int
main(int argc, char *argv[]) {
char *me, **name;
int lenName, ni, reverse, quiet, noAction, mac;
hestOpt *hopt = NULL;
airArray *mop;
me = argv[0];
hestOptAdd(&hopt, "r", NULL, airTypeInt, 0, 0, &reverse, NULL,
"convert back to DOS, instead of converting from DOS to normal");
hestOptAdd(&hopt, "q", NULL, airTypeInt, 0, 0, &quiet, NULL,
"never print anything to stderr, even for errors.");
hestOptAdd(&hopt, "m", NULL, airTypeInt, 0, 0, &mac, NULL,
"deal with legacy MAC text files.");
hestOptAdd(&hopt, "n", NULL, airTypeInt, 0, 0, &noAction, NULL,
"don't actually write converted files, just pretend to. "
"This is useful to see which files WOULD be converted. ");
hestOptAdd(&hopt, NULL, "file", airTypeString, 1, -1, &name, NULL,
"all the files to convert. Each file will be over-written "
"with its converted contents. Use \"-\" to read from stdin "
"and write to stdout", &lenName);
hestParseOrDie(hopt, argc-1, argv+1, NULL, me, info,
AIR_TRUE, AIR_TRUE, AIR_TRUE);
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
for (ni=0; ni<lenName; ni++) {
undosConvert(me, name[ni], reverse, mac, quiet, noAction);
}
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt = NULL;
int center;
double minPos, maxPos, pos, index, size;
me = argv[0];
hestOptAdd(&hopt, NULL, "center", airTypeEnum, 1, 1, ¢er, NULL,
"which centering applies to the quantized position.\n "
"Possibilities are:\n "
"\b\bo \"cell\": for histogram bins, quantized values, and "
"pixels-as-squares\n "
"\b\bo \"node\": for non-trivially interpolated "
"sample points", NULL, nrrdCenter);
hestOptAdd(&hopt, NULL, "minPos", airTypeDouble, 1, 1, &minPos, NULL,
"smallest position associated with index 0");
hestOptAdd(&hopt, NULL, "maxPos", airTypeDouble, 1, 1, &maxPos, NULL,
"highest position associated with highest index");
hestOptAdd(&hopt, NULL, "num", airTypeDouble, 1, 1, &size, NULL,
"number of intervals into which position has been quantized");
hestOptAdd(&hopt, NULL, "index", airTypeDouble, 1, 1, &index, NULL,
"the input index, to be converted to position");
hestParseOrDie(hopt, argc-1, argv+1, NULL, me, info,
AIR_TRUE, AIR_TRUE, AIR_TRUE);
pos = NRRD_POS(center, minPos, maxPos, size, index);
printf("%g\n", pos);
hestParseFree(hopt);
hestOptFree(hopt);
exit(0);
}
int
unrrdu_shuffleMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
unsigned int di, axis, permLen, *perm, *iperm, *whichperm;
size_t *realperm;
int inverse, pret;
airArray *mop;
/* so that long permutations can be read from file */
hparm->respFileEnable = AIR_TRUE;
hestOptAdd(&opt, "p,permute", "slc0 slc1", airTypeUInt, 1, -1, &perm, NULL,
"new slice ordering", &permLen);
hestOptAdd(&opt, "inv,inverse", NULL, airTypeInt, 0, 0, &inverse, NULL,
"use inverse of given permutation");
OPT_ADD_AXIS(axis, "axis to shuffle along");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_shuffleInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
/* we have to do error checking on axis in order to do error
checking on length of permutation */
if (!( axis < nin->dim )) {
fprintf(stderr, "%s: axis %d not in valid range [0,%d]\n",
me, axis, nin->dim-1);
airMopError(mop);
return 1;
}
if (!( permLen == nin->axis[axis].size )) {
char stmp[AIR_STRLEN_SMALL];
fprintf(stderr, "%s: permutation length (%u) != axis %d's size (%s)\n",
me, permLen, axis,
airSprintSize_t(stmp, nin->axis[axis].size));
airMopError(mop);
return 1;
}
if (inverse) {
iperm = AIR_CALLOC(permLen, unsigned int);
airMopAdd(mop, iperm, airFree, airMopAlways);
if (nrrdInvertPerm(iperm, perm, permLen)) {
fprintf(stderr,
"%s: couldn't compute inverse of given permutation\n", me);
airMopError(mop);
return 1;
}
whichperm = iperm;
} else {
int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt=NULL;
airArray *mop;
unsigned int *srcA, *srcB, *dstC, *_srcA, *_srcB, numA, numB, numC, idx;
me = argv[0];
hestOptAdd(&hopt, "a", "vals", airTypeUInt, 1, -1, &srcA, NULL,
"list of values", &numA);
hestOptAdd(&hopt, "b", "vals", airTypeUInt, 1, -1, &srcB, NULL,
"list of values", &numB);
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
fprintf(stderr, "a =");
for (idx=0; idx<numA; idx++) {
fprintf(stderr, " %u", srcA[idx]);
}
fprintf(stderr, "\n");
fprintf(stderr, "b =");
for (idx=0; idx<numB; idx++) {
fprintf(stderr, " %u", srcB[idx]);
}
fprintf(stderr, "\n");
_srcA = AIR_CAST(unsigned int*, calloc(1+numA, sizeof(unsigned int)));
airMopAdd(mop, _srcA, airFree, airMopAlways);
_srcB = AIR_CAST(unsigned int*, calloc(1+numB, sizeof(unsigned int)));
airMopAdd(mop, _srcB, airFree, airMopAlways);
dstC = AIR_CAST(unsigned int*, calloc(1+AIR_MAX(numA,numB),
sizeof(unsigned int)));
airMopAdd(mop, dstC, airFree, airMopAlways);
_srcA[0] = numA;
for (idx=0; idx<numA; idx++) {
_srcA[1+idx] = srcA[idx];
}
_srcB[0] = numB;
for (idx=0; idx<numB; idx++) {
_srcB[1+idx] = srcB[idx];
}
numC = flipListIntx(dstC, _srcA, _srcB);
fprintf(stderr, "intx(a,b) =");
for (idx=0; idx<numC; idx++) {
fprintf(stderr, " %u", dstC[idx]);
}
fprintf(stderr, "\n");
airMopOkay(mop);
return 0;
}
int
unrrdu_ccfindMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err, *valS;
Nrrd *nin, *nout, *nval=NULL;
airArray *mop;
int type, pret;
unsigned int conny;
hestOptAdd(&opt, "v,values", "filename", airTypeString, 1, 1, &valS, "",
"Giving a filename here allows you to save out the values "
"associated with each connect component. This can be used "
"later with \"ccmerge -d\". By default, no record of the "
"original CC values is kept.");
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &type, "default",
"type to use for output, to store the CC ID values. By default "
"(not using this option), the type used will be the smallest of "
"uchar, ushort, or int, that can represent all the CC ID values. "
"Using this option allows one to specify the integral type to "
"be used.",
NULL, NULL, &unrrduHestMaybeTypeCB);
hestOptAdd(&opt, "c,connect", "connectivity", airTypeUInt, 1, 1,
&conny, NULL,
"what kind of connectivity to use: the number of coordinates "
"that vary in order to traverse the neighborhood of a given "
"sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_ccfindInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCCFind(nout, airStrlen(valS) ? &nval : NULL, nin, type, conny)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error doing connected components:\n%s", me, err);
airMopError(mop);
return 1;
}
if (nval) {
airMopAdd(mop, nval, (airMopper)nrrdNuke, airMopAlways);
}
if (airStrlen(valS)) {
SAVE(valS, nval, NULL);
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
hestOpt *hopt=NULL;
airArray *mop;
const char *me;
char *outS, *err;
Nrrd *nin, *nout;
NrrdIoState *nio;
float heqamount;
me = argv[0];
mop = airMopNew();
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input nrrd to project. Must be three dimensional.",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "amt", "heq", airTypeFloat, 1, 1, &heqamount, "0.5",
"how much to apply histogram equalization to projection images");
hestOptAdd(&hopt, "o", "img out", airTypeString, 1, 1, &outS,
NULL, "output image to save to. Will try to use whatever "
"format is implied by extension, but will fall back to PPM.");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, 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);
nio = nrrdIoStateNew();
airMopAdd(mop, nio, (airMopper)nrrdIoStateNix, airMopAlways);
nrrdStateDisableContent = AIR_TRUE;
if (doit(nout, nin, 1, heqamount)) {
err=biffGetDone(NINSPECT);
airMopAdd(mop, err, airFree, airMopAlways);
fprintf(stderr, "%s: trouble creating output:\n%s", me, err);
airMopError(mop); return 1;
}
if (nrrdFormatPNG->nameLooksLike(outS)
&& !nrrdFormatPNG->available()) {
fprintf(stderr, "(%s: using PPM format for output)\n", me);
nio->format = nrrdFormatPNM;
}
if (nrrdSave(outS, nout, nio)) {
err=biffGetDone(NRRD);
airMopAdd(mop, err, airFree, airMopAlways);
fprintf(stderr, "%s: trouble saving output image \"%s\":\n%s",
me, outS, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
unrrdu_spliceMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout, *nslice;
unsigned int axis;
int pret;
long int _pos[2];
size_t pos;
airArray *mop;
OPT_ADD_AXIS(axis, "axis to splice along");
hestOptAdd(&opt, "p,position", "pos", airTypeOther, 1, 1, _pos, NULL,
"position to splice at:\n "
"\b\bo <int> gives 0-based index\n "
"\b\bo M-<int> give index relative "
"to the last sample on the axis (M == #samples-1).",
NULL, NULL, &unrrduHestPosCB);
hestOptAdd(&opt, "s,slice", "nslice", airTypeOther, 1, 1, &(nslice), NULL,
"slice nrrd. This the slice to be inserted in \"nin\"",
NULL, NULL, nrrdHestNrrd);
OPT_ADD_NIN(nin, "input nrrd. This the nrrd into which the slice will "
"be inserted");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_spliceInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
if (!( axis < nin->dim )) {
fprintf(stderr, "%s: axis %u not in range [0,%u]\n", me, axis, nin->dim-1);
return 1;
}
if (_pos[0] == -1) {
fprintf(stderr, "%s: m+<int> specification format meaningless here\n", me);
return 1;
}
pos = _pos[0]*(nin->axis[axis].size-1) + _pos[1];
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdSplice(nout, nin, nslice, axis, pos)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error splicing nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
airArray *mop;
hestOpt *hopt=NULL;
int i, N, M, P, yes, *year;
unsigned int E;
const char *me;
double crct;
me = argv[0];
mop = airMopNew();
hestOptAdd(&hopt, "N", "days", airTypeInt, 1, 1, &N, "365",
"# of days in year");
/* E != P */
hestOptAdd(&hopt, "E", "exps", airTypeInt, 1, 1, &P, "100000",
"number of experiments after which to print out newly "
"computed probability");
hestOptAdd(&hopt, NULL, "people", airTypeInt, 1, 1, &M, NULL,
"# of people in room");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!( N > 1 && M > 0 && P > 1)) {
fprintf(stderr, "%s: need both M, P all > 1, M > 0\n", me);
airMopError(mop); exit(1);
}
if (!(year = (int*)calloc(N, sizeof(int)))) {
fprintf(stderr, "%s: couldn't calloc(%d,sizeof(int))\n", me, N);
airMopError(mop); exit(1);
}
airMopMem(mop, year, airMopAlways);
crct = 1;
for (i=0; i<M; i++) {
crct *= (double)(N-i)/N;
}
crct = 1-crct;
yes = 0;
E = 1;
airSrandMT((int)airTime());
while (E) {
yes += runexp(year, N, M);
if (!(E % P)) {
printf("P = %10d/%10d = %22.20f =?= %22.20f\n",
yes, E, (double)yes/E, crct);
}
E++;
}
airMopOkay(mop);
exit(0);
}
int
main(int argc, const char *argv[]) {
const char *me;
char *err, *outS;
hestOpt *hopt=NULL;
airArray *mop;
limnPolyData *pld;
FILE *file;
Nrrd *nin;
double thresh;
int bitflag;
me = argv[0];
hestOptAdd(&hopt, "vi", "nin", airTypeOther, 1, 1, &nin, NULL,
"input values",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "pi", "lpld", airTypeOther, 1, 1, &pld, NULL,
"input polydata",
NULL, NULL, limnHestPolyDataLMPD);
hestOptAdd(&hopt, "th", "thresh", airTypeDouble, 1, 1, &thresh, NULL,
"threshold value");
hestOptAdd(&hopt, "o", "output LMPD", airTypeString, 1, 1, &outS, "out.lmpd",
"output file to save LMPD into");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
bitflag = limnPolyDataInfoBitFlag(pld);
fprintf(stderr, "!%s: bitflag = %d\n", me, bitflag);
fprintf(stderr, "!%s: rgba %d, norm %d, tex2 %d\n", me,
(1 << limnPolyDataInfoRGBA) & bitflag,
(1 << limnPolyDataInfoNorm) & bitflag,
(1 << limnPolyDataInfoTex2) & bitflag);
file = airFopen(outS, stdout, "w");
if (!file) {
fprintf(stderr, "%s: couldn't open \"%s\" for writing", me, outS);
airMopError(mop); return 1;
}
airMopAdd(mop, file, (airMopper)airFclose, airMopAlways);
if (limnPolyDataClip(pld, nin, thresh)
|| limnPolyDataWriteLMPD(file, pld)) {
airMopAdd(mop, err = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
unrrdu_histaxMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
int type, bins, pret, blind8BitRange;
unsigned int axis;
double min, max;
airArray *mop;
NrrdRange *range;
OPT_ADD_AXIS(axis, "axis to histogram along");
hestOptAdd(&opt, "b,bin", "bins", airTypeInt, 1, 1, &bins, NULL,
"# of bins in histogram");
OPT_ADD_TYPE(type, "output type", "uchar");
hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
"Value at low end of histogram. Defaults to lowest value "
"found in input nrrd.");
hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
"Value at high end of histogram. Defaults to highest value "
"found in input nrrd.");
hestOptAdd(&opt, "blind8", "bool", airTypeBool, 1, 1, &blind8BitRange,
nrrdStateBlind8BitRange ? "true" : "false",
"Whether to know the range of 8-bit data blindly "
"(uchar is always [0,255], signed char is [-128,127]).");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_histaxInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
if (nrrdHistoAxis(nout, nin, range, axis, bins, type)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error doing axis histogramming:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
unrrdu_dhistoMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
int pret, nolog, notick;
unsigned int size;
airArray *mop;
double max;
hestOptAdd(&opt, "h,height", "height", airTypeUInt, 1, 1, &size, NULL,
"height of output image (horizontal size is determined by "
"number of bins in input histogram).");
hestOptAdd(&opt, "nolog", NULL, airTypeInt, 0, 0, &nolog, NULL,
"do not show the log-scaled histogram with decade tick-marks");
hestOptAdd(&opt, "notick", NULL, airTypeInt, 0, 0, ¬ick, NULL,
"do not draw the log decade tick marks");
hestOptAdd(&opt, "max,maximum", "max # hits", airTypeDouble, 1, 1,
&max, "nan",
"constrain the top of the drawn histogram to be at this "
"number of hits. This will either scale the drawn histogram "
"downward or clip its top, depending on whether the given max "
"is higher or lower than the actual maximum bin count. By "
"not using this option (the default), the actual maximum bin "
"count is used");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_dhistoInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdHistoDraw(nout, nin, size,
nolog ? AIR_FALSE : (notick ? 2 : AIR_TRUE),
max)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error drawing histogram nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
tend_evqMain(int argc, char **argv, char *me, hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
int which, aniso, dontScaleByAniso;
Nrrd *nin, *nout;
char *outS;
hestOptAdd(&hopt, "c", "evec index", airTypeInt, 1, 1, &which, "0",
"Which eigenvector should be quantized: \"0\" for the "
"direction of fastest diffusion (eigenvector associated "
"with largest eigenvalue), \"1\" or \"2\" for other two "
"eigenvectors (associated with middle and smallest eigenvalue)");
hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &aniso, NULL,
"Which anisotropy metric to scale the eigenvector "
"with. " TEN_ANISO_DESC,
NULL, tenAniso);
hestOptAdd(&hopt, "ns", NULL, airTypeInt, 0, 0, &dontScaleByAniso, NULL,
"Don't attenuate the color by anisotropy. By default (not "
"using this option), regions with low or no anisotropy are "
"very dark colors or black");
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
"input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_evqInfoL);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (tenEvqVolume(nout, nin, which, aniso, !dontScaleByAniso)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble quantizing eigenvectors:\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 writing:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me;
hestOpt *hopt=NULL;
airArray *mop;
int *itype, itypeNum, ii;
double src[3], last[3], dst[3];
char space[] = " ";
me = argv[0];
hestOptAdd(&hopt, NULL, "v1 v2 v3", airTypeDouble, 3, 3, src, NULL,
"source triple");
hestOptAdd(&hopt, "t", "type", airTypeEnum, 2, -1, &itype, NULL,
"sequence of triple types to convert through",
&itypeNum, tenTripleType);
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
printf("%s", space + strlen(airEnumStr(tenTripleType, itype[0])));
printf("%s", airEnumStr(tenTripleType, itype[0]));
ell_3v_print_d(stdout, src);
ELL_3V_COPY(last, src);
for (ii=1; ii<itypeNum; ii++) {
tenTripleConvertSingle_d(dst, itype[ii], src, itype[ii-1]);
printf("%s", space + strlen(airEnumStr(tenTripleType, itype[ii])));
printf("%s", airEnumStr(tenTripleType, itype[ii]));
ell_3v_print_d(stdout, dst);
ELL_3V_COPY(src, dst);
}
/*
tenTripleConvert_d(dst, dstType, src, srcType);
tenTripleConvert_d(tst, srcType, dst, dstType);
*/
/*
printf("%s: %s %s --> %s --> %s\n", me,
tenTriple->name,
airEnumStr(tenTriple, srcType),
airEnumStr(tenTriple, dstType),
airEnumStr(tenTriple, srcType));
ell_3v_print_d(stdout, src);
ell_3v_print_d(stdout, dst);
ell_3v_print_d(stdout, tst);
*/
airMopOkay(mop);
return 0;
}
int
unrrdu_gammaMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
double min, max, gamma;
airArray *mop;
int pret, blind8BitRange;
NrrdRange *range;
hestOptAdd(&opt, "g,gamma", "gamma", airTypeDouble, 1, 1, &gamma, NULL,
"gamma > 1.0 brightens; gamma < 1.0 darkens. "
"Negative gammas invert values (like in xv). ");
hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
"Value to implicitly map to 0.0 prior to calling pow(). "
"Defaults to lowest value found in input nrrd.");
hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
"Value to implicitly map to 1.0 prior to calling pow(). "
"Defaults to highest value found in input nrrd.");
hestOptAdd(&opt, "blind8", "bool", airTypeBool, 1, 1, &blind8BitRange,
nrrdStateBlind8BitRange ? "true" : "false",
"Whether to know the range of 8-bit data blindly "
"(uchar is always [0,255], signed char is [-128,127]).");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_gammaInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
if (nrrdArithGamma(nout, nin, range, gamma)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error doing gamma:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
unrrdu_distMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
int pret;
int E, typeOut, invert, sign;
double thresh;
airArray *mop;
hestOptAdd(&opt, "th,thresh", "val", airTypeDouble, 1, 1, &thresh, NULL,
"threshold value to separate inside from outside");
hestOptAdd(&opt, "t,type", "type", airTypeEnum, 1, 1, &typeOut, "float",
"type to save output in", NULL, nrrdType);
hestOptAdd(&opt, "sgn", NULL, airTypeInt, 0, 0, &sign, NULL,
"also compute signed (negative) distances inside objects, "
"instead of leaving them as zero");
hestOptAdd(&opt, "inv", NULL, airTypeInt, 0, 0, &invert, NULL,
"values *below* threshold are considered interior to object. "
"By default (not using this option), values above threshold "
"are considered interior. ");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_distInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (sign) {
E = nrrdDistanceL2Signed(nout, nin, typeOut, NULL, thresh, !invert);
} else {
E = nrrdDistanceL2(nout, nin, typeOut, NULL, thresh, !invert);
}
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error doing distance transform:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
const char *me;
char *err;
limnCamera *cam;
float mat[16];
hestOpt *hopt=NULL;
airArray *mop;
mop = airMopNew();
cam = limnCameraNew();
airMopAdd(mop, cam, (airMopper)limnCameraNix, airMopAlways);
me = argv[0];
hestOptAdd(&hopt, "fr", "eye pos", airTypeDouble, 3, 3, cam->from,
NULL, "camera eye point");
hestOptAdd(&hopt, "at", "at pos", airTypeDouble, 3, 3, cam->at,
"0 0 0", "camera look-at point");
hestOptAdd(&hopt, "up", "up dir", airTypeDouble, 3, 3, cam->up,
"0 0 1", "camera pseudo up vector");
hestOptAdd(&hopt, "rh", NULL, airTypeInt, 0, 0, &(cam->rightHanded), NULL,
"use a right-handed UVN frame (V points down)");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
cam->neer = -1;
cam->dist = 0;
cam->faar = 1;
cam->atRelative = AIR_TRUE;
if (limnCameraUpdate(cam)) {
fprintf(stderr, "%s: trouble:\n%s\n", me, err = biffGet(LIMN));
free(err);
return 1;
}
printf("%s: W2V:\n", me);
ELL_4M_COPY(mat, cam->W2V);
ell_4m_print_f(stdout, mat);
printf("\n");
printf("%s: V2W:\n", me);
ELL_4M_COPY(mat, cam->V2W);
ell_4m_print_f(stdout, mat);
airMopOkay(mop);
return 0;
}
int
baneGkms_miteMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *perr;
Nrrd *nin, *nout;
airArray *mop;
int pret, E;
hestOptAdd(&opt, "i", "opacIn", airTypeOther, 1, 1, &nin, NULL,
"input opacity function (1 or 2 dimensional), from "
"\"gkms opac\"",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "o", "opacOut", airTypeString, 1, 1, &out, NULL,
"output opacity function filename");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_baneGkms_miteInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
if (1 == nin->axis[0].size && nin->axis[0].label &&
!strcmp("A", nin->axis[0].label)) {
fprintf(stderr, "%s: already\n", me);
nout = nin;
} else {
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
E = 0;
if (!E) E |= nrrdAxesInsert(nout, nin, 0);
if (!E) E |= !(nout->axis[0].label = airStrdup("A"));
if (!E) E |= !(nout->axis[1].label = airStrdup("gage(v)"));
if (3 == nout->dim) {
if (!E) E |= !(nout->axis[2].label = airStrdup("gage(gm)"));
}
if (E) {
biffMovef(BANE, NRRD,
"%s: trouble modifying opacity function nrrd", me);
airMopError(mop); return 1;
}
}
if (nrrdSave(out, nout, NULL)) {
biffMovef(BANE, NRRD, "%s: trouble saving opacity function", me);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
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
unrrdu_joinMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err, *label;
Nrrd **nin;
Nrrd *nout;
int incrDim, pret;
unsigned int ninLen, axis;
double mm[2], spc;
airArray *mop;
hparm->respFileEnable = AIR_TRUE;
hestOptAdd(&opt, "i,input", "nin0", airTypeOther, 1, -1, &nin, NULL,
"everything to be joined together",
&ninLen, NULL, nrrdHestNrrd);
OPT_ADD_AXIS(axis, "axis to join along");
hestOptAdd(&opt, "incr", NULL, airTypeInt, 0, 0, &incrDim, NULL,
"in situations where the join axis is *not* among the existing "
"axes of the input nrrds, then this flag signifies that the join "
"axis should be *inserted*, and the output dimension should "
"be one greater than input dimension. Without this flag, the "
"nrrds are joined side-by-side, along an existing axis.");
hestOptAdd(&opt, "l,label", "label", airTypeString, 1, 1, &label, "",
"label to associate with join axis");
hestOptAdd(&opt, "mm,minmax", "min max", airTypeDouble, 2, 2, mm, "nan nan",
"min and max values along join axis");
hestOptAdd(&opt, "sp,spacing", "spc", airTypeDouble, 1, 1, &spc, "nan",
"spacing between samples along join axis");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_joinInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdJoin(nout, AIR_CAST(const Nrrd*const*, nin), ninLen,
axis, incrDim)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error joining nrrds:\n%s", me, err);
airMopError(mop);
return 1;
}
int
baneGkms_infoMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *outS, *perr, err[BIFF_STRLEN];
Nrrd *hvol, *nout;
airArray *mop;
int pret, one, measr;
hestOptAdd(&opt, "m", "measr", airTypeEnum, 1, 1, &measr, "mean",
"How to project along the 2nd derivative axis. Possibilities "
"include:\n "
"\b\bo \"mean\": average value\n "
"\b\bo \"median\": value at 50th percentile\n "
"\b\bo \"mode\": most common value\n "
"\b\bo \"min\", \"max\": probably not useful",
NULL, baneGkmsMeasr);
hestOptAdd(&opt, "one", NULL, airTypeInt, 0, 0, &one, NULL,
"Create 1-dimensional info file; default is 2-dimensional");
hestOptAdd(&opt, "i", "hvolIn", airTypeOther, 1, 1, &hvol, NULL,
"input histogram volume (from \"gkms hvol\")",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "o", "infoOut", airTypeString, 1, 1, &outS, NULL,
"output info file, used by \"gkms pvg\" and \"gkms opac\"");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_baneGkms_infoInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (baneOpacInfo(nout, hvol, one ? 1 : 2, measr)) {
sprintf(err, "%s: trouble distilling histogram info", me);
biffAdd(BANE, err);
airMopError(mop);
return 1;
}
if (nrrdSave(outS, nout, NULL)) {
sprintf(err, "%s: trouble saving info file", me);
biffMove(BANE, err, NRRD);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
tend_normMain(int argc, char **argv, char *me, hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
Nrrd *nin, *nout;
char *outS;
float amount, target;
double weight[3];
hestOptAdd(&hopt, "w", "w0 w1 w2", airTypeDouble, 3, 3, weight, NULL,
"relative weights to put on major, medium, and minor "
"eigenvalue when performing normalization (internally "
"rescaled to have a 1.0 L1 norm). These weightings determine "
"the tensors's \"size\".");
hestOptAdd(&hopt, "a", "amount", airTypeFloat, 1, 1, &amount, "1.0",
"how much of the normalization to perform");
hestOptAdd(&hopt, "t", "target", airTypeFloat, 1, 1, &target, "1.0",
"target size, post normalization");
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
"input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_normInfoL);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (tenSizeNormalize(nout, nin, weight, amount, target)) {
airMopAdd(mop, err=biffGetDone(TEN), 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 writing:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
tend_evecrgbMain(int argc, char **argv, char *me, hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
tenEvecRGBParm *rgbp;
Nrrd *nin, *nout;
char *outS;
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
rgbp = tenEvecRGBParmNew();
airMopAdd(mop, rgbp, AIR_CAST(airMopper, tenEvecRGBParmNix), airMopAlways);
hestOptAdd(&hopt, "c", "evec index", airTypeUInt, 1, 1, &(rgbp->which), NULL,
"which eigenvector will be colored. \"0\" for the "
"principal, \"1\" for the middle, \"2\" for the minor");
hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &(rgbp->aniso), NULL,
"Which anisotropy to use for modulating the saturation "
"of the colors. " TEN_ANISO_DESC,
NULL, tenAniso);
hestOptAdd(&hopt, "t", "thresh", airTypeDouble, 1, 1, &(rgbp->confThresh),
"0.5", "confidence threshold");
hestOptAdd(&hopt, "bg", "background", airTypeDouble, 1, 1, &(rgbp->bgGray),
"0", "gray level to use for voxels who's confidence is zero ");
hestOptAdd(&hopt, "gr", "gray", airTypeDouble, 1, 1, &(rgbp->isoGray), "0",
"the gray level to desaturate towards as anisotropy "
"decreases (while confidence remains 1.0)");
hestOptAdd(&hopt, "gam", "gamma", airTypeDouble, 1, 1, &(rgbp->gamma), "1",
"gamma to use on color components");
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
"input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output image (floating point)");
USAGE(_tend_evecrgbInfoL);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (tenEvecRGB(nout, nin, rgbp)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble doing colormapping:\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 writing:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
tend_anscaleMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
Nrrd *nin, *nout;
char *outS;
float scale;
int fixDet, makePositive;
hestOptAdd(&hopt, "s", "scale", airTypeFloat, 1, 1, &scale, NULL,
"Amount by which to scale deviatoric component of tensor.");
hestOptAdd(&hopt, "fd", NULL, airTypeInt, 0, 0, &fixDet, NULL,
"instead of fixing the per-sample trace (the default), fix the "
"determinant (ellipsoid volume)");
hestOptAdd(&hopt, "mp", NULL, airTypeInt, 0, 0, &makePositive, NULL,
"after changing the eigenvalues of the tensor, enforce their "
"non-negative-ness. By default, no such constraint is imposed.");
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
"input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_anscaleInfoL);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (tenAnisoScale(nout, nin, scale, fixDet, makePositive)) {
airMopAdd(mop, err=biffGetDone(TEN), 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 writing:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 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;
}
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
unrrdu_axdeleteMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout, *ntmp;
int pret, _axis;
unsigned axis;
airArray *mop;
hestOptAdd(&opt, "a,axis", "axis", airTypeInt, 1, 1, &_axis, NULL,
"dimension (axis index) of the axis to remove");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_axdeleteInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (-1 == _axis) {
ntmp = nrrdNew();
airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error copying axis:\n%s", me, err);
airMopError(mop); return 1;
}
for (axis=0;
axis<nout->dim && nout->axis[axis].size > 1;
axis++);
while (axis<nout->dim) {
if (nrrdAxesDelete(ntmp, nout, axis)
|| nrrdCopy(nout, ntmp)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error deleting axis:\n%s", me, err);
airMopError(mop); return 1;
}
for (axis=0;
axis<nout->dim && nout->axis[axis].size > 1;
axis++);
}
} else {
if (nrrdAxesDelete(nout, nin, _axis)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error deleting axis:\n%s", me, err);
airMopError(mop); return 1;
}
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
unrrdu_dataMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *err, *inS=NULL;
Nrrd *nin;
NrrdIoState *nio;
airArray *mop;
int car, pret;
mop = airMopNew();
hestOptAdd(&opt, NULL, "nin", airTypeString, 1, 1, &inS, NULL,
"input nrrd");
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_dataInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nio = nrrdIoStateNew();
airMopAdd(mop, nio, (airMopper)nrrdIoStateNix, airMopAlways);
nio->skipData = AIR_TRUE;
nio->keepNrrdDataFileOpen = AIR_TRUE;
nin = nrrdNew();
airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nin, inS, nio)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error reading header:\n%s", me, err);
airMopError(mop);
return 1;
}
if (_nrrdDataFNNumber(nio) > 1) {
fprintf(stderr, "%s: sorry, currently can't operate with multiple "
"detached datafiles\n", me);
airMopError(mop);
return 1;
}
if (!( nrrdFormatNRRD == nio->format )) {
fprintf(stderr, "%s: can only print data of NRRD format files\n", me);
airMopError(mop); return 1;
}
car = fgetc(nio->dataFile);
#ifdef _MSC_VER
/* needed because otherwise printing a carraige return will
automatically also produce a newline */
_setmode(_fileno(stdout), _O_BINARY);
#endif
while (EOF != car) {
fputc(car, stdout);
car = fgetc(nio->dataFile);
}
airFclose(nio->dataFile);
airMopOkay(mop);
return 0;
}
int
unrrdu_projectMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
unsigned int axis;
int measr, pret, type;
airArray *mop;
OPT_ADD_AXIS(axis, "axis to project along");
hestOptAdd(&opt, "m,measure", "measr", airTypeEnum, 1, 1, &measr, NULL,
"How to \"measure\" a scanline, by summarizing all its values "
"with a single scalar. " NRRD_MEASURE_DESC,
NULL, nrrdMeasure);
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &type, "default",
"type to use for output. By default (not using this option), "
"the output type is determined auto-magically",
NULL, NULL, &unrrduHestMaybeTypeCB);
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_projectInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdProject(nout, nin, axis, measr, type)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error projecting nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
limnpu_sortMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *hopt = NULL;
char *err, *perr;
airArray *mop;
int pret;
limnPolyData *pld;
Nrrd *nin;
char *out;
hestOptAdd(&hopt, NULL, "input lpld", airTypeOther, 1, 1, &pld, NULL,
"input polydata filename",
NULL, NULL, limnHestPolyDataLMPD);
hestOptAdd(&hopt, NULL, "input nrrd", airTypeOther, 1, 1, &nin, NULL,
"input nrrd filename",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
"output lpld filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(myinfo);
PARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (limnPolyDataPrimitiveSort(pld, nin)) {
airMopAdd(mop, err = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:%s", me, err);
airMopError(mop);
return 1;
}
if (limnPolyDataSave(out, pld)) {
airMopAdd(mop, err = biffGetDone(LIMN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:%s", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
unrrdu_ccsettleMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err, *valS;
Nrrd *nin, *nout, *nval=NULL;
airArray *mop;
int pret;
mop = airMopNew();
hestOptAdd(&opt, "i,input", "nin", airTypeOther, 1, 1, &nin, NULL,
"input nrrd",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "v,values", "filename", airTypeString, 1, 1, &valS, "",
"Giving a filename here allows you to save out the mapping "
"from new (settled) values to old values, in the form of a "
"1-D lookup table");
OPT_ADD_NOUT(out, "output nrrd");
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_ccsettleInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCCSettle(nout, airStrlen(valS) ? &nval : NULL, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error settling connected components:\n%s", me, err);
airMopError(mop);
return 1;
}
if (nval) {
airMopAdd(mop, nval, (airMopper)nrrdNuke, airMopAlways);
}
if (airStrlen(valS)) {
SAVE(valS, nval, NULL);
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
