int
nrrdApplyMulti1DRegMap(Nrrd *nout, const Nrrd *nin,
const NrrdRange *_range, const Nrrd *nmmap,
int typeOut, int rescale) {
char me[]="nrrdApplyMulti1DRegMap", err[BIFF_STRLEN];
NrrdRange *range;
airArray *mop;
if (!(nout && nmmap && nin)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(NRRD, err); return 1;
}
mop = airMopNew();
if (_range) {
range = nrrdRangeCopy(_range);
nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
} else {
range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
}
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
if (_nrrdApply1DSetUp(nout, nin, range, nmmap, kindRmap, typeOut,
rescale, AIR_TRUE)
|| _nrrdApply1DLutOrRegMap(nout, nin, range, nmmap, AIR_TRUE,
rescale, AIR_TRUE)) {
sprintf(err, "%s:", me);
biffAdd(NRRD, 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_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_imapMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nmap, *nacl, *nout;
airArray *mop;
NrrdRange *range=NULL;
unsigned int aclLen;
int typeOut, rescale, pret, blind8BitRange;
double min, max;
hestOptAdd(&opt, "m,map", "map", airTypeOther, 1, 1, &nmap, NULL,
"irregular map to map input nrrd through",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "l,length", "aclLen", airTypeUInt, 1, 1, &aclLen, "0",
"length of accelerator array, used to try to speed-up "
"task of finding between which pair of control points "
"a given value lies. Not terribly useful for small maps "
"(about 10 points or less). Use 0 to turn accelorator off. ");
hestOptAdd(&opt, "r,rescale", NULL, airTypeInt, 0, 0, &rescale, NULL,
"rescale the input values from the input range to the "
"map domain");
hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
"Low end of input range. Defaults to lowest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
"High end of input range. Defaults to highest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
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]). "
"Explicitly setting this is useful only with rescaling (\"-r\")");
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &typeOut, "default",
"specify the type (\"int\", \"float\", etc.) of the "
"output nrrd. "
"By default (not using this option), the output type "
"is the map's type.",
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_imapInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (aclLen) {
nacl = nrrdNew();
airMopAdd(mop, nacl, (airMopper)nrrdNuke, airMopAlways);
if (nrrd1DIrregAclGenerate(nacl, nmap, aclLen)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble generating accelerator:\n%s", me, err);
airMopError(mop);
return 1;
}
} else {
nacl = NULL;
}
if (rescale) {
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
}
if (nrrdTypeDefault == typeOut) {
typeOut = nmap->type;
}
/* some very non-exhaustive tests seemed to indicate that the
accelerator does not in fact reliably speed anything up.
This of course depends on the size of the imap (# points),
but chances are most imaps will have only a handful of points,
in which case the binary search in _nrrd1DIrregFindInterval()
will finish quickly ... */
if (nrrdApply1DIrregMap(nout, nin, range, nmap, nacl, typeOut, rescale)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble applying map:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
unrrdu_lutMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nlut, *nout;
airArray *mop;
int typeOut, rescale, pret, blind8BitRange;
double min, max;
NrrdRange *range=NULL;
hestOptAdd(&opt, "m,map", "lut", airTypeOther, 1, 1, &nlut, NULL,
"lookup table to map input nrrd through",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "r,rescale", NULL, airTypeInt, 0, 0, &rescale, NULL,
"rescale the input values from the input range to the "
"lut domain. The lut domain is either explicitly "
"defined by the axis min,max along axis 0 or 1, or, it "
"is implicitly defined as zero to the length of that axis "
"minus one.");
hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
"Low end of input range. Defaults to lowest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
"High end of input range. Defaults to highest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
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]). "
"Explicitly setting this is useful only with rescaling (\"-r\")");
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &typeOut, "default",
"specify the type (\"int\", \"float\", etc.) of the "
"output nrrd. "
"By default (not using this option), the output type "
"is the lut's type.",
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_lutInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
/* see comment rmap.c */
if (!( AIR_EXISTS(nlut->axis[nlut->dim - 1].min) &&
AIR_EXISTS(nlut->axis[nlut->dim - 1].max) )) {
rescale = AIR_TRUE;
}
if (rescale) {
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
}
if (nrrdTypeDefault == typeOut) {
typeOut = nlut->type;
}
if (nrrdApply1DLut(nout, nin, range, nlut, typeOut, rescale)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble applying LUT:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
unrrdu_rmapMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nmap, *nout;
airArray *mop;
NrrdRange *range=NULL;
int typeOut, rescale, pret, blind8BitRange;
double min, max;
hestOptAdd(&opt, "m,map", "map", airTypeOther, 1, 1, &nmap, NULL,
"regular map to map input nrrd through",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "r,rescale", NULL, airTypeInt, 0, 0, &rescale, NULL,
"rescale the input values from the input range to the "
"map domain. The map domain is either explicitly "
"defined by the axis min,max along axis 0 or 1, or, it "
"is implicitly defined as zero to the length of "
"that axis minus one.");
hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
"Low end of input range. Defaults to lowest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\") or if the map domain is only "
"implicitly defined");
hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
"High end of input range. Defaults to highest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\") or if the map domain is only "
"implicitly defined");
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]). "
"Explicitly setting this is useful "
"only with rescaling (\"-r\") or if the map domain is only "
"implicitly defined");
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &typeOut, "default",
"specify the type (\"int\", \"float\", etc.) of the "
"output nrrd. "
"By default (not using this option), the output type "
"is the map's type.",
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_rmapInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
/* here is a big difference between unu and nrrd: we enforce
rescaling any time that the map domain is implicit. This
is how the pre-1.6 functionality is recreated. Also, whenever
there is rescaling we pass a NrrdRange to reflect the (optional)
user range specification, instead of letting nrrdApply1DRegMap
find the input range itself (by passing a NULL NrrdRange).
*/
if (!( AIR_EXISTS(nmap->axis[nmap->dim - 1].min) &&
AIR_EXISTS(nmap->axis[nmap->dim - 1].max) )) {
rescale = AIR_TRUE;
}
if (rescale) {
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
}
if (nrrdTypeDefault == typeOut) {
typeOut = nmap->type;
}
if (nrrdApply1DRegMap(nout, nin, range, nmap, typeOut, rescale)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble applying map:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
/*
******** nrrdApply1DIrregMap()
**
** Linear interpolation between irregularly spaced control points.
** Obviously, the location of the control point has to be given
** explicitly. The map nrrd must have dimension 2, and each
** control point is represented by a scanline along axis 0. The
** first value is the position of the control point, and the remaining
** value(s) are linearly weighted according to the position of the
** input value among the control point locations.
**
** To allow "coloring" of non-existant values -inf, NaN, and +inf, if
** the very first value of the map (the location of the first control
** point) is non-existant, then the first three control point locations
** must be -inf, NaN, and +inf, in that order, and the information
** about these points will be used for corresponding input values.
** Doing this makes everything slower, however, because airFPClass_f()
** is called on every single value.
**
** This assumes that nrrd1DIrregMapCheck has been called on "nmap",
** and that nrrd1DIrregAclCheck has been called on "nacl" (if it is
** non-NULL).
*/
int
nrrdApply1DIrregMap(Nrrd *nout, const Nrrd *nin, const NrrdRange *_range,
const Nrrd *nmap, const Nrrd *nacl,
int typeOut, int rescale) {
char me[]="nrrdApply1DIrregMap", err[BIFF_STRLEN];
size_t N, I;
int i, *acl, entLen, posLen, aclLen, mapIdx, aclIdx,
entSize, colSize, inSize, lo, hi, baseI;
double val, *pos, domMin, domMax, mapIdxFrac,
(*mapLup)(const void *v, size_t I),
(*inLoad)(const void *v), (*outInsert)(void *v, size_t I, double d);
char *inData, *outData, *entData0, *entData1;
NrrdRange *range;
airArray *mop;
if (!(nout && nmap && nin)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(NRRD, err); return 1;
}
mop = airMopNew();
if (_range) {
range = nrrdRangeCopy(_range);
nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
} else {
range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
}
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
if (_nrrdApply1DSetUp(nout, nin, range, nmap,
kindImap, typeOut, rescale, AIR_FALSE)) {
sprintf(err, "%s:", me);
biffAdd(NRRD, err); airMopError(mop); return 1;
}
if (nacl && nrrd1DIrregAclCheck(nacl)) {
sprintf(err, "%s: given acl isn't valid", me);
biffAdd(NRRD, err); airMopError(mop); return 1;
}
if (nacl) {
acl = (int *)nacl->data;
aclLen = nacl->axis[1].size;
} else {
acl = NULL;
aclLen = 0;
}
pos = _nrrd1DIrregMapDomain(&posLen, &baseI, nmap);
if (!pos) {
sprintf(err, "%s: couldn't determine domain", me);
biffAdd(NRRD, err); airMopError(mop); return 1;
}
airMopAdd(mop, pos, airFree, airMopAlways);
mapLup = nrrdDLookup[nmap->type];
inData = (char *)nin->data;
inLoad = nrrdDLoad[nin->type];
inSize = nrrdElementSize(nin);
mapLup = nrrdDLookup[nmap->type];
entLen = nmap->axis[0].size; /* entLen is really 1 + entry length */
entSize = entLen*nrrdElementSize(nmap);
colSize = (entLen-1)*nrrdTypeSize[typeOut];
outData = (char *)nout->data;
outInsert = nrrdDInsert[nout->type];
domMin = pos[0];
domMax = pos[posLen-1];
N = nrrdElementNumber(nin);
for (I=0;
I<N;
I++, inData += inSize, outData += colSize) {
val = inLoad(inData);
/* _VV = ( (AIR_EXISTS(val) && (21 == (int)(-val)))
|| 22400 < I ); */
/* if (_VV)
fprintf(stderr, "##%s: (%d) val = % 31.15f\n", me, (int)I, val); */
if (!AIR_EXISTS(val)) {
/* got a non-existant value */
if (baseI) {
/* and we know how to deal with them */
switch (airFPClass_d(val)) {
case airFP_NEG_INF:
mapIdx = 0;
break;
case airFP_SNAN:
case airFP_QNAN:
mapIdx = 1;
break;
case airFP_POS_INF:
mapIdx = 2;
break;
default:
mapIdx = 0;
fprintf(stderr, "%s: PANIC: non-existant value/class %g/%d "
"not handled\n",
me, val, airFPClass_d(val));
exit(1);
}
entData0 = (char*)(nmap->data) + mapIdx*entSize;
for (i=1; i<entLen; i++) {
outInsert(outData, i-1, mapLup(entData0, i));
}
continue; /* we're done! (with this value) */
} else {
/* we don't know how to properly deal with this non-existant value:
we use the first entry, and then fall through to code below */
mapIdx = 0;
mapIdxFrac = 0.0;
}
} else {
/* we have an existant value */
if (rescale) {
val = AIR_AFFINE(range->min, val, range->max, domMin, domMax);
/* if (_VV) fprintf(stderr, " rescaled --> % 31.15f\n", val); */
}
val = AIR_CLAMP(domMin, val, domMax);
if (acl) {
aclIdx = airIndex(domMin, val, domMax, aclLen);
lo = acl[0 + 2*aclIdx];
hi = acl[1 + 2*aclIdx];
} else {
lo = 0;
hi = posLen-2;
}
if (lo < hi) {
mapIdx = _nrrd1DIrregFindInterval(pos, val, lo, hi);
} else {
/* acl did its job ==> lo == hi */
mapIdx = lo;
}
}
mapIdxFrac = AIR_AFFINE(pos[mapIdx], val, pos[mapIdx+1], 0.0, 1.0);
/* if (_VV) fprintf(stderr, "##%s: val=\n% 31.15f --> "
"mapIdx,frac = %d,\n% 31.15f\n",
me, val, mapIdx, mapIdxFrac); */
entData0 = (char*)(nmap->data) + (baseI+mapIdx)*entSize;
entData1 = (char*)(nmap->data) + (baseI+mapIdx+1)*entSize;
/* if (_VV) fprintf(stderr, "##%s: 2; %d/\n% 31.15f --> entLen=%d "
"baseI=%d -->\n",
me, mapIdx, mapIdxFrac, entLen, baseI); */
for (i=1; i<entLen; i++) {
val = ((1-mapIdxFrac)*mapLup(entData0, i) +
mapIdxFrac*mapLup(entData1, i));
/* if (_VV) fprintf(stderr, "% 31.15f\n", val); */
outInsert(outData, i-1, val);
}
/* if (_VV) fprintf(stderr, "##%s: 3\n", me); */
}
airMopOkay(mop);
return 0;
}
/*
******** nrrdHisto()
**
** makes a 1D histogram of a given size and type
**
** pre-NrrdRange policy:
** this looks at nin->min and nin->max to see if they are both non-NaN.
** If so, it uses these as the range of the histogram, otherwise it
** finds the min and max present in the volume. If nin->min and nin->max
** are being used as the histogram range, then values which fall outside
** this are ignored (they don't contribute to the histogram).
**
** post-NrrdRange policy:
*/
int
nrrdHisto(Nrrd *nout, const Nrrd *nin, const NrrdRange *_range,
const Nrrd *nwght, size_t bins, int type) {
static const char me[]="nrrdHisto", func[]="histo";
size_t I, num, idx;
airArray *mop;
NrrdRange *range;
double min, max, eps, val, count, incr, (*lup)(const void *v, size_t I);
if (!(nin && nout)) {
/* _range and nwght can be NULL */
biffAddf(NRRD, "%s: got NULL pointer", me);
return 1;
}
if (nout == nin) {
biffAddf(NRRD, "%s: nout==nin disallowed", me);
return 1;
}
if (!(bins > 0)) {
biffAddf(NRRD, "%s: bins value (" _AIR_SIZE_T_CNV ") invalid", me, bins);
return 1;
}
if (airEnumValCheck(nrrdType, type) || nrrdTypeBlock == type) {
biffAddf(NRRD, "%s: invalid nrrd type %d", me, type);
return 1;
}
if (nwght) {
if (nout==nwght) {
biffAddf(NRRD, "%s: nout==nwght disallowed", me);
return 1;
}
if (nrrdTypeBlock == nwght->type) {
biffAddf(NRRD, "%s: nwght type %s invalid", me,
airEnumStr(nrrdType, nrrdTypeBlock));
return 1;
}
if (!nrrdSameSize(nin, nwght, AIR_TRUE)) {
biffAddf(NRRD, "%s: nwght size mismatch with nin", me);
return 1;
}
lup = nrrdDLookup[nwght->type];
} else {
lup = NULL;
}
if (nrrdMaybeAlloc_va(nout, type, 1, bins)) {
biffAddf(NRRD, "%s: failed to alloc histo array (len " _AIR_SIZE_T_CNV
")", me, bins);
return 1;
}
mop = airMopNew();
/* nout->axis[0].size set */
nout->axis[0].spacing = AIR_NAN;
nout->axis[0].thickness = AIR_NAN;
if (nout && AIR_EXISTS(nout->axis[0].min) && AIR_EXISTS(nout->axis[0].max)) {
/* HEY: total hack to externally nail down min and max of histogram:
use the min and max already set on axis[0] */
/* HEY: shouldn't this blatent hack be further restricted by also
checking the existence of range->min and range->max ? */
min = nout->axis[0].min;
max = nout->axis[0].max;
} else {
if (_range) {
range = nrrdRangeCopy(_range);
nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
} else {
range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
}
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
min = range->min;
max = range->max;
nout->axis[0].min = min;
nout->axis[0].max = max;
}
eps = (min == max ? 1.0 : 0.0);
nout->axis[0].center = nrrdCenterCell;
/* nout->axis[0].label set below */
/* make histogram */
num = nrrdElementNumber(nin);
for (I=0; I<num; I++) {
val = nrrdDLookup[nin->type](nin->data, I);
if (AIR_EXISTS(val)) {
if (val < min || val > max+eps) {
/* value is outside range; ignore it */
continue;
}
if (AIR_IN_CL(min, val, max)) {
idx = airIndex(min, val, max+eps, AIR_CAST(unsigned int, bins));
/*
printf("!%s: %d: index(%g, %g, %g, %d) = %d\n",
me, (int)I, min, val, max, bins, idx);
*/
/* count is a double in order to simplify clamping the
hit values to the representable range for nout->type */
count = nrrdDLookup[nout->type](nout->data, idx);
incr = nwght ? lup(nwght->data, I) : 1;
count = nrrdDClamp[nout->type](count + incr);
nrrdDInsert[nout->type](nout->data, idx, count);
}
}
}
if (nrrdContentSet_va(nout, func, nin, "%d", bins)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
nout->axis[0].label = (char *)airFree(nout->axis[0].label);
nout->axis[0].label = (char *)airStrdup(nout->content);
if (!nrrdStateKindNoop) {
nout->axis[0].kind = nrrdKindDomain;
}
airMopOkay(mop);
return 0;
}
/*
******** nrrdHistoAxis
**
** replace scanlines along one scanline with a histogram of the scanline
**
** this looks at nin->min and nin->max to see if they are both non-NaN.
** If so, it uses these as the range of the histogram, otherwise it
** finds the min and max present in the volume
**
** By its very nature, and by the simplicity of this implemention,
** this can be a slow process due to terrible memory locality. User
** may want to permute axes before and after this, but that can be
** slow too...
*/
int
nrrdHistoAxis(Nrrd *nout, const Nrrd *nin, const NrrdRange *_range,
unsigned int hax, size_t bins, int type) {
static const char me[]="nrrdHistoAxis", func[]="histax";
int map[NRRD_DIM_MAX];
unsigned int ai, hidx;
size_t szIn[NRRD_DIM_MAX], szOut[NRRD_DIM_MAX], size[NRRD_DIM_MAX],
coordIn[NRRD_DIM_MAX], coordOut[NRRD_DIM_MAX];
size_t I, hI, num;
double val, count;
airArray *mop;
NrrdRange *range;
if (!(nin && nout)) {
biffAddf(NRRD, "%s: got NULL pointer", me);
return 1;
}
if (nout == nin) {
biffAddf(NRRD, "%s: nout==nin disallowed", me);
return 1;
}
if (!(bins > 0)) {
biffAddf(NRRD, "%s: bins value (" _AIR_SIZE_T_CNV ") invalid", me, bins);
return 1;
}
if (airEnumValCheck(nrrdType, type) || nrrdTypeBlock == type) {
biffAddf(NRRD, "%s: invalid nrrd type %d", me, type);
return 1;
}
if (!( hax <= nin->dim-1 )) {
biffAddf(NRRD, "%s: axis %d is not in range [0,%d]",
me, hax, nin->dim-1);
return 1;
}
mop = airMopNew();
if (_range) {
range = nrrdRangeCopy(_range);
nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
} else {
range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeState);
}
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdAxisInfoGet_nva(nin, nrrdAxisInfoSize, size);
size[hax] = bins;
if (nrrdMaybeAlloc_nva(nout, type, nin->dim, size)) {
biffAddf(NRRD, "%s: failed to alloc output nrrd", me);
airMopError(mop); return 1;
}
/* copy axis information */
for (ai=0; ai<nin->dim; ai++) {
map[ai] = ai != hax ? (int)ai : -1;
}
nrrdAxisInfoCopy(nout, nin, map, NRRD_AXIS_INFO_NONE);
/* axis hax now has to be set manually */
nout->axis[hax].size = bins;
nout->axis[hax].spacing = AIR_NAN; /* min and max convey the information */
nout->axis[hax].thickness = AIR_NAN;
nout->axis[hax].min = range->min;
nout->axis[hax].max = range->max;
nout->axis[hax].center = nrrdCenterCell;
if (nin->axis[hax].label) {
nout->axis[hax].label = (char *)calloc(strlen("histax()")
+ strlen(nin->axis[hax].label)
+ 1, sizeof(char));
if (nout->axis[hax].label) {
sprintf(nout->axis[hax].label, "histax(%s)", nin->axis[hax].label);
} else {
biffAddf(NRRD, "%s: couldn't allocate output label", me);
airMopError(mop); return 1;
}
} else {
nout->axis[hax].label = NULL;
}
if (!nrrdStateKindNoop) {
nout->axis[hax].kind = nrrdKindDomain;
}
/* the skinny: we traverse the input samples in linear order, and
increment the bin in the histogram for the scanline we're in.
This is not terribly clever, and the memory locality is a
disaster */
nrrdAxisInfoGet_nva(nin, nrrdAxisInfoSize, szIn);
nrrdAxisInfoGet_nva(nout, nrrdAxisInfoSize, szOut);
memset(coordIn, 0, NRRD_DIM_MAX*sizeof(size_t));
num = nrrdElementNumber(nin);
for (I=0; I<num; I++) {
/* get input nrrd value and compute its histogram index */
val = nrrdDLookup[nin->type](nin->data, I);
if (AIR_EXISTS(val) && AIR_IN_CL(range->min, val, range->max)) {
hidx = airIndex(range->min, val, range->max, AIR_CAST(unsigned int, bins));
memcpy(coordOut, coordIn, nin->dim*sizeof(size_t));
coordOut[hax] = (unsigned int)hidx;
NRRD_INDEX_GEN(hI, coordOut, szOut, nout->dim);
count = nrrdDLookup[nout->type](nout->data, hI);
count = nrrdDClamp[nout->type](count + 1);
nrrdDInsert[nout->type](nout->data, hI, count);
}
NRRD_COORD_INCR(coordIn, szIn, nin->dim, 0);
}
int
unrrdu_mlutMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, **_nmlut, *nmlut, *nout;
airArray *mop;
int typeOut, rescale, pret, blind8BitRange;
unsigned int _nmlutLen, mapAxis;
double min, max;
NrrdRange *range=NULL;
hestOptAdd(&opt, "m,map", "mlut", airTypeOther, 1, -1, &_nmlut, NULL,
"one nrrd of lookup tables to map input nrrd through, or, "
"list of nrrds which contain the individual entries of "
"the lookup table at each voxel, which will be joined together.",
&_nmlutLen, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "r,rescale", NULL, airTypeInt, 0, 0, &rescale, NULL,
"rescale the input values from the input range to the "
"lut domain. The lut domain is either explicitly "
"defined by the axis min,max along axis 0 or 1, or, it "
"is implicitly defined as zero to the length of that axis "
"minus one.");
hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
"Low end of input range. Defaults to lowest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
"High end of input range. Defaults to highest value "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
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]). "
"Explicitly setting this is useful only with rescaling (\"-r\")");
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &typeOut, "default",
"specify the type (\"int\", \"float\", etc.) of the "
"output nrrd. "
"By default (not using this option), the output type "
"is the lut's type.",
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_mlutInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
/* by the end of this block we need to have nmlut and mapAxis */
if (1 == _nmlutLen) {
/* we got the mlut as a single nrrd */
nmlut = _nmlut[0];
mapAxis = nmlut->dim - nin->dim - 1;
/* its not our job to do real error checking ... */
mapAxis = AIR_MIN(mapAxis, nmlut->dim - 1);
} else {
/* we have to join together multiple nrrds to get the mlut */
nmlut = nrrdNew();
airMopAdd(mop, nmlut, (airMopper)nrrdNuke, airMopAlways);
/* assume that mlut component nrrds are all compatible sizes,
nrrdJoin will fail if they aren't */
mapAxis = _nmlut[0]->dim - nin->dim;
if (nrrdJoin(nmlut, (const Nrrd**)_nmlut, _nmlutLen, mapAxis, AIR_TRUE)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble joining mlut:\n%s", me, err);
airMopError(mop);
return 1;
}
/* set these if they were given, they'll be NaN otherwise */
nmlut->axis[mapAxis].min = min;
nmlut->axis[mapAxis].max = max;
}
if (!( AIR_EXISTS(nmlut->axis[mapAxis].min) &&
AIR_EXISTS(nmlut->axis[mapAxis].max) )) {
rescale = AIR_TRUE;
}
if (rescale) {
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
}
if (nrrdTypeDefault == typeOut) {
typeOut = nmlut->type;
}
if (nrrdApplyMulti1DLut(nout, nin, range, nmlut, typeOut, rescale)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble applying multi-LUT:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
int
unrrdu_histoMain(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout, *nwght;
int type, pret, blind8BitRange;
unsigned int bins;
double min, max;
NrrdRange *range;
airArray *mop;
hestOptAdd(&opt, "b,bins", "num", airTypeUInt, 1, 1, &bins, NULL,
"# of bins in histogram");
hestOptAdd(&opt, "w,weight", "nweight", airTypeOther, 1, 1, &nwght, "",
"how to weigh contributions to histogram. By default "
"(not using this option), the increment is one bin count per "
"sample, but by giving a nrrd, the value in the nrrd at the "
"corresponding location will be the bin count increment ",
NULL, NULL, nrrdHestNrrd);
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_TYPE(type, "type to use for bins in output histogram", "uint");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
USAGE(_unrrdu_histoInfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
/* If the input nrrd never specified min and max, then they'll be
AIR_NAN, and nrrdRangeSafeSet will find them, and will do so
according to blind8BitRange */
range = nrrdRangeNew(min, max);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range, nin, blind8BitRange);
if (nrrdHisto(nout, nin, range, nwght, bins, type)) {
err = biffGet(NRRD);
fprintf(stderr, "%s: error calculating histogram:\n%s", me, err);
free(err);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
/*
******** nrrdArithGamma()
**
** map the values in a nrrd through a power function; essentially:
** val = pow(val, 1/gamma), but this is after the val has been normalized
** to be in the range of 0.0 to 1.0 (assuming that the given min and
** max really are the full range of the values in the nrrd). Thus,
** the given min and max values are fixed points of this
** transformation. Using a negative gamma means that after the pow()
** function has been applied, the value is inverted with respect to
** min and max (like in xv).
*/
int
nrrdArithGamma(Nrrd *nout, const Nrrd *nin,
const NrrdRange *_range, double Gamma) {
static const char me[]="nrrdArithGamma", func[]="gamma";
double val, min, max;
size_t I, num;
NrrdRange *range;
airArray *mop;
double (*lup)(const void *, size_t);
double (*ins)(void *, size_t, double);
if (!(nout && nin)) {
/* _range can be NULL */
biffAddf(NRRD, "%s: got NULL pointer", me);
return 1;
}
if (!( AIR_EXISTS(Gamma) )) {
biffAddf(NRRD, "%s: gamma doesn't exist", me);
return 1;
}
if (!( nrrdTypeBlock != nin->type && nrrdTypeBlock != nout->type )) {
biffAddf(NRRD, "%s: can't deal with %s type", me,
airEnumStr(nrrdType, nrrdTypeBlock));
return 1;
}
if (nout != nin) {
if (nrrdCopy(nout, nin)) {
biffAddf(NRRD, "%s: couldn't initialize by copy to output", me);
return 1;
}
}
mop = airMopNew();
if (_range) {
range = nrrdRangeCopy(_range);
nrrdRangeSafeSet(range, nin, nrrdBlind8BitRangeState);
} else {
range = nrrdRangeNewSet(nin, nrrdBlind8BitRangeTrue);
}
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
min = range->min;
max = range->max;
if (min == max) {
/* this is stupid. We want min < max to avoid making NaNs */
max += 1;
}
lup = nrrdDLookup[nin->type];
ins = nrrdDInsert[nout->type];
Gamma = 1/Gamma;
num = nrrdElementNumber(nin);
if (Gamma < 0.0) {
Gamma = -Gamma;
for (I=0; I<num; I++) {
val = lup(nin->data, I);
val = AIR_AFFINE(min, val, max, 0.0, 1.0);
val = pow(val, Gamma);
val = AIR_AFFINE(1.0, val, 0.0, min, max);
ins(nout->data, I, val);
}
} else {
for (I=0; I<num; I++) {
val = lup(nin->data, I);
val = AIR_AFFINE(min, val, max, 0.0, 1.0);
val = pow(val, Gamma);
val = AIR_AFFINE(0.0, val, 1.0, min, max);
ins(nout->data, I, val);
}
}
if (nrrdContentSet_va(nout, func, nin, "%g,%g,%g", min, max, Gamma)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
if (nout != nin) {
nrrdAxisInfoCopy(nout, nin, NULL, NRRD_AXIS_INFO_NONE);
}
/* basic info handled by nrrdCopy above */
airMopOkay(mop);
return 0;
}
int
unrrdu_lut2Main(int argc, char **argv, char *me, hestParm *hparm) {
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nlut, *nout, *ntmp[2];
airArray *mop;
int typeOut, rescale[2], pret, blind8BitRange;
double min[2], max[2];
NrrdRange *range[2]={NULL,NULL};
unsigned int mapAxis, rai;
hestOptAdd(&opt, "m,map", "lut", airTypeOther, 1, 1, &nlut, NULL,
"lookup table to map input nrrd through",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&opt, "r,rescale", "bool bool", airTypeBool, 2, 2, rescale,
"false false",
"rescale one or both of the input values from the "
"input range to the lut domain. The lut domain is either "
"explicitly defined by the axis min,max along axis 0 or 1, "
"or, it is implicitly defined as zero to the length of that axis "
"minus one.");
hestOptAdd(&opt, "min,minimum", "min0 min1", airTypeDouble, 2, 2, min,
"nan nan",
"Low ends of input range. Defaults to lowest values "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
hestOptAdd(&opt, "max,maximum", "max0 max1", airTypeDouble, 2, 2, max,
"nan nan",
"High end of input range. Defaults to highest values "
"found in input nrrd. Explicitly setting this is useful "
"only with rescaling (\"-r\")");
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]). "
"Explicitly setting this is useful only with rescaling (\"-r\")");
hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &typeOut, "default",
"specify the type (\"int\", \"float\", etc.) of the "
"output nrrd. "
"By default (not using this option), the output type "
"is the lut's type.",
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_lut2InfoL);
PARSE();
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (!( nin->dim > 1 && 2 == nin->axis[0].size )) {
fprintf(stderr, "%s: input nrrd dim must be > 1, and axis[0].size "
"must be 2 (not " _AIR_SIZE_T_CNV ")", me, nin->axis[0].size);
airMopError(mop);
return 1;
}
mapAxis = nlut->dim - 2;
if (!(0 == mapAxis || 1 == mapAxis)) {
fprintf(stderr, "%s: dimension of lut should be 2 or 3, not %d",
me, nlut->dim);
airMopError(mop);
return 1;
}
/* see comment in rmap.c */
for (rai=0; rai<=1; rai++) {
if (!( AIR_EXISTS(nlut->axis[mapAxis + rai].min) &&
AIR_EXISTS(nlut->axis[mapAxis + rai].max) )) {
rescale[rai] = AIR_TRUE;
}
if (rescale[rai]) {
ntmp[rai] = nrrdNew();
airMopAdd(mop, ntmp[rai], AIR_CAST(airMopper, nrrdNuke), airMopAlways);
if (nrrdSlice(ntmp[rai], nin, 0, rai)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble slicing input value %u:\n%s",
me, rai, err);
airMopError(mop);
return 1;
}
range[rai] = nrrdRangeNew(min[rai], max[rai]);
airMopAdd(mop, range[rai], (airMopper)nrrdRangeNix, airMopAlways);
nrrdRangeSafeSet(range[rai], ntmp[rai], blind8BitRange);
}
}
if (nrrdTypeDefault == typeOut) {
typeOut = nlut->type;
}
if (nrrdApply2DLut(nout, nin, 0, range[0], range[1], nlut, typeOut,
rescale[0], rescale[1])) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble applying 2-D LUT:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
