int
ninspect_proj(Nrrd *nout, Nrrd *nin, int axis, int smart, float amount) {
static const char me[]="ninspect_proj";
airArray *mop;
Nrrd *ntmpA, *ntmpB, **nrgb;
int bins;
if (!(nout && nin)) {
biffAddf(NINSPECT, "%s: got NULL pointer", me);
return 1;
}
if (!( AIR_IN_CL(0, axis, 2) )) {
biffAddf(NINSPECT, "%s: given axis %d outside valid range [0,1,2]",
me, axis);
return 1;
}
/* allocate a bunch of nrrds to use as basically temp variables */
mop = airMopNew();
airMopAdd(mop, ntmpA = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, ntmpB = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
/* HEY: this used to be nrgb[3], but its passing to nrrdJoin caused
"dereferencing type-punned pointer might break strict-aliasing rules"
warning; GLK not sure how else to fix it */
nrgb = AIR_CALLOC(3, Nrrd*);
airMopAdd(mop, nrgb, airFree, airMopAlways);
airMopAdd(mop, nrgb[0] = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nrgb[1] = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nrgb[2] = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
/* these arguments to nrrdHistoEq will control its behavior */
bins = 3000; /* equalization will use a histogram with this many bins */
/* the following idiom is one way of handling the fact that any
non-trivial nrrd call can fail, and if it does, then any subsequent
nrrd calls should be avoided (to be perfectly safe), so that you can
get the error message from biff. Because of the left-to-right ordering
ensured for logical expressions, this will all be called in sequence
until one of them has a non-zero return. If he had exception handling,
we'd put all the nrrd calls in one "try" block. */
if (nrrdProject(ntmpA, nin, axis, nrrdMeasureSum, nrrdTypeDefault)
|| nrrdHistoEq(ntmpB, ntmpA, NULL, bins, smart, amount)
|| nrrdQuantize(nrgb[0], ntmpB, NULL, 8)
|| nrrdProject(ntmpA, nin, axis, nrrdMeasureVariance, nrrdTypeDefault)
|| nrrdHistoEq(ntmpB, ntmpA, NULL, bins, smart, amount)
|| nrrdQuantize(nrgb[1], ntmpB, NULL, 8)
|| nrrdProject(ntmpA, nin, axis, nrrdMeasureMax, nrrdTypeDefault)
|| nrrdQuantize(nrgb[2], ntmpA, NULL, 8)
|| nrrdJoin(nout, (const Nrrd*const*)nrgb, 3, 0, AIR_TRUE)) {
biffMovef(NINSPECT, NRRD, "%s: trouble with nrrd operations", me);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
_alanPerIteration(alanContext *actx, int iter) {
char me[]="_alanPerIteration", fname[AIR_STRLEN_MED];
Nrrd *nslc, *nimg;
if (!(actx->saveInterval || actx->frameInterval)) {
if (actx->verbose && !(iter % 100)) {
fprintf(stderr, "%s: iter = %d, averageChange = %g\n",
me, iter, actx->averageChange);
}
}
if (actx->saveInterval && !(iter % actx->saveInterval)) {
sprintf(fname, "%06d.nrrd", actx->constFilename ? 0 : iter);
nrrdSave(fname, actx->_nlev[(iter+1) % 2], NULL);
fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
me, iter, actx->averageChange, fname);
}
if (actx->frameInterval && !(iter % actx->frameInterval)) {
nrrdSlice(nslc=nrrdNew(), actx->_nlev[(iter+1) % 2], 0, 0);
nrrdQuantize(nimg=nrrdNew(), nslc, NULL, 8);
sprintf(fname, (2 == actx->dim ? "%06d.png" : "%06d.nrrd"),
actx->constFilename ? 0 : iter);
nrrdSave(fname, nimg, NULL);
fprintf(stderr, "%s: iter = %d, averageChange = %g, saved %s\n",
me, iter, actx->averageChange, fname);
nrrdNuke(nslc);
nrrdNuke(nimg);
}
return 0;
}
int
main(int argc, char *argv[]) {
Nrrd *map, *ppm;
NrrdRange *range;
AIR_UNUSED(argc);
me = argv[0];
if (limnEnvMapFill(map=nrrdNew(), cb, limnQN16checker, NULL)) {
fprintf(stderr, "%s: trouble:\n%s", me, biffGet(LIMN));
exit(1);
}
range = nrrdRangeNew(0, 1);
if (nrrdQuantize(ppm=nrrdNew(), map, range, 8)) {
fprintf(stderr, "%s: trouble:\n%s", me, biffGet(NRRD));
exit(1);
}
if (nrrdSave("map.ppm", ppm, NULL)) {
fprintf(stderr, "%s: trouble:\n%s", me, biffGet(NRRD));
exit(1);
}
nrrdNuke(map);
nrrdNuke(ppm);
nrrdRangeNix(range);
exit(0);
}
void WriteFile(Nrrd *nData, int type, char *Outfile){
if(type == 0){
if(nrrdSave(Outfile, nData, NULL)) {
exit(1);
}
}
else{
Nrrd *ntmp = nrrdNew();
nrrdQuantize(ntmp, nData, NULL, 8);
nrrdSave(Outfile, ntmp, NULL);
}
nrrdNuke(nData);
return;
}
int main(int argc, char * argv[])
{
Nrrd *nin = nrrdNew();
Nrrd *nquantized = nrrdNew();
char *biffErr;
if(argc < 4) {
fprintf(stderr,"Usage: %s centerx centery nrrd\n",argv[0]);
return 1;
}
cx = atoi(argv[1]);
cy = atoi(argv[2]);
if(nrrdLoad(nin, argv[3], NULL)) {
biffErr = biffGetDone(NRRD);
fprintf(stderr, "Error reading file: %s\n", biffErr);
free(biffErr);
return 1;
}
printf("Read %d-dimensional nrrd of type %d (%s)\n",
nin->dim, nin->type, airEnumStr(nrrdType, nin->type));
printf("Axis dimensions: %d x %d x %d\n", nin->axis[0].size,
nin->axis[1].size, nin->axis[2].size);
NrrdRange *range = nrrdRangeNewSet(nin, 0);
printf("min: %g\tmax: %g\n", range->min, range->max);
if(nrrdQuantize(nquantized, nin, range, 8)) {
biffErr = biffGetDone(NRRD);
fprintf(stderr, "Error quantizing: %s\n", biffErr);
return 1;
}
process_slices(nquantized);
nrrdRangeNix(range);
nrrdNuke(nin);
nrrdNuke(nquantized);
return 0;
}
int
baneGkms_scatMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out[2], *perr, err[BIFF_STRLEN];
Nrrd *hvol, *nvgRaw, *nvhRaw, *nvgQuant, *nvhQuant;
NrrdRange *vgRange, *vhRange;
airArray *mop;
int pret, E;
double gamma;
hestOptAdd(&opt, "g", "gamma", airTypeDouble, 1, 1, &gamma, "1.0",
"gamma used to brighten/darken scatterplots. "
"gamma > 1.0 brightens; gamma < 1.0 darkens. "
"Negative gammas invert values (like in xv). ");
hestOptAdd(&opt, "i", "hvolIn", airTypeOther, 1, 1, &hvol, NULL,
"input histogram volume (from \"gkms hvol\")",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "o", "vgOut vhOut", airTypeString, 2, 2, out, NULL,
"Filenames to use for two output scatterplots, (gradient "
"magnitude versus value, and 2nd derivative versus value); "
"can use PGM or PNG format");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_baneGkms_scatInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nvgRaw = nrrdNew();
nvhRaw = nrrdNew();
nvgQuant = nrrdNew();
nvhQuant = nrrdNew();
airMopAdd(mop, nvgRaw, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nvhRaw, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nvgQuant, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nvhQuant, (airMopper)nrrdNuke, airMopAlways);
if (baneRawScatterplots(nvgRaw, nvhRaw, hvol, AIR_TRUE)) {
sprintf(err, "%s: trouble creating raw scatterplots", me);
biffAdd(BANE, err); airMopError(mop); return 1;
}
vgRange = nrrdRangeNewSet(nvgRaw, nrrdBlind8BitRangeFalse);
vhRange = nrrdRangeNewSet(nvhRaw, nrrdBlind8BitRangeFalse);
airMopAdd(mop, vgRange, (airMopper)nrrdRangeNix, airMopAlways);
airMopAdd(mop, vhRange, (airMopper)nrrdRangeNix, airMopAlways);
E = 0;
if (!E) E |= nrrdArithGamma(nvgRaw, nvgRaw, vgRange, gamma);
if (!E) E |= nrrdArithGamma(nvhRaw, nvhRaw, vhRange, gamma);
if (!E) E |= nrrdQuantize(nvgQuant, nvgRaw, vgRange, 8);
if (!E) E |= nrrdQuantize(nvhQuant, nvhRaw, vhRange, 8);
if (E) {
sprintf(err, "%s: trouble doing gamma or quantization", me);
biffMove(BANE, err, NRRD); airMopError(mop); return 1;
}
if (!E) E |= nrrdSave(out[0], nvgQuant, NULL);
if (!E) E |= nrrdSave(out[1], nvhQuant, NULL);
if (E) {
sprintf(err, "%s: trouble saving scatterplot images", me);
biffMove(BANE, err, NRRD); airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int
main() {
airArray *mop, *submop;
char *err;
int typi;
unsigned int supi, probePass, cti /* context copy index */,
pvlIdx[NRRD_TYPE_MAX+1], sx, sy, sz, subnum;
size_t sizes[3] = {42,61,50} /* one of these must be even */,
ii, nn;
Nrrd *norigScl, *nucharScl, *nunquant, *nqdiff,
*nconvScl[NRRD_TYPE_MAX+1];
unsigned char *ucharScl;
gageContext *gctx[2][KERN_SIZE_MAX+1];
gagePerVolume *gpvl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1];
const double *vansScl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1],
*gansScl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1],
*hansScl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1];
double *origScl, omin, omax, dsx, dsy, dsz,
spcOrig[NRRD_SPACE_DIM_MAX] = {0.0, 0.0, 0.0},
spcVec[3][NRRD_SPACE_DIM_MAX] = {
{1.1, 0.0, 0.0},
{0.0, 2.2, 0.0},
{0.0, 0.0, 3.3}};
mop = airMopNew();
#define NRRD_NEW(name, mop) \
(name) = nrrdNew(); \
airMopAdd((mop), (name), (airMopper)nrrdNuke, airMopAlways)
/* --------------------------------------------------------------- */
/* Creating initial volume */
NRRD_NEW(norigScl, mop);
if (nrrdMaybeAlloc_nva(norigScl, nrrdTypeDouble, 3, sizes)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "trouble allocating:\n%s", err);
airMopError(mop); return 1;
}
origScl = AIR_CAST(double *, norigScl->data);
nn = nrrdElementNumber(norigScl);
airSrandMT(42*42);
for (ii=0; ii<nn/2; ii++) {
airNormalRand(origScl + 2*ii + 0, origScl + 2*ii + 1);
}
/* learn real range */
omin = omax = origScl[0];
for (ii=1; ii<nn; ii++) {
omin = AIR_MIN(omin, origScl[ii]);
omax = AIR_MAX(omax, origScl[ii]);
}
ELL_3V_SET(spcOrig, 0.0, 0.0, 0.0);
if (nrrdSpaceSet(norigScl, nrrdSpaceRightAnteriorSuperior)
|| nrrdSpaceOriginSet(norigScl, spcOrig)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "trouble setting space:\n%s", err);
airMopError(mop); return 1;
}
nrrdAxisInfoSet_nva(norigScl, nrrdAxisInfoSpaceDirection, spcVec);
dsx = AIR_CAST(double, sizes[0]);
dsy = AIR_CAST(double, sizes[1]);
dsz = AIR_CAST(double, sizes[2]);
sx = AIR_CAST(unsigned int, sizes[0]);
sy = AIR_CAST(unsigned int, sizes[1]);
sz = AIR_CAST(unsigned int, sizes[2]);
subnum = AIR_CAST(unsigned int, PROBE_NUM*0.9);
/* --------------------------------------------------------------- */
/* Quantizing to 8-bits and checking */
submop = airMopNew();
NRRD_NEW(nucharScl, mop);
NRRD_NEW(nunquant, submop);
NRRD_NEW(nqdiff, submop);
if (nrrdQuantize(nucharScl, norigScl, NULL, 8)
|| nrrdUnquantize(nunquant, nucharScl, nrrdTypeDouble)
|| nrrdArithBinaryOp(nqdiff, nrrdBinaryOpSubtract,
norigScl, nunquant)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "trouble quantizing and back:\n%s", err);
airMopError(submop); airMopError(mop); return 1;
}
if (!( nucharScl->oldMin == omin
&& nucharScl->oldMax == omax )) {
fprintf(stderr, "quantization range [%g,%g] != real range [%g,%g]\n",
nucharScl->oldMin, nucharScl->oldMax, omin, omax);
airMopError(submop); airMopError(mop); return 1;
}
{
double *qdiff, *unquant;
/* empirically determined tolerance, which had to be increased in
order to work under valgrind (!)- perhaps because of a
difference in the use of 80-bit registers */
double epsilon=0.50000000000004;
qdiff = AIR_CAST(double *, nqdiff->data);
unquant = AIR_CAST(double *, nunquant->data);
for (ii=0; ii<nn; ii++) {
double dd;
/* with infinite precision, the max difference between original and
quantized values should be exactly half the width (in value)
of 1/256 of value range ==> dd = 0.5 */
dd = qdiff[ii]*256/(omax - omin);
if (AIR_ABS(dd) > epsilon) {
unsigned int ui;
ui = AIR_CAST(unsigned int, ii);
fprintf(stderr, "|orig[%u]=%.17g - unquant=%.17g|*256/%.17g "
"= %.17g > %.17g!\n", ui, origScl[ii], unquant[ii],
omax - omin, AIR_ABS(dd), epsilon);
airMopError(submop); airMopError(mop); return 1;
}
}
}
int
unrrdu_quantizeMain(int argc, const char **argv, const char *me,
hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout;
char *minStr, *maxStr;
int pret, blind8BitRange;
unsigned int bits, hbins;
NrrdRange *range;
airArray *mop;
hestOptAdd(&opt, "b,bits", "bits", airTypeOther, 1, 1, &bits, NULL,
"Number of bits to quantize down to; determines the type "
"of the output nrrd:\n "
"\b\bo \"8\": unsigned char\n "
"\b\bo \"16\": unsigned short\n "
"\b\bo \"32\": unsigned int",
NULL, NULL, &unrrduHestBitsCB);
hestOptAdd(&opt, "min,minimum", "value", airTypeString, 1, 1,
&minStr, "nan",
"The value to map to zero, given explicitly as a regular number, "
"*or*, if the number is given with a \"" NRRD_MINMAX_PERC_SUFF
"\" suffix, this "
"minimum is specified in terms of the percentage of samples in "
"input that are lower. "
"\"0" NRRD_MINMAX_PERC_SUFF "\" means the "
"lowest input value is used, "
"\"1" NRRD_MINMAX_PERC_SUFF "\" means that the "
"1% of the lowest values are all mapped to zero. "
"By default (not using this option), the lowest input value is "
"used.");
hestOptAdd(&opt, "max,maximum", "value", airTypeString, 1, 1,
&maxStr, "nan",
"The value to map to the highest unsigned integral value, given "
"explicitly as a regular number, "
"*or*, if the number is given with "
"a \"" NRRD_MINMAX_PERC_SUFF "\" suffix, "
"this maximum is specified "
"in terms of the percentage of samples in input that are higher. "
"\"0" NRRD_MINMAX_PERC_SUFF "\" means the highest input value is "
"used, which is also the default "
"behavior (same as not using this option).");
hestOptAdd(&opt, "hb,bins", "bins", airTypeUInt, 1, 1, &hbins, "5000",
"number of bins in histogram of values, for determining min "
"or max by percentiles. This has to be large enough so that "
"any errant very high or very low values do not compress the "
"interesting part of the histogram to an inscrutably small "
"number of bins.");
hestOptAdd(&opt, "blind8", "bool", airTypeBool, 1, 1, &blind8BitRange,
nrrdStateBlind8BitRange ? "true" : "false",
"if not using \"-min\" or \"-max\", 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_quantizeInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
range = nrrdRangeNew(AIR_NAN, AIR_NAN);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdRangePercentileFromStringSet(range, nin, minStr, maxStr,
hbins, blind8BitRange)
|| nrrdQuantize(nout, nin, range, bits)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error with range or quantizing:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
