/*
******** nrrdSlice()
**
** slices a nrrd along a given axis, at a given position.
**
** This is a newer version of the procedure, which is simpler, faster,
** and requires less memory overhead than the first one. It is based
** on the observation that any slice is a periodic square-wave pattern
** in the original data (viewed as a one- dimensional array). The
** characteristics of that periodic pattern are how far from the
** beginning it starts (offset), the length of the "on" part (length),
** the period (period), and the number of periods (numper).
*/
int
nrrdSlice(Nrrd *nout, const Nrrd *cnin, unsigned int saxi, size_t pos) {
static const char me[]="nrrdSlice", func[]="slice";
size_t
I,
rowLen, /* length of segment */
colStep, /* distance between start of each segment */
colLen, /* number of periods */
szOut[NRRD_DIM_MAX];
unsigned int ai, outdim;
int map[NRRD_DIM_MAX];
const char *src;
char *dest, stmp[2][AIR_STRLEN_SMALL];
airArray *mop;
Nrrd *nin;
if (!(cnin && nout)) {
biffAddf(NRRD, "%s: got NULL pointer", me);
return 1;
}
if (nout == cnin) {
biffAddf(NRRD, "%s: nout==nin disallowed", me);
return 1;
}
if (1 == cnin->dim) {
if (0 != saxi) {
biffAddf(NRRD, "%s: slice axis must be 0, not %u, for 1-D array",
me, saxi);
return 1;
}
} else {
if (!( saxi < cnin->dim )) {
biffAddf(NRRD, "%s: slice axis %d out of bounds (0 to %d)",
me, saxi, cnin->dim-1);
return 1;
}
}
if (!( pos < cnin->axis[saxi].size )) {
biffAddf(NRRD, "%s: position %s out of bounds (0 to %s)", me,
airSprintSize_t(stmp[0], pos),
airSprintSize_t(stmp[1], cnin->axis[saxi].size-1));
return 1;
}
/* this shouldn't actually be necessary .. */
if (!nrrdElementSize(cnin)) {
biffAddf(NRRD, "%s: nrrd reports zero element size!", me);
return 1;
}
/* HEY: copy and paste from measure.c/nrrdProject */
mop = airMopNew();
if (1 == cnin->dim) {
/* There are more efficient ways of dealing with this case; this way is
easy to implement because it leaves most of the established code below
only superficially changed; uniformly replacing nin with (nin ? nin :
cnin), even if pointlessly so; this expression that can't be assigned
to a new variable because of the difference in const. */
nin = nrrdNew();
airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
if (nrrdAxesInsert(nin, cnin, 1)) {
biffAddf(NRRD, "%s: trouble inserting axis on 1-D array", me);
airMopError(mop); return 1;
}
} else {
nin = NULL;
}
/* set up control variables */
rowLen = colLen = 1;
for (ai=0; ai<(nin ? nin : cnin)->dim; ai++) {
if (ai < saxi) {
rowLen *= (nin ? nin : cnin)->axis[ai].size;
} else if (ai > saxi) {
colLen *= (nin ? nin : cnin)->axis[ai].size;
}
}
rowLen *= nrrdElementSize(nin ? nin : cnin);
colStep = rowLen*(nin ? nin : cnin)->axis[saxi].size;
outdim = (nin ? nin : cnin)->dim-1;
for (ai=0; ai<outdim; ai++) {
map[ai] = AIR_INT(ai) + (ai >= saxi);
szOut[ai] = (nin ? nin : cnin)->axis[map[ai]].size;
}
nout->blockSize = (nin ? nin : cnin)->blockSize;
if (nrrdMaybeAlloc_nva(nout, (nin ? nin : cnin)->type, outdim, szOut)) {
biffAddf(NRRD, "%s: failed to create slice", me);
airMopError(mop); return 1;
}
/* the skinny */
src = AIR_CAST(const char *, (nin ? nin : cnin)->data);
dest = AIR_CAST(char *, nout->data);
src += rowLen*pos;
for (I=0; I<colLen; I++) {
/* HEY: replace with AIR_MEMCPY() or similar, when applicable */
memcpy(dest, src, rowLen);
src += colStep;
dest += rowLen;
}
/* copy the peripheral information */
if (nrrdAxisInfoCopy(nout, (nin ? nin : cnin), map, NRRD_AXIS_INFO_NONE)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
if (nrrdContentSet_va(nout, func, cnin /* hide possible axinsert*/,
"%d,%d", saxi, pos)) {
biffAddf(NRRD, "%s:", me);
airMopError(mop); return 1;
}
if (nrrdBasicInfoCopy(nout, (nin ? nin : cnin),
NRRD_BASIC_INFO_DATA_BIT
| NRRD_BASIC_INFO_TYPE_BIT
| NRRD_BASIC_INFO_BLOCKSIZE_BIT
| NRRD_BASIC_INFO_DIMENSION_BIT
| NRRD_BASIC_INFO_SPACEORIGIN_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;
}
/* translate origin if this was a spatial axis, otherwise copy */
/* note that if there is no spatial info at all, this is all harmless */
if (AIR_EXISTS((nin ? nin : cnin)->axis[saxi].spaceDirection[0])) {
nrrdSpaceVecScaleAdd2(nout->spaceOrigin,
1.0, (nin ? nin : cnin)->spaceOrigin,
AIR_CAST(double, pos),
(nin ? nin : cnin)->axis[saxi].spaceDirection);
} 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;
}
