCRC32(nin, airEndianBig);
if (refCRC != gotCRC) {
fprintf(stderr, "%s: got CRC %u but wanted %u\n", me, gotCRC, refCRC);
airMopError(mop); return 1;
}
fprintf(stderr, "(all ok)\n");
/* HEY: to test gzip reading, we really want to do a system call to
gzip compress the data, and write a new header to point to the
compressed data, and make sure we can read in that just the same */
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *outS, *err;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
Nrrd *nin, *nmat, *ninv, *nidn;
int (*func)(Nrrd *, Nrrd *);
double m3[9], m4[16];
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, NULL, "matrix", airTypeOther, 1, 1, &nin, NULL,
"transform(s) to apply to image",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write output nrrd to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, invInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
ninv = nrrdNew();
airMopAdd(mop, ninv, (airMopper)nrrdNuke, airMopAlways);
nidn = nrrdNew();
airMopAdd(mop, nidn, (airMopper)nrrdNuke, airMopAlways);
nmat = nrrdNew();
airMopAdd(mop, nmat, (airMopper)nrrdNuke, airMopAlways);
nrrdConvert(nmat, nin, nrrdTypeDouble);
if (3 == nmat->axis[0].size && 3 == nmat->axis[1].size) {
ell_3m_inv_d(m3, (double *)nmat->data);
fprintf(stderr, "%s: input:\n", me);
ell_3m_print_d(stderr, (double *)nmat->data);
fprintf(stderr, "%s: inverse:\n", me);
ell_3m_print_d(stderr, m3);
}
if (4 == nmat->axis[0].size && 4 == nmat->axis[1].size) {
ell_4m_inv_d(m4, (double *)nmat->data);
fprintf(stderr, "%s: input:\n", me);
ell_4m_print_d(stderr, (double *)nmat->data);
fprintf(stderr, "%s: inverse:\n", me);
ell_4m_print_d(stderr, m4);
}
func = (nmat->axis[0].size == nmat->axis[1].size
? ell_Nm_inv
: ell_Nm_pseudo_inv);
if (func(ninv, nmat)) {
airMopAdd(mop, err = biffGetDone(ELL), airFree, airMopAlways);
fprintf(stderr, "%s: problem inverting:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (nrrdSave(outS, ninv, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: problem saving output:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, char **argv) {
int res[2], v, numIn;
char **in, *out, *blah[3], *option = NULL;
int n, *ints, numN;
hestOpt *opt = NULL;
hestParm *parm;
char *err = NULL, info[] =
"This program does nothing in particular, though it does attempt "
"to pose as some sort of command-line image processing program. "
"As usual, any implied functionality is purely coincidental, "
"especially since this is the output of a unicyclist.";
parm = hestParmNew();
parm->respFileEnable = AIR_TRUE;
parm->verbosity = 3;
opt = NULL;
hestOptAdd(&opt, "v,verbose", "level", airTypeInt, 0, 1, &v, "0",
"verbosity level");
hestOptAdd(&opt, "out", "file", airTypeString, 1, 1, &out, "output.ppm",
"PPM image output");
hestOptAdd(&opt, "blah", "input", airTypeString, 3, 3, blah, "a b c",
"input image file(s)");
hestOptAdd(&opt, "option","opt", airTypeString, 0, 1, &option, "default",
"this is just a test");
hestOptAdd(&opt, NULL, "input", airTypeString, 1, -1, &in, NULL,
"input image file(s)", &numIn);
hestOptAdd(&opt, "ints", "N", airTypeInt, 1, -1, &ints, "10 20 30",
"a list of integers", &numN);
hestOptAdd(&opt, "res", "sx sy", airTypeInt, 2, 2, res, NULL,
"image resolution");
printf("what 0\n");
if (1 == argc) {
/* didn't get anything at all on command line */
/* print program information ... */
hestInfo(stderr, argv[0], info, parm);
/* ... and usage information ... */
hestUsage(stderr, opt, argv[0], parm);
hestGlossary(stderr, opt, parm);
/* ... and avoid memory leaks */
opt = hestOptFree(opt);
parm = hestParmFree(parm);
exit(1);
}
printf("what 1\n");
/* else we got something, see if we can parse it */
if (hestParse(opt, argc-1, argv+1, &err, parm)) {
fprintf(stderr, "ERROR: %s\n", err); free(err);
/* print usage information ... */
hestUsage(stderr, opt, argv[0], parm);
hestGlossary(stderr, opt, parm);
/* ... and then avoid memory leaks */
opt = hestOptFree(opt);
parm = hestParmFree(parm);
printf(" ---- in = %lx\n", (unsigned long)in);
printf(" ---- blah[0] = %lx\n", (unsigned long)(blah[0]));
printf(" ---- option = %lx\n", (unsigned long)option);
exit(1);
}
printf("what 2\n");
printf("(err = %s)\n", err ? err : "(null)");
printf(" v = %d\n", v);
printf("out = \"%s\"\n", out ? out : "(null)");
printf("blah = \"%s\" \"%s\" \"%s\"\n", blah[0], blah[1], blah[2]);
printf("option = \"%s\"\n", option ? option : "(null)");
printf("res = %d %d\n", res[0], res[1]);
/*
printf(" ---- in = %lx\n", (unsigned long)in);
printf(" in = %d files:", numIn);
for (n=0; n<=numIn-1; n++) {
printf(" \"%s\"", in[n] ? in[n] : "(null)");
}
printf("\n");
*/
printf(" ints = %d ints:", numN);
for (n=0; n<=numN-1; n++) {
printf(" %d", ints[n]);
}
printf("\n");
printf("what 3\n");
/* free the memory allocated by parsing ... */
hestParseFree(opt);
/* ... and the other stuff */
opt = hestOptFree(opt);
parm = hestParmFree(parm);
exit(0);
}
int
main(int argc, const char *argv[]) {
const char *me;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, *outS;
double sigmaMax, convEps, cutoff;
int measr[2], tentRecon;
unsigned int sampleNumMax, dim, measrSampleNum, maxIter, num, ii;
gageOptimSigParm *osparm;
double *scalePos, *out, info[512];
Nrrd *nout;
double *plotPos; unsigned int plotPosNum;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "num", "# samp", airTypeUInt, 1, 1, &sampleNumMax, NULL,
"maximum number of samples to optimize");
hestOptAdd(&hopt, "dim", "dimension", airTypeUInt, 1, 1, &dim, "3",
"dimension of image to work with");
hestOptAdd(&hopt, "max", "sigma", airTypeDouble, 1, 1, &sigmaMax, NULL,
"sigma to use for top sample (using 0 for bottom sample)");
hestOptAdd(&hopt, "cut", "cut", airTypeDouble, 1, 1, &cutoff, "4",
"at how many sigmas to cut-off discrete gaussian");
hestOptAdd(&hopt, "mi", "max", airTypeUInt, 1, 1, &maxIter, "1000",
"maximum # iterations");
hestOptAdd(&hopt, "N", "# samp", airTypeUInt, 1, 1, &measrSampleNum, "300",
"number of samples in the measurement of error across scales");
hestOptAdd(&hopt, "eps", "eps", airTypeDouble, 1, 1, &convEps, "0.0001",
"convergence threshold for optimization");
hestOptAdd(&hopt, "m", "m1 m2", airTypeEnum, 2, 2, measr, "l2 l2",
"how to measure error across image, and across scales",
NULL, nrrdMeasure);
hestOptAdd(&hopt, "p", "s0 s1", airTypeDouble, 2, -1, &plotPos, "nan nan",
"hack: dont do optimization; just plot the recon error given "
"these samples along scale", &plotPosNum);
hestOptAdd(&hopt, "tent", NULL, airTypeInt, 0, 0, &tentRecon, NULL,
"same hack: plot error with tent recon, not hermite");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL,
"output array");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, optsigInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, AIR_CAST(airMopper, nrrdNuke), airMopAlways);
osparm = gageOptimSigParmNew(sampleNumMax);
airMopAdd(mop, osparm, AIR_CAST(airMopper, gageOptimSigParmNix),
airMopAlways);
scalePos = AIR_CAST(double *, calloc(sampleNumMax, sizeof(double)));
airMopAdd(mop, scalePos, airFree, airMopAlways);
osparm->plotting = (AIR_EXISTS(plotPos[0]) && AIR_EXISTS(plotPos[1]));
if (gageOptimSigTruthSet(osparm, dim, sigmaMax, cutoff, measrSampleNum)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
if (osparm->plotting) {
if (gageOptimSigPlot(osparm, nout, plotPos, plotPosNum,
measr[0], tentRecon)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
} else {
/* do sample position optimization */
if (nrrdMaybeAlloc_va(nout, nrrdTypeDouble, 2,
AIR_CAST(size_t, sampleNumMax+1),
AIR_CAST(size_t, sampleNumMax+1))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating output:\n%s", me, err);
airMopError(mop); return 1;
}
out = AIR_CAST(double *, nout->data);
/* hacky way of saving some of the computation information */
info[0] = cutoff;
info[1] = measrSampleNum;
info[2] = measr[0];
info[3] = measr[1];
info[4] = convEps;
info[5] = maxIter;
for (ii=0; ii<sampleNumMax+1; ii++) {
out[ii] = info[ii];
}
for (num=2; num<=sampleNumMax; num++) {
printf("\n%s: ======= optimizing %u/%u samples (sigmaMax %g) \n\n",
me, num, sampleNumMax, sigmaMax);
if (gageOptimSigCalculate(osparm, scalePos, num,
measr[0], measr[1],
convEps, maxIter)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s", me, err);
airMopError(mop); return 1;
}
out[sampleNumMax + (sampleNumMax+1)*num] = osparm->finalErr;
for (ii=0; ii<num; ii++) {
out[ii + (sampleNumMax+1)*num] = scalePos[ii];
}
}
}
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble saving output:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
exit(0);
}
void
hestGlossary(FILE *f, hestOpt *opt, hestParm *_parm) {
int i, j, len, maxlen, numOpts;
char buff[2*AIR_STRLEN_HUGE], tmpS[AIR_STRLEN_HUGE];
hestParm *parm;
parm = !_parm ? hestParmNew() : _parm;
if (_hestPanic(opt, NULL, parm)) {
/* we can't continue; the opt array is botched */
parm = !_parm ? hestParmFree(parm) : NULL;
return;
}
numOpts = _hestNumOpts(opt);
maxlen = 0;
if (numOpts) {
fprintf(f, "\n");
}
for (i=0; i<numOpts; i++) {
strcpy(buff, "");
_hestSetBuff(buff, opt + i, parm, AIR_TRUE, AIR_FALSE);
maxlen = AIR_MAX((int)strlen(buff), maxlen);
}
if (parm && parm->respFileEnable) {
sprintf(buff, "%cfile ...", parm->respFileFlag);
len = strlen(buff);
for (j=len; j<maxlen; j++) {
fprintf(f, " ");
}
fprintf(f, "%s = ", buff);
strcpy(buff, "response file(s) containing command-line arguments");
_hestPrintStr(f, maxlen + 3, maxlen + 3, parm->columns, buff, AIR_FALSE);
}
for (i=0; i<numOpts; i++) {
strcpy(buff, "");
_hestSetBuff(buff, opt + i, parm, AIR_TRUE, AIR_FALSE);
airOneLinify(buff);
len = strlen(buff);
for (j=len; j<maxlen; j++) {
fprintf(f, " ");
}
fprintf(f, "%s", buff);
strcpy(buff, "");
#if 1
if (opt[i].flag && strchr(opt[i].flag, parm->multiFlagSep)) {
/* there is a long-form flag as well as short */
_hestSetBuff(buff, opt + i, parm, AIR_FALSE, AIR_TRUE);
strcat(buff, " = ");
fprintf(f, " , ");
} else {
/* there is only a short-form flag */
fprintf(f, " = ");
}
#else
fprintf(f, " = ");
#endif
if (opt[i].info) {
strcat(buff, opt[i].info);
}
if ((opt[i].min || _hestMax(opt[i].max))
&& (!( 2 == opt[i].kind
&& airTypeEnum == opt[i].type
&& parm->elideSingleEnumType ))
&& (!( 2 == opt[i].kind
&& airTypeOther == opt[i].type
&& parm->elideSingleOtherType ))
) {
/* if there are newlines in the info, then we want to clarify the
type by printing it on its own line */
if (opt[i].info && strchr(opt[i].info, '\n')) {
strcat(buff, "\n ");
}
else {
strcat(buff, " ");
}
strcat(buff, "(");
if (opt[i].min == 0 && _hestMax(opt[i].max) == 1) {
strcat(buff, "optional\t");
}
else {
if ((int)opt[i].min == _hestMax(opt[i].max) && _hestMax(opt[i].max) > 1) { /* HEY scrutinize casts */
sprintf(tmpS, "%d\t", _hestMax(opt[i].max));
strcat(buff, tmpS);
}
else if ((int)opt[i].min < _hestMax(opt[i].max)) { /* HEY scrutinize casts */
if (-1 == opt[i].max) {
sprintf(tmpS, "%d\tor\tmore\t", opt[i].min);
}
else {
sprintf(tmpS, "%d..%d\t", opt[i].min, _hestMax(opt[i].max));
}
strcat(buff, tmpS);
}
}
sprintf(tmpS, "%s%s",
(airTypeEnum == opt[i].type
? opt[i].enm->name
: (airTypeOther == opt[i].type
? opt[i].CB->type
: airTypeStr[opt[i].type])),
(_hestMax(opt[i].max) > 1
? (airTypeOther == opt[i].type
&& 'y' == opt[i].CB->type[airStrlen(opt[i].CB->type)-1]
&& parm->cleverPluralizeOtherY
? "\bies"
: "s")
: ""));
strcat(buff, tmpS);
strcat(buff, ")");
}
/*
fprintf(stderr, "!%s: parm->elideSingleOtherDefault = %d\n",
"hestGlossary", parm->elideSingleOtherDefault);
*/
if (opt[i].dflt
&& (opt[i].min || _hestMax(opt[i].max))
&& (!( 2 == opt[i].kind
&& (airTypeFloat == opt[i].type || airTypeDouble == opt[i].type)
&& !AIR_EXISTS(airAtod(opt[i].dflt))
&& parm->elideSingleNonExistFloatDefault ))
&& (!( (3 == opt[i].kind || 5 == opt[i].kind)
&& (airTypeFloat == opt[i].type || airTypeDouble == opt[i].type)
&& !AIR_EXISTS(airAtod(opt[i].dflt))
&& parm->elideMultipleNonExistFloatDefault ))
&& (!( 2 == opt[i].kind
&& airTypeOther == opt[i].type
&& parm->elideSingleOtherDefault ))
&& (!( 2 == opt[i].kind
&& airTypeString == opt[i].type
&& parm->elideSingleEmptyStringDefault
&& 0 == airStrlen(opt[i].dflt) ))
&& (!( (3 == opt[i].kind || 5 == opt[i].kind)
&& airTypeString == opt[i].type
&& parm->elideMultipleEmptyStringDefault
&& 0 == airStrlen(opt[i].dflt) ))
) {
/* if there are newlines in the info, then we want to clarify the
default by printing it on its own line */
if (opt[i].info && strchr(opt[i].info, '\n')) {
strcat(buff, "\n ");
}
else {
strcat(buff, "; ");
}
strcat(buff, "default:\t");
strcpy(tmpS, opt[i].dflt);
airStrtrans(tmpS, ' ', '\t');
strcat(buff, "\"");
strcat(buff, tmpS);
strcat(buff, "\"");
}
_hestPrintStr(f, maxlen + 3, maxlen + 3, parm->columns, buff, AIR_FALSE);
}
parm = !_parm ? hestParmFree(parm) : NULL;
return;
}
int
main(int argc, const char *argv[]) {
const char *me;
char *err, *out;
int size[3], xi, yi, zi;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
float min[3], max[3], AB[2], x, y, z, *data, off;
Nrrd *nout;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "s", "sx sy sz", airTypeInt, 3, 3, size, "128 128 128",
"dimensions of output volume");
hestOptAdd(&hopt, "min", "x y z", airTypeFloat, 3, 3, min, "-1 -1 -1",
"lower bounding corner of volume");
hestOptAdd(&hopt, "max", "x y z", airTypeFloat, 3, 3, max, "1 1 1",
"upper bounding corner of volume");
hestOptAdd(&hopt, "c", "A B", airTypeFloat, 2, 2, AB, NULL,
"A and B quadratic coefficients");
hestOptAdd(&hopt, "off", "z offset", airTypeFloat, 1, 1, &off, "0.0",
"vertical offset");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &out, "-",
"file to write output nrrd to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, quadInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdAlloc_va(nout, nrrdTypeFloat, 3,
AIR_CAST(size_t, size[0]),
AIR_CAST(size_t, size[1]),
AIR_CAST(size_t, size[2]))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: problem allocating volume:\n%s\n", me, err);
airMopError(mop); return 1;
}
data = (float *)nout->data;
for (zi=0; zi<size[2]; zi++) {
z = AIR_AFFINE(0, zi, size[2]-1, min[2], max[2]);
for (yi=0; yi<size[1]; yi++) {
y = AIR_AFFINE(0, yi, size[1]-1, min[1], max[1]);
for (xi=0; xi<size[0]; xi++) {
x = AIR_AFFINE(0, xi, size[0]-1, min[0], max[0]);
*data = quadFunc(x,y,z, AB[0], AB[1], off);
data += 1;
}
}
}
nrrdAxisInfoSet_va(nout, nrrdAxisInfoMin, min[0], min[1], min[2]);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoMax, max[0], max[1], max[2]);
nrrdAxisInfoSpacingSet(nout, 0);
nrrdAxisInfoSpacingSet(nout, 1);
nrrdAxisInfoSpacingSet(nout, 2);
if (nrrdSave(out, nout, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: problem saving output:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, done[13];
Nrrd *nin, *ndist, *nmask, *nupdate, *nout;
NrrdKernelSpec *k00, *k11, *k22;
int E;
unsigned int sx, sy, sz, xi, yi, zi, si, iter, maxIter;
gageContext *ctx;
gagePerVolume *pvl;
double dt, *dist, *mask, *update, thresh, eps, rmsMin;
const double *valu, *gmag, *mcrv;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &k00,
"tent", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &k11,
"cubicd:0,0.5", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "dt", "step", airTypeDouble, 1, 1, &dt, "0.17",
"time step size");
hestOptAdd(&hopt, "th", "val", airTypeDouble, 1, 1, &thresh, "0.0",
"the value to use for thresholding the input "
"volume, to create the binary constraint image.");
hestOptAdd(&hopt, "eps", "val", airTypeDouble, 1, 1, &eps, "0.05",
"width of value bracket around threshold, to constrain the "
"the update from letting to value, originally on either "
"side of the threshold, from getting too close.");
hestOptAdd(&hopt, "rms", "thresh", airTypeDouble, 1, 1, &rmsMin, "0.01",
"RMS change below this terminates updates.");
hestOptAdd(&hopt, "mi", "max", airTypeUInt, 1, 1, &maxIter, "100",
"maximum # iterations");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"fixed volume output");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, aaliasInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
ndist = nrrdNew();
nmask = nrrdNew();
nupdate = nrrdNew();
airMopAdd(mop, ndist, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nmask, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nupdate, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ndist, nin, nrrdTypeDouble)
|| nrrdConvert(nmask, nin, nrrdTypeDouble)
|| nrrdConvert(nupdate, nin, nrrdTypeDouble)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate buffers:\n%s", me, err);
airMopError(mop); return 1;
}
dist = AIR_CAST(double *, ndist->data);
mask = AIR_CAST(double *, nmask->data);
update = AIR_CAST(double *, nupdate->data);
ctx = gageContextNew();
airMopAdd(mop, ctx, (airMopper)gageContextNix, airMopAlways);
gageParmSet(ctx, gageParmRenormalize, AIR_TRUE);
gageParmSet(ctx, gageParmCheckIntegrals, AIR_TRUE);
E = 0;
if (!E) E |= !(pvl = gagePerVolumeNew(ctx, ndist, gageKindScl));
if (!E) E |= gagePerVolumeAttach(ctx, pvl);
if (!E) E |= gageKernelSet(ctx, gageKernel00, k00->kernel, k00->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel11, k11->kernel, k11->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel22, k22->kernel, k22->parm);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclValue);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradMag);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclMeanCurv);
if (!E) E |= gageUpdate(ctx);
if (E) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
valu = gageAnswerPointer(ctx, pvl, gageSclValue);
gmag = gageAnswerPointer(ctx, pvl, gageSclGradMag);
mcrv = gageAnswerPointer(ctx, pvl, gageSclMeanCurv);
sx = nin->axis[0].size;
sy = nin->axis[1].size;
sz = nin->axis[2].size;
for (iter=0; iter<maxIter; iter++) {
double rms;
unsigned count;
fprintf(stderr, "%s: iter %u: ", me, iter);
fflush(stderr);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
fflush(stderr);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
si = xi + sx*(yi + sy*zi);
gageProbe(ctx, xi, yi, zi);
update[si] = -dt*(*gmag)*(*mcrv);
}
}
}
rms = 0;
count = 0;
for (si=0; si<sx*sy*sz; si++) {
double newval;
if (update[si]) {
/* NOTE: this update behavior is only slightly different than
what's described in Equation 18 of the paper. That update
rule ensures that the value never changes "sign" (with
respect to the threshold value), by clamping the values
above or below to 0.0. But worst-case scenario is that two
adjacent samples that were on other side of the threshold
(i.e. 0), could then equal the threshold, which would
confuse a marching-cubes type algorithm. So the "eps"
enforces a small value range around the treshold, and keeps
the values on either side of it. */
newval = dist[si] + update[si];
if (mask[si] > thresh) {
newval = AIR_MAX(newval, thresh+eps/2);
} else {
newval = AIR_MIN(newval, thresh-eps/2);
}
rms += (dist[si] - newval)*(dist[si] - newval);
dist[si] = newval;
count++;
}
}
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
rms /= count;
rms = sqrt(rms);
if (rms < rmsMin) {
fprintf(stderr, "\n%s: RMS %g below threshold %g\n", me, rms, rmsMin);
break;
} else {
fprintf(stderr, " rms = %g > %g\n", rms, rmsMin);
}
}
if (iter == maxIter) {
fprintf(stderr, "%s: hit max iter %u\n", me, maxIter);
}
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, ndist)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, char **argv) {
int i, ret;
char *me, *argv0 = NULL, *err;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for how Teem was built here.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_FALSE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->cleverPluralizeOtherY = AIR_TRUE;
hparm->columns = 78;
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
tendUsage(TEND, hparm);
airMopError(mop);
exit(1);
}
/* else, we see if its --version */
if (!strcmp("--version", argv[1])) {
printf("Teem version %s (%s)\n",
airTeemVersion, airTeemReleaseDate);
exit(0);
}
/* else, we should see if they're asking for a command we know about */
for (i=0; tendCmdList[i]; i++) {
if (!strcmp(argv[1], tendCmdList[i]->name))
break;
if (!strcmp("--help", argv[1])
&& !strcmp("about", tendCmdList[i]->name)) {
break;
}
}
if (tendCmdList[i]) {
/* yes, we have that command */
/* initialize variables used by the various commands */
argv0 = (char *)calloc(strlen(TEND) + strlen(argv[1]) + 2, sizeof(char));
airMopMem(mop, &argv0, airMopAlways);
sprintf(argv0, "%s %s", TEND, argv[1]);
/* run the individual unu program, saving its exit status */
ret = tendCmdList[i]->main(argc-2, argv+2, argv0, hparm);
} else {
fprintf(stderr, "%s: unrecognized command: \"%s\"; type \"%s\" for "
"complete list\n", me, argv[1], me);
ret = 1;
}
airMopDone(mop, ret);
return ret;
}
/*
******** unrrduCmdMain
**
** A "main" function for unu-like programs, which is very similar to
** teem/src/bin/unu.c:main(), and
** teem/src/bin/tend.c:main(), and
** teem/src/limn/test/lpu.c:main().
** With more time (and a major Teem release), this function may change,
** and those programs may use this.
**
** A sneaky but basic issue is the const-correctness of how the hestParm
** is used; we'd like to take a const hestParm* to communicate parameters
** the caller has set, but the show-stopper is that unrrduCmd->main()
** takes a non-const hestParm, and it has to be that way, because some
** unu commands alter the given hparm (which probably shouldn't happen).
** Until that's fixed, we have a non-const hestParm* coming in here.
*/
int
unrrduCmdMain(int argc, const char **argv,
const char *cmd, const char *title,
const unrrduCmd *const *cmdList,
hestParm *_hparm, FILE *fusage) {
int i, ret;
const char *me;
char *argv0 = NULL;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* unu does some unu-specific environment-variable handling here */
nrrdSanityOrDie(me);
mop = airMopNew();
if (_hparm) {
hparm = _hparm;
} else {
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_FALSE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->cleverPluralizeOtherY = AIR_TRUE;
/* learning columns from current window; if ioctl is available
if (1) {
struct winsize ws;
ioctl(1, TIOCGWINSZ, &ws);
hparm->columns = ws.ws_col - 1;
}
*/
hparm->columns = 78;
}
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
/* this is like unrrduUsageUnu() */
unsigned int ii, maxlen = 0;
char *buff, *fmt, tdash[] = "--- %s ---";
for (ii=0; cmdList[ii]; ii++) {
if (cmdList[ii]->hidden) {
continue;
}
maxlen = AIR_MAX(maxlen, AIR_UINT(strlen(cmdList[ii]->name)));
}
if (!maxlen) {
fprintf(fusage, "%s: problem: maxlen = %u\n", me, maxlen);
airMopError(mop); return 1;
}
buff = AIR_CALLOC(strlen(tdash) + strlen(title) + 1, char);
airMopAdd(mop, buff, airFree, airMopAlways);
sprintf(buff, tdash, title);
fmt = AIR_CALLOC(hparm->columns + strlen(buff) + 1, char); /* generous */
airMopAdd(mop, buff, airFree, airMopAlways);
sprintf(fmt, "%%%us\n",
AIR_UINT((hparm->columns-strlen(buff))/2 + strlen(buff) - 1));
fprintf(fusage, fmt, buff);
for (ii=0; cmdList[ii]; ii++) {
unsigned int cc, len;
if (cmdList[ii]->hidden) {
continue;
}
len = AIR_UINT(strlen(cmdList[ii]->name));
strcpy(buff, "");
for (cc=len; cc<maxlen; cc++)
strcat(buff, " ");
strcat(buff, cmd);
strcat(buff, " ");
strcat(buff, cmdList[ii]->name);
strcat(buff, " ... ");
len = strlen(buff);
fprintf(fusage, "%s", buff);
_hestPrintStr(fusage, len, len, hparm->columns,
cmdList[ii]->info, AIR_FALSE);
}
airMopError(mop);
return 1;
}
int
main(int argc, char **argv) {
static int res[2], v, numIn;
static char **in, *out;
static int *mm, mmm;
int n;
hestOpt opt[] = {
{"res", "sx sy", airTypeInt, 2, 2, res, NULL,
"image resolution"},
{"v", "level", airTypeInt, 0, 1, &v, NULL /* "0" */,
"verbosity level"},
{"VV", "level", airTypeInt, 0, 5, &mm, "33 22 11",
"gonzo level", &mmm},
{"out", "file", airTypeString, 1, 1, &out, "output.ppm",
"PPM image output"},
{NULL, "input", airTypeString, 1, -1, &in, NULL,
"input image file(s)", &numIn},
{NULL, NULL, 0}
};
hestParm *parm;
char *err = NULL, info[] =
"This program does nothing in particular, though it does attempt "
"to pose as some sort of command-line image processing program. "
"Any implied functionality is purely coincidental, especially since "
"this software was written by a sleep-deprived grad student.";
parm = hestParmNew();
parm->respFileEnable = AIR_TRUE;
if (1 == argc) {
/* didn't get anything at all on command line */
hestInfo(stderr, argv[0], info, parm);
hestUsage(stderr, opt, argv[0], parm);
hestGlossary(stderr, opt, parm);
parm = hestParmFree(parm);
exit(1);
}
/* else we got something, see if we can parse it */
if (hestParse(opt, argc-1, argv+1, &err, parm)) {
fprintf(stderr, "ERROR: %s\n", err); free(err);
hestUsage(stderr, opt, argv[0], parm);
hestGlossary(stderr, opt, parm);
parm = hestParmFree(parm);
exit(1);
}
printf("(err = %s)\n", err);
printf("res = %d %d\n", res[0], res[1]);
printf(" v = %d\n", v);
printf("out = \"%s\"\n", out);
printf(" mm = %d ints:", mmm);
for (n=0; n<=mmm-1; n++) {
printf(" %d", mm[n]);
}
printf("\n");
printf(" in = %d files:", numIn);
for (n=0; n<=numIn-1; n++) {
printf(" \"%s\"", in[n]);
}
printf("\n");
hestParseFree(opt);
parm = hestParmFree(parm);
exit(0);
}
int
main(int argc, char *argv[]) {
gageKind *kind;
char *me, *whatS, *err, *outS, *stackSavePath;
hestParm *hparm;
hestOpt *hopt = NULL;
NrrdKernelSpec *k00, *k11, *k22, *kSS, *kSSblur;
float pos[3], lineInfo[4];
double gmc, rangeSS[2], posSS, *scalePos;
unsigned int ansLen, numSS, ninSSIdx, lineStepNum;
int what, E=0, renorm, SSrenorm, SSuniform, verbose;
const double *answer;
Nrrd *nin, **ninSS=NULL, *nout=NULL;
gageContext *ctx;
gagePerVolume *pvl;
limnPolyData *lpld=NULL;
airArray *mop;
int worldSpace;
Nrrd *ngrad=NULL, *nbmat=NULL;
double bval, eps;
unsigned int *skip, skipNum;
mop = airMopNew();
me = argv[0];
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
"\"kind\" of volume (\"scalar\", \"vector\", or \"tensor\")",
NULL, NULL, &probeKindHestCB);
hestOptAdd(&hopt, "p", "x y z", airTypeFloat, 3, 3, pos, NULL,
"the position in space at which to probe");
hestOptAdd(&hopt, "wsp", NULL, airTypeInt, 0, 0, &worldSpace, NULL,
"if using this option, position (\"-p\") will be in world "
"space, instead of index space (the default)");
hestOptAdd(&hopt, "pi", "lpld in", airTypeOther, 1, 1, &lpld, "",
"input polydata (overrides \"-p\")",
NULL, NULL, limnHestPolyDataLMPD);
hestOptAdd(&hopt, "pl", "x y z s", airTypeFloat, 4, 4, lineInfo, "0 0 0 0",
"probe along line, instead of at point. "
"The \"-p\" three coords are the line start point. "
"If \"s\" is zero, (x,y,z) is the line end point. "
"If \"s\" is non-zero, (x,y,z) is the line direction, "
"which is scaled to have length \"s\", "
"and then used as the step between line samples. ");
hestOptAdd(&hopt, "pln", "num", airTypeUInt, 1, 1, &lineStepNum, "0",
"if non-zero, number of steps of probing to do along line, "
"which overrides \"-p\" and \"-pi\"");
hestOptAdd(&hopt, "v", "verbosity", airTypeInt, 1, 1, &verbose, "1",
"verbosity level");
hestOptAdd(&hopt, "q", "query", airTypeString, 1, 1, &whatS, NULL,
"the quantity (scalar, vector, or matrix) to learn by probing");
hestOptAdd(&hopt, "eps", "epsilon", airTypeDouble, 1, 1, &eps, "0",
"if non-zero, and if query is a scalar, epsilon around probe "
"location where we will do discrete differences to find the "
"gradient and hessian (for debugging)");
hestOptAdd(&hopt, "k00", "kern00", airTypeOther, 1, 1, &k00,
"tent", "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(&hopt, "ssn", "SS #", airTypeUInt, 1, 1, &numSS,
"0", "how many scale-space samples to evaluate, or, "
"0 to turn-off all scale-space behavior");
hestOptAdd(&hopt, "ssr", "scale range", airTypeDouble, 2, 2, rangeSS,
"nan nan", "range of scales in scale-space");
hestOptAdd(&hopt, "sss", "scale save path", airTypeString, 1, 1,
&stackSavePath, "",
"give a non-empty path string (like \"./\") to save out "
"the pre-blurred volumes computed for the stack");
hestOptAdd(&hopt, "ssp", "SS pos", airTypeDouble, 1, 1, &posSS, "0",
"position at which to sample in scale-space");
hestOptAdd(&hopt, "kssblur", "kernel", airTypeOther, 1, 1, &kSSblur,
"dgauss:1,5", "blurring kernel, to sample scale space",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "kss", "kernel", airTypeOther, 1, 1, &kSS,
"tent", "kernel for reconstructing from scale space samples",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "ssrn", "ssrn", airTypeInt, 1, 1, &SSrenorm, "0",
"enable derivative normalization based on scale space");
hestOptAdd(&hopt, "ssu", NULL, airTypeInt, 0, 0, &SSuniform, NULL,
"do uniform samples along sigma, and not (by default) "
"samples according to the logarithm of diffusion time");
hestOptAdd(&hopt, "rn", NULL, airTypeInt, 0, 0, &renorm, NULL,
"renormalize kernel weights at each new sample location. "
"\"Accurate\" kernels don't need this; doing it always "
"makes things go slower");
hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc,
"0.0", "For curvature-based queries, use zero when gradient "
"magnitude is below this");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output array, when probing on polydata vertices");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, probeInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
what = airEnumVal(kind->enm, whatS);
if (!what) {
/* 0 indeed always means "unknown" for any gageKind */
fprintf(stderr, "%s: couldn't parse \"%s\" as measure of \"%s\" volume\n",
me, whatS, kind->name);
hestUsage(stderr, hopt, me, hparm);
hestGlossary(stderr, hopt, hparm);
airMopError(mop);
return 1;
}
if (ELL_4V_LEN(lineInfo) && !lineStepNum) {
fprintf(stderr, "%s: gave line info (\"-pl\") but not "
"# samples (\"-pln\")", me);
hestUsage(stderr, hopt, me, hparm);
hestGlossary(stderr, hopt, hparm);
airMopError(mop);
return 1;
}
/* special set-up required for DWI kind */
if (!strcmp(TEN_DWI_GAGE_KIND_NAME, kind->name)) {
if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &bval, &skip, &skipNum, nin)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing DWI info:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (skipNum) {
fprintf(stderr, "%s: sorry, can't do DWI skipping in tenDwiGage", me);
airMopError(mop); return 1;
}
/* this could stand to use some more command-line arguments */
if (tenDwiGageKindSet(kind, 50, 1, bval, 0.001, ngrad, nbmat,
tenEstimate1MethodLLS,
tenEstimate2MethodQSegLLS,
/* randSeed */ 7919)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing DWI info:\n%s\n", me, err);
airMopError(mop); return 1;
}
}
ansLen = kind->table[what].answerLength;
/* for setting up pre-blurred scale-space samples */
if (numSS) {
unsigned int vi;
ninSS = AIR_CAST(Nrrd **, calloc(numSS, sizeof(Nrrd *)));
scalePos = AIR_CAST(double *, calloc(numSS, sizeof(double)));
if (!(ninSS && scalePos)) {
fprintf(stderr, "%s: couldn't allocate ninSS", me);
airMopError(mop); return 1;
}
for (ninSSIdx=0; ninSSIdx<numSS; ninSSIdx++) {
ninSS[ninSSIdx] = nrrdNew();
airMopAdd(mop, ninSS[ninSSIdx], (airMopper)nrrdNuke, airMopAlways);
}
if (SSuniform) {
for (vi=0; vi<numSS; vi++) {
scalePos[vi] = AIR_AFFINE(0, vi, numSS-1, rangeSS[0], rangeSS[1]);
}
} else {
double rangeTau[2], tau;
rangeTau[0] = gageTauOfSig(rangeSS[0]);
rangeTau[1] = gageTauOfSig(rangeSS[1]);
for (vi=0; vi<numSS; vi++) {
tau = AIR_AFFINE(0, vi, numSS-1, rangeTau[0], rangeTau[1]);
scalePos[vi] = gageSigOfTau(tau);
}
}
if (verbose > 2) {
fprintf(stderr, "%s: sampling scale range %g--%g %suniformly:\n", me,
rangeSS[0], rangeSS[1], SSuniform ? "" : "non-");
for (vi=0; vi<numSS; vi++) {
fprintf(stderr, " scalePos[%u] = %g\n", vi, scalePos[vi]);
}
}
if (gageStackBlur(ninSS, scalePos, numSS,
nin, kind->baseDim, kSSblur,
nrrdBoundaryBleed, AIR_TRUE,
verbose)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble pre-computing blurrings:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (airStrlen(stackSavePath)) {
char fnform[AIR_STRLEN_LARGE];
sprintf(fnform, "%s/blur-%%02u.nrrd", stackSavePath);
fprintf(stderr, "%s: |%s|\n", me, fnform);
if (nrrdSaveMulti(fnform, AIR_CAST(const Nrrd *const *, ninSS),
numSS, 0, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble saving blurrings:\n%s\n", me, err);
airMopError(mop); return 1;
}
}
} else {
int
main(int argc, const char *argv[]) {
gageKind *kind;
const char *me;
char *whatS, *err, *outS, *stackReadFormat, *stackSaveFormat;
hestParm *hparm;
hestOpt *hopt = NULL;
NrrdKernelSpec *k00, *k11, *k22, *kSS, *kSSblur;
int what, E=0, renorm, SSuniform, SSoptim, verbose, zeroZ,
orientationFromSpacing, SSnormd;
unsigned int iBaseDim, oBaseDim, axi, numSS, ninSSIdx, seed;
const double *answer;
Nrrd *nin, *nout, **ninSS=NULL;
Nrrd *ngrad=NULL, *nbmat=NULL;
size_t ai, ansLen, idx, xi, yi, zi, six, siy, siz, sox, soy, soz;
double bval=0, gmc, rangeSS[2], wrlSS, idxSS=AIR_NAN,
dsix, dsiy, dsiz, dsox, dsoy, dsoz;
gageContext *ctx;
gagePerVolume *pvl=NULL;
double t0, t1, x, y, z, scale[3], rscl[3], min[3], maxOut[3], maxIn[3];
airArray *mop;
unsigned int hackZi, *skip, skipNum;
double (*ins)(void *v, size_t I, double d);
gageStackBlurParm *sbp;
char hackKeyStr[]="TEEM_VPROBE_HACK_ZI", *hackValStr;
int otype, hackSet;
char stmp[4][AIR_STRLEN_SMALL];
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for how Teem was built here.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, AIR_CAST(airMopper, hestParmFree), airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
"\"kind\" of volume (\"scalar\", \"vector\", "
"\"tensor\", or \"dwi\")",
NULL, NULL, meetHestGageKind);
hestOptAdd(&hopt, "v", "verbosity", airTypeInt, 1, 1, &verbose, "1",
"verbosity level");
hestOptAdd(&hopt, "q", "query", airTypeString, 1, 1, &whatS, NULL,
"the quantity (scalar, vector, or matrix) to learn by probing");
hestOptAdd(&hopt, "s", "sclX sclY sxlZ", airTypeDouble, 3, 3, scale,
"1.0 1.0 1.0",
"scaling factor for resampling on each axis "
"(>1.0 : supersampling)");
hestOptAdd(&hopt, "k00", "kern00", airTypeOther, 1, 1, &k00,
"tent", "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(&hopt, "seed", "N", airTypeUInt, 1, 1, &seed, "42",
"RNG seed; mostly for debugging");
hestOptAdd(&hopt, "zz", "bool", airTypeBool, 1, 1, &zeroZ, "false",
"enable \"zeroZ\" behavior in gage that partially "
"implements working with 3D images as if they are 2D");
hestOptAdd(&hopt, "ssn", "SS #", airTypeUInt, 1, 1, &numSS,
"0", "how many scale-space samples to evaluate, or, "
"0 to turn-off all scale-space behavior");
hestOptAdd(&hopt, "ssr", "scale range", airTypeDouble, 2, 2, rangeSS,
"nan nan", "range of scales in scale-space");
hestOptAdd(&hopt, "ssrf", "SS read format", airTypeString, 1, 1,
&stackReadFormat, "",
"printf-style format (including a \"%u\") for the "
"filenames from which to *read* "
"pre-blurred volumes computed for the stack");
hestOptAdd(&hopt, "sssf", "SS save format", airTypeString, 1, 1,
&stackSaveFormat, "",
"printf-style format (including a \"%u\") for the "
"filenames in which to *save* "
"pre-blurred volumes computed for the stack");
hestOptAdd(&hopt, "ssw", "SS pos", airTypeDouble, 1, 1, &wrlSS, "0",
"\"world\"-space position (true sigma) "
"at which to sample in scale-space");
hestOptAdd(&hopt, "kssb", "kernel", airTypeOther, 1, 1, &kSSblur,
"dgauss:1,5", "blurring kernel, to sample scale space",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "kssr", "kernel", airTypeOther, 1, 1, &kSS,
"hermite", "kernel for reconstructing from scale space samples",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "ssu", NULL, airTypeInt, 0, 0, &SSuniform, NULL,
"do uniform samples along sigma, and not (by default) "
"samples according to the effective diffusion scale");
hestOptAdd(&hopt, "sso", NULL, airTypeInt, 0, 0, &SSoptim, NULL,
"if not using \"-ssu\", use pre-computed optimal "
"sigmas when possible");
hestOptAdd(&hopt, "ssnd", NULL, airTypeInt, 0, 0, &SSnormd, NULL,
"normalize derivatives by scale");
hestOptAdd(&hopt, "rn", NULL, airTypeInt, 0, 0, &renorm, NULL,
"renormalize kernel weights at each new sample location. "
"\"Accurate\" kernels don't need this; doing it always "
"makes things go slower");
hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc,
"0.0", "For curvature-based queries, use zero when gradient "
"magnitude is below this");
hestOptAdd(&hopt, "ofs", "ofs", airTypeInt, 0, 0, &orientationFromSpacing,
NULL, "If only per-axis spacing is available, use that to "
"contrive full orientation info");
hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &otype, "float",
"type of output volume", NULL, nrrdType);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output volume");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, probeInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestOptFree), airMopAlways);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestParseFree), airMopAlways);
what = airEnumVal(kind->enm, whatS);
if (!what) {
/* 0 indeed always means "unknown" for any gageKind */
fprintf(stderr, "%s: couldn't parse \"%s\" as measure of \"%s\" volume\n",
me, whatS, kind->name);
hestUsage(stderr, hopt, me, hparm);
hestGlossary(stderr, hopt, hparm);
airMopError(mop);
return 1;
}
/* special set-up required for DWI kind */
if (!strcmp(TEN_DWI_GAGE_KIND_NAME, kind->name)) {
if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &bval, &skip, &skipNum, nin)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing DWI info:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (skipNum) {
fprintf(stderr, "%s: sorry, can't do DWI skipping in tenDwiGage", me);
airMopError(mop); return 1;
}
/* this could stand to use some more command-line arguments */
if (tenDwiGageKindSet(kind, 50, 1, bval, 0.001, ngrad, nbmat,
tenEstimate1MethodLLS,
tenEstimate2MethodQSegLLS, seed)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing DWI info:\n%s\n", me, err);
airMopError(mop); return 1;
}
}
/* for setting up pre-blurred scale-space samples */
if (numSS) {
unsigned int vi;
sbp = gageStackBlurParmNew();
airMopAdd(mop, sbp, (airMopper)gageStackBlurParmNix, airMopAlways);
ninSS = AIR_CAST(Nrrd **, calloc(numSS, sizeof(Nrrd *)));
if (!ninSS) {
fprintf(stderr, "%s: couldn't allocate ninSS", me);
airMopError(mop); return 1;
}
for (ninSSIdx=0; ninSSIdx<numSS; ninSSIdx++) {
ninSS[ninSSIdx] = nrrdNew();
airMopAdd(mop, ninSS[ninSSIdx], (airMopper)nrrdNuke, airMopAlways);
}
if (gageStackBlurParmScaleSet(sbp, numSS, rangeSS[0], rangeSS[1],
SSuniform, SSoptim)
|| gageStackBlurParmKernelSet(sbp, kSSblur)
|| gageStackBlurParmRenormalizeSet(sbp, AIR_TRUE)
|| gageStackBlurParmBoundarySet(sbp, nrrdBoundaryBleed, AIR_NAN)
|| gageStackBlurParmVerboseSet(sbp, verbose)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble with stack blur info:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (airStrlen(stackReadFormat)) {
if (nrrdLoadMulti(ninSS, numSS,
stackReadFormat, 0, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble loading blurrings:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (gageStackBlurCheck(AIR_CAST(const Nrrd *const*, ninSS),
sbp, nin, kind)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
} else {
if (gageStackBlur(ninSS, sbp, nin, kind)) {
