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 {
/*
******** nrrdAxesPermute
**
** changes the scanline ordering of the data in a nrrd
**
** The basic means by which data is moved around is with memcpy().
** The goal is to call memcpy() as few times as possible, on memory
** segments as large as possible. Currently, this is done by
** detecting how many of the low-index axes are left untouched by
** the permutation- this constitutes a "scanline" which can be
** copied around as a unit. For permuting the y and z axes of a
** matrix-x-y-z order matrix volume, this optimization produced a
** factor of 5 speed up (exhaustive multi-platform tests, of course).
**
** The axes[] array determines the permutation of the axes.
** axis[i] = j means: axis i in the output will be the input's axis j
** (axis[i] answers: "what do I put here", from the standpoint of the output,
** not "where do I put this", from the standpoint of the input)
*/
int
nrrdAxesPermute(Nrrd *nout, const Nrrd *nin, const unsigned int *axes) {
static const char me[]="nrrdAxesPermute", func[]="permute";
char buff1[NRRD_DIM_MAX*30], buff2[AIR_STRLEN_SMALL];
size_t idxOut, idxInA=0, /* indices for input and output scanlines */
lineSize, /* size of block of memory which can be
moved contiguously from input to output,
thought of as a "scanline" */
numLines, /* how many "scanlines" there are to permute */
szIn[NRRD_DIM_MAX], *lszIn,
szOut[NRRD_DIM_MAX], *lszOut,
cIn[NRRD_DIM_MAX],
cOut[NRRD_DIM_MAX];
char *dataIn, *dataOut;
int axmap[NRRD_DIM_MAX];
unsigned int
ai, /* running index along dimensions */
lowPax, /* lowest axis which is "p"ermutated */
ldim, /* nin->dim - lowPax */
ip[NRRD_DIM_MAX+1], /* inverse of permutation in "axes" */
laxes[NRRD_DIM_MAX+1]; /* copy of axes[], but shifted down by lowPax
elements, to remove i such that i == axes[i] */
airArray *mop;
mop = airMopNew();
if (!(nin && nout && axes)) {
biffAddf(NRRD, "%s: got NULL pointer", me);
airMopError(mop); return 1;
}
/* we don't actually need ip[], computing it is for error checking */
if (nrrdInvertPerm(ip, axes, nin->dim)) {
biffAddf(NRRD, "%s: couldn't compute axis permutation inverse", me);
airMopError(mop); return 1;
}
/* this shouldn't actually be necessary .. */
if (!nrrdElementSize(nin)) {
biffAddf(NRRD, "%s: nrrd reports zero element size!", me);
airMopError(mop); return 1;
}
for (ai=0; ai<nin->dim && axes[ai] == ai; ai++)
;
lowPax = ai;
/* allocate output by initial copy */
if (nout != nin) {
if (nrrdCopy(nout, nin)) {
biffAddf(NRRD, "%s: trouble copying input", me);
airMopError(mop); return 1;
}
dataIn = (char*)nin->data;
} else {
dataIn = (char*)calloc(nrrdElementNumber(nin), nrrdElementSize(nin));
if (!dataIn) {
biffAddf(NRRD, "%s: couldn't create local copy of data", me);
airMopError(mop); return 1;
}
airMopAdd(mop, dataIn, airFree, airMopAlways);
memcpy(dataIn, nin->data, nrrdElementNumber(nin)*nrrdElementSize(nin));
}
if (lowPax < nin->dim) {
/* if lowPax == nin->dim, then we were given the identity permutation, so
there's nothing to do other than the copy already done. Otherwise,
here we are (actually, lowPax < nin->dim-1) */
for (ai=0; ai<nin->dim; ai++) {
axmap[ai] = AIR_INT(axes[ai]);
}
nrrdAxisInfoGet_nva(nin, nrrdAxisInfoSize, szIn);
if (nrrdAxisInfoCopy(nout, nin, axmap, NRRD_AXIS_INFO_NONE)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
nrrdAxisInfoGet_nva(nout, nrrdAxisInfoSize, szOut);
/* the skinny */
lineSize = 1;
for (ai=0; ai<lowPax; ai++) {
lineSize *= szIn[ai];
}
numLines = nrrdElementNumber(nin)/lineSize;
lineSize *= nrrdElementSize(nin);
lszIn = szIn + lowPax;
lszOut = szOut + lowPax;
ldim = nin->dim - lowPax;
memset(laxes, 0, sizeof(laxes));
for (ai=0; ai<ldim; ai++) {
laxes[ai] = axes[ai+lowPax]-lowPax;
}
dataOut = AIR_CAST(char *, nout->data);
memset(cIn, 0, sizeof(cIn));
memset(cOut, 0, sizeof(cOut));
for (idxOut=0; idxOut<numLines; idxOut++) {
/* in our representation of the coordinates of the start of the
scanlines that we're copying, we are not even storing all the
zeros in the coordinates prior to lowPax, and when we go to
a linear index for the memcpy(), we multiply by lineSize */
for (ai=0; ai<ldim; ai++) {
cIn[laxes[ai]] = cOut[ai];
}
NRRD_INDEX_GEN(idxInA, cIn, lszIn, ldim);
memcpy(dataOut + idxOut*lineSize, dataIn + idxInA*lineSize, lineSize);
NRRD_COORD_INCR(cOut, lszOut, ldim, 0);
}
/* set content */
strcpy(buff1, "");
for (ai=0; ai<nin->dim; ai++) {
sprintf(buff2, "%s%d", (ai ? "," : ""), axes[ai]);
strcat(buff1, buff2);
}
if (nrrdContentSet_va(nout, func, nin, "%s", buff1)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
if (nout != nin) {
if (nrrdBasicInfoCopy(nout, nin,
NRRD_BASIC_INFO_DATA_BIT
| NRRD_BASIC_INFO_TYPE_BIT
| NRRD_BASIC_INFO_BLOCKSIZE_BIT
| NRRD_BASIC_INFO_DIMENSION_BIT
| NRRD_BASIC_INFO_CONTENT_BIT
| NRRD_BASIC_INFO_COMMENTS_BIT
| (nrrdStateKeyValuePairsPropagate
? 0
: NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
}
}
airMopOkay(mop);
return 0;
}
int
unrrdu_shuffleMain(int argc, char **argv, 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 )) {
fprintf(stderr, "%s: permutation length (%u) != axis %d's size ("
_AIR_SIZE_T_CNV ")\n",
me, permLen, axis, nin->axis[axis].size);
airMopError(mop);
return 1;
}
if (inverse) {
iperm = (unsigned int*)calloc(permLen, sizeof(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 {
whichperm = perm;
}
realperm = (size_t*)calloc(permLen, sizeof(size_t));
airMopAdd(mop, realperm, airFree, airMopAlways);
for (di=0; di<permLen; di++) {
realperm[di] = whichperm[di];
}
if (nrrdShuffle(nout, nin, axis, realperm)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error shuffling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
SAVE(out, nout, NULL);
airMopOkay(mop);
return 0;
}
