int
unrrdu_minmaxDoit(char *me, char *inS, int blind8BitRange, FILE *fout) {
char err[BIFF_STRLEN];
Nrrd *nrrd;
NrrdRange *range;
airArray *mop;
mop = airMopNew();
airMopAdd(mop, nrrd=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nrrd, inS, NULL)) {
sprintf(err, "%s: trouble loading \"%s\"", me, inS);
biffMove(me, err, NRRD); airMopError(mop); return 1;
}
range = nrrdRangeNewSet(nrrd, blind8BitRange);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
airSinglePrintf(fout, NULL, "min: %g\n", range->min);
airSinglePrintf(fout, NULL, "max: %g\n", range->max);
if (0 == range->min && 0 == range->max) {
fprintf(fout, "# min == max == 0.0 exactly\n");
}
if (range->hasNonExist) {
fprintf(fout, "# has non-existent values\n");
}
airMopOkay(mop);
return 0;
}
int
main(int argc, char **argv) {
char *me, *err;
Nrrd *nrrd;
NrrdRange *range;
me = argv[0];
if (2 != argc)
usage(me);
nrrdStateVerboseIO = 10;
if (nrrdLoad(nrrd=nrrdNew(), argv[1], NULL)) {
fprintf(stderr, "%s: trouble loading \"%s\":\n%s",
me, argv[1], err = biffGet(NRRD));
free(err);
exit(1);
}
range = nrrdRangeNewSet(nrrd, nrrdBlind8BitRangeState);
printf("%s: min = %g; max = %g, hasNonExist = %d\n", me,
range->min, range->max, range->hasNonExist);
nrrdNuke(nrrd);
exit(0);
}
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 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(int argc, const char **argv) {
const char *me;
char *err;
hestOpt *hopt=NULL;
hestParm *hparm;
airArray *mop;
/* variables learned via hest */
Nrrd *nin;
float camfr[3], camat[3], camup[3], camnc, camfc, camFOV;
int camortho, hitandquit;
unsigned int camsize[2];
double isovalue, sliso, isomin, isomax;
/* boilerplate hest code */
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hparm->respFileEnable = AIR_TRUE;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
/* setting up the command-line options */
hparm->respFileEnable = AIR_TRUE;
hestOptAdd(&hopt, "i", "volume", airTypeOther, 1, 1, &nin, NULL,
"input volume to isosurface", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "v", "isovalue", airTypeDouble, 1, 1, &isovalue, "nan",
"isovalue at which to run Marching Cubes");
hestOptAdd(&hopt, "fr", "x y z", airTypeFloat, 3, 3, camfr, "3 4 5",
"look-from point");
hestOptAdd(&hopt, "at", "x y z", airTypeFloat, 3, 3, camat, "0 0 0",
"look-at point");
hestOptAdd(&hopt, "up", "x y z", airTypeFloat, 3, 3, camup, "0 0 1",
"up direction");
hestOptAdd(&hopt, "nc", "dist", airTypeFloat, 1, 1, &(camnc), "-2",
"at-relative near clipping distance");
hestOptAdd(&hopt, "fc", "dist", airTypeFloat, 1, 1, &(camfc), "2",
"at-relative far clipping distance");
hestOptAdd(&hopt, "fov", "angle", airTypeFloat, 1, 1, &(camFOV), "20",
"vertical field-of-view, in degrees. Full vertical "
"extent of image plane subtends this angle.");
hestOptAdd(&hopt, "sz", "s0 s1", airTypeUInt, 2, 2, &(camsize), "640 480",
"# samples (horz vert) of image plane. ");
hestOptAdd(&hopt, "ortho", NULL, airTypeInt, 0, 0, &(camortho), NULL,
"use orthographic instead of (the default) "
"perspective projection ");
hestOptAdd(&hopt, "haq", NULL, airTypeBool, 0, 0, &(hitandquit), NULL,
"save a screenshot rather than display the viewer");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, "demo program", AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
/* learn value range, and set initial isovalue if needed */
NrrdRange *range = nrrdRangeNewSet(nin, AIR_FALSE);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
isomin = range->min;
isomax = range->max;
if (!AIR_EXISTS(isovalue)) {
isovalue = (isomin + isomax)/2;
}
/* first, make sure we can isosurface ok */
limnPolyData *lpld = limnPolyDataNew();
seekContext *sctx = seekContextNew();
airMopAdd(mop, sctx, (airMopper)seekContextNix, airMopAlways);
sctx->pldArrIncr = nrrdElementNumber(nin);
seekVerboseSet(sctx, 0);
seekNormalsFindSet(sctx, AIR_TRUE);
if (seekDataSet(sctx, nin, NULL, 0)
|| seekTypeSet(sctx, seekTypeIsocontour)
|| seekIsovalueSet(sctx, isovalue)
|| seekUpdate(sctx)
|| seekExtract(sctx, lpld)) {
airMopAdd(mop, err=biffGetDone(SEEK), airFree, airMopAlways);
fprintf(stderr, "trouble with isosurfacing:\n%s", err);
airMopError(mop);
return 1;
}
if (!lpld->xyzwNum) {
fprintf(stderr, "%s: warning: No isocontour generated at isovalue %g\n",
me, isovalue);
}
/* then create empty scene */
Hale::init();
Hale::Scene scene;
/* then create viewer (in order to create the OpenGL context) */
Hale::Viewer viewer(camsize[0], camsize[1], "Iso", &scene);
viewer.lightDir(glm::vec3(-1.0f, 1.0f, 3.0f));
viewer.camera.init(glm::vec3(camfr[0], camfr[1], camfr[2]),
glm::vec3(camat[0], camat[1], camat[2]),
glm::vec3(camup[0], camup[1], camup[2]),
camFOV, (float)camsize[0]/camsize[1],
camnc, camfc, camortho);
viewer.refreshCB((Hale::ViewerRefresher)render);
viewer.refreshData(&viewer);
sliso = isovalue;
viewer.slider(&sliso, isomin, isomax);
viewer.current();
/* then create geometry, and add it to scene */
Hale::Polydata hply(lpld, true, // hply now owns lpld
Hale::ProgramLib(Hale::preprogramAmbDiff2SideSolid));
scene.add(&hply);
scene.drawInit();
render(&viewer);
if (hitandquit) {
seekIsovalueSet(sctx, isovalue);
seekUpdate(sctx);
seekExtract(sctx, lpld);
hply.rebuffer();
render(&viewer);
glfwWaitEvents();
render(&viewer);
viewer.snap();
Hale::done();
airMopOkay(mop);
return 0;
}
while(!Hale::finishing){
glfwWaitEvents();
if (viewer.sliding() && sliso != isovalue) {
isovalue = sliso;
printf("%s: isosurfacing at %g\n", me, isovalue);
seekIsovalueSet(sctx, isovalue);
seekUpdate(sctx);
seekExtract(sctx, lpld);
hply.rebuffer();
}
render(&viewer);
}
/* clean exit; all okay */
Hale::done();
airMopOkay(mop);
return 0;
}
/*
******** 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
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err;
Nrrd *nin, *nhist;
double vmin, vmax, rmax, val, cent[2], rad;
int bins[2], sx, sy, xi, yi, ridx, hidx, rbins, hbins;
NrrdRange *range;
double (*lup)(const void *v, size_t I), *hist;
me = argv[0];
mop = airMopNew();
hparm = hestParmNew();
hopt = NULL;
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input image", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "rbins hbins", airTypeInt, 2, 2, bins, NULL,
"# of histogram bins: radial and value");
hestOptAdd(&hopt, "min", "value", airTypeDouble, 1, 1, &vmin, "nan",
"Value at low end of histogram. Defaults to lowest value "
"found in input nrrd.");
hestOptAdd(&hopt, "max", "value", airTypeDouble, 1, 1, &vmax, "nan",
"Value at high end of histogram. Defaults to highest value "
"found in input nrrd.");
hestOptAdd(&hopt, "rmax", "max radius", airTypeDouble, 1, 1, &rmax, "nan",
"largest radius to include in histogram");
hestOptAdd(&hopt, "c", "center x, y", airTypeDouble, 2, 2, cent, NULL,
"The center point around which to build radial histogram");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"file to write histogram to");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, histradInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (2 != nin->dim) {
fprintf(stderr, "%s: need 2-D input (not %d-D)\n", me, nin->dim);
airMopError(mop); return 1;
}
rbins = bins[0];
hbins = bins[1];
nhist = nrrdNew();
airMopAdd(mop, nhist, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nhist, nrrdTypeDouble, 2,
AIR_CAST(size_t, rbins),
AIR_CAST(size_t, hbins))) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate histogram:\n%s", me, err);
airMopError(mop); return 1;
}
if (!( AIR_EXISTS(vmin) && AIR_EXISTS(vmax) )) {
range = nrrdRangeNewSet(nin, nrrdStateBlind8BitRange);
airMopAdd(mop, range, (airMopper)nrrdRangeNix, airMopAlways);
vmin = AIR_EXISTS(vmin) ? vmin : range->min;
vmax = AIR_EXISTS(vmax) ? vmax : range->max;
}
#define DIST(x0, y0, x1, y1) (sqrt((x0-x1)*(x0-x1) + (y0-y1)*(y0-y1)))
sx = nin->axis[0].size;
sy = nin->axis[1].size;
if (!AIR_EXISTS(rmax)) {
rmax = 0;
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], 0, 0));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], sx-1, 0));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], 0, sy-1));
rmax = AIR_MAX(rmax, DIST(cent[0], cent[1], sx-1, sy-1));
}
lup = nrrdDLookup[nin->type];
hist = (double*)(nhist->data);
for (xi=0; xi<sx; xi++) {
for (yi=0; yi<sy; yi++) {
rad = DIST(cent[0], cent[1], xi, yi);
if (!AIR_IN_OP(0, rad, rmax)) {
continue;
}
val = lup(nin->data, xi + sx*yi);
if (!AIR_IN_OP(vmin, val, vmax)) {
continue;
}
ridx = airIndex(0, rad, rmax, rbins);
hidx = airIndex(vmin, val, vmax, hbins);
hist[ridx + rbins*hidx] += 1;
}
}
nhist->axis[0].min = 0;
nhist->axis[0].max = rmax;
nhist->axis[1].min = vmin;
nhist->axis[1].max = vmax;
if (nrrdSave(outS, nhist, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't save output:\n%s", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
exit(0);
}
/*
******** 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;
}