int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, done[13];
Nrrd *nin, *ndist, *nmask, *nupdate, *nout;
NrrdKernelSpec *k00, *k11, *k22;
int E;
unsigned int sx, sy, sz, xi, yi, zi, si, iter, maxIter;
gageContext *ctx;
gagePerVolume *pvl;
double dt, *dist, *mask, *update, thresh, eps, rmsMin;
const double *valu, *gmag, *mcrv;
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 volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &k00,
"tent", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &k11,
"cubicd:0,0.5", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "dt", "step", airTypeDouble, 1, 1, &dt, "0.17",
"time step size");
hestOptAdd(&hopt, "th", "val", airTypeDouble, 1, 1, &thresh, "0.0",
"the value to use for thresholding the input "
"volume, to create the binary constraint image.");
hestOptAdd(&hopt, "eps", "val", airTypeDouble, 1, 1, &eps, "0.05",
"width of value bracket around threshold, to constrain the "
"the update from letting to value, originally on either "
"side of the threshold, from getting too close.");
hestOptAdd(&hopt, "rms", "thresh", airTypeDouble, 1, 1, &rmsMin, "0.01",
"RMS change below this terminates updates.");
hestOptAdd(&hopt, "mi", "max", airTypeUInt, 1, 1, &maxIter, "100",
"maximum # iterations");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"fixed volume output");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, aaliasInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
ndist = nrrdNew();
nmask = nrrdNew();
nupdate = nrrdNew();
airMopAdd(mop, ndist, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nmask, (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nupdate, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ndist, nin, nrrdTypeDouble)
|| nrrdConvert(nmask, nin, nrrdTypeDouble)
|| nrrdConvert(nupdate, nin, nrrdTypeDouble)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate buffers:\n%s", me, err);
airMopError(mop); return 1;
}
dist = AIR_CAST(double *, ndist->data);
mask = AIR_CAST(double *, nmask->data);
update = AIR_CAST(double *, nupdate->data);
ctx = gageContextNew();
airMopAdd(mop, ctx, (airMopper)gageContextNix, airMopAlways);
gageParmSet(ctx, gageParmRenormalize, AIR_TRUE);
gageParmSet(ctx, gageParmCheckIntegrals, AIR_TRUE);
E = 0;
if (!E) E |= !(pvl = gagePerVolumeNew(ctx, ndist, gageKindScl));
if (!E) E |= gagePerVolumeAttach(ctx, pvl);
if (!E) E |= gageKernelSet(ctx, gageKernel00, k00->kernel, k00->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel11, k11->kernel, k11->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel22, k22->kernel, k22->parm);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclValue);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradMag);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclMeanCurv);
if (!E) E |= gageUpdate(ctx);
if (E) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
valu = gageAnswerPointer(ctx, pvl, gageSclValue);
gmag = gageAnswerPointer(ctx, pvl, gageSclGradMag);
mcrv = gageAnswerPointer(ctx, pvl, gageSclMeanCurv);
sx = nin->axis[0].size;
sy = nin->axis[1].size;
sz = nin->axis[2].size;
for (iter=0; iter<maxIter; iter++) {
double rms;
unsigned count;
fprintf(stderr, "%s: iter %u: ", me, iter);
fflush(stderr);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
fflush(stderr);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
si = xi + sx*(yi + sy*zi);
gageProbe(ctx, xi, yi, zi);
update[si] = -dt*(*gmag)*(*mcrv);
}
}
}
rms = 0;
count = 0;
for (si=0; si<sx*sy*sz; si++) {
double newval;
if (update[si]) {
/* NOTE: this update behavior is only slightly different than
what's described in Equation 18 of the paper. That update
rule ensures that the value never changes "sign" (with
respect to the threshold value), by clamping the values
above or below to 0.0. But worst-case scenario is that two
adjacent samples that were on other side of the threshold
(i.e. 0), could then equal the threshold, which would
confuse a marching-cubes type algorithm. So the "eps"
enforces a small value range around the treshold, and keeps
the values on either side of it. */
newval = dist[si] + update[si];
if (mask[si] > thresh) {
newval = AIR_MAX(newval, thresh+eps/2);
} else {
newval = AIR_MIN(newval, thresh-eps/2);
}
rms += (dist[si] - newval)*(dist[si] - newval);
dist[si] = newval;
count++;
}
}
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
rms /= count;
rms = sqrt(rms);
if (rms < rmsMin) {
fprintf(stderr, "\n%s: RMS %g below threshold %g\n", me, rms, rmsMin);
break;
} else {
fprintf(stderr, " rms = %g > %g\n", rms, rmsMin);
}
}
if (iter == maxIter) {
fprintf(stderr, "%s: hit max iter %u\n", me, maxIter);
}
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, ndist)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
if (nrrdSave(outS, nout, 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);
}
int
main(int argc, const char **argv) {
/* stock variables */
char me[] = BKEY;
hestOpt *hopt=NULL;
hestParm *hparm;
airArray *mop;
/* variables specific to this program */
int negskip, progress;
Nrrd *nref, *nin;
size_t *size, ii, nn, tick, pad[2];
unsigned int axi, refCRC, gotCRC, sizeNum;
char *berr, *outS[2], stmp[AIR_STRLEN_SMALL], doneStr[AIR_STRLEN_SMALL];
airRandMTState *rng;
unsigned int seed, *rdata, printbytes;
unsigned char *dataUC;
double time0, time1;
FILE *fout;
/* start-up */
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
/* learn things from hest */
hestOptAdd(&hopt, "seed", "N", airTypeUInt, 1, 1, &seed, "42",
"seed for RNG");
hestOptAdd(&hopt, "s", "sz0", airTypeSize_t, 1, -1, &size, NULL,
"sizes of desired output", &sizeNum);
hestOptAdd(&hopt, "p", "pb pa", airTypeSize_t, 2, 2, pad, "0 0",
"bytes of padding before, and after, the data segment "
"in the written data");
hestOptAdd(&hopt, "ns", "bool", airTypeInt, 0, 0, &negskip, NULL,
"skipping should be relative to end of file");
hestOptAdd(&hopt, "pb", "print", airTypeUInt, 1, 1, &printbytes, "0",
"bytes to print at beginning and end of data, to help "
"debug problems");
hestOptAdd(&hopt, "o", "out.data out.nhdr", airTypeString, 2, 2,
outS, NULL, "output filenames of data and header");
hestParseOrDie(hopt, argc-1, argv+1, hparm, me, tskipInfo,
AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
/* generate reference nrrd data */
nref = nrrdNew();
airMopAdd(mop, nref, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_nva(nref, nrrdTypeUInt, sizeNum, size)) {
airMopAdd(mop, berr=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error allocating data: %s\n", me, berr);
airMopError(mop); return 1;
}
rng = airRandMTStateNew(seed);
airMopAdd(mop, rng, (airMopper)airRandMTStateNix, airMopAlways);
nn = nrrdElementNumber(nref);
rdata = AIR_CAST(unsigned int *, nref->data);
fprintf(stderr, "generating data: . . . "); fflush(stderr);
time0 = airTime();
progress = AIR_FALSE;
tick = nn/100;
for (ii=0; ii<nn; ii++) {
rdata[ii] = airUIrandMT_r(rng);
if (ii && tick && !(ii % tick)) {
time1 = airTime();
if (time1 - time0 > 1.0) {
/* if it took more than a second to do 1% of the thing,
would be good to generate some progress indication */
progress = AIR_TRUE;
}
if (progress) {
fprintf(stderr, "%s", airDoneStr(0, ii, nn, doneStr)); fflush(stderr);
}
}
}
if (progress) {
fprintf(stderr, "%s\n", airDoneStr(0, ii, nn, doneStr)); fflush(stderr);
} else {
fprintf(stderr, "\n");
}
fprintf(stderr, "finding reference (big-endian) CRC: "); fflush(stderr);
refCRC = nrrdCRC32(nref, airEndianBig);
fprintf(stderr, "%u\n", refCRC);
/* write data, with padding */
fprintf(stderr, "saving data . . . "); fflush(stderr);
if (!(fout = fopen(outS[0], "wb" COMMIT))) {
fprintf(stderr, "\n%s: couldn't open %s for writing: %s\n", me,
outS[0], strerror(errno));
airMopError(mop); return 1;
}
airMopAdd(mop, fout, (airMopper)airFclose, airMopAlways);
for (ii=0; ii<pad[0]; ii++) {
if (EOF == fputc(1, fout)) {
fprintf(stderr, "\n%s: error doing pre-padding\n", me);
airMopError(mop); return 1;
}
}
if (nn != fwrite(nref->data, nrrdElementSize(nref), nn, fout)) {
fprintf(stderr, "\n%s: error writing data\n", me);
airMopError(mop); return 1;
}
for (ii=0; ii<pad[1]; ii++) {
if (EOF == fputc(2, fout)) {
fprintf(stderr, "\n%s: error doing post-padding\n", me);
airMopError(mop); return 1;
}
}
if (EOF == fflush(fout)) {
fprintf(stderr, "\n%s: error fflushing data: %s\n", me,
strerror(errno));
}
fprintf(stderr, "\n");
if (printbytes) {
size_t bi, rpb, nn;
char stmp[AIR_STRLEN_SMALL];
nn = nrrdElementSize(nref)*nrrdElementNumber(nref);
rpb = AIR_MIN(printbytes, nn);
dataUC = AIR_CAST(unsigned char *, nref->data);
fprintf(stderr, "CORRECT %s bytes at beginning:\n",
airSprintSize_t(stmp, rpb));
for (bi=0; bi<rpb; bi++) {
fprintf(stderr, "%x ", dataUC[bi]);
}
fprintf(stderr, "...\n");
fprintf(stderr, "CORRECT %s bytes at end:\n",
airSprintSize_t(stmp, rpb));
fprintf(stderr, "...");
for (bi=nn - rpb; bi<nn; bi++) {
fprintf(stderr, " %x", dataUC[bi]);
}
fprintf(stderr, "\n");
}
airMopSingleOkay(mop, fout);
airMopSingleOkay(mop, nref); nref = NULL;
/* write header; for now just writing the header directly */
fprintf(stderr, "writing header . . . \n");
if (!(fout = fopen(outS[1], "w"))) {
fprintf(stderr, "%s: couldn't open %s for writing: %s\n", me,
outS[1], strerror(errno));
airMopError(mop); return 1;
}
airMopAdd(mop, fout, (airMopper)airFclose, airMopAlways);
fprintf(fout, "NRRD0005\n");
fprintf(fout, "type: unsigned int\n");
fprintf(fout, "dimension: %u\n", sizeNum);
fprintf(fout, "sizes:");
for (axi=0; axi<sizeNum; axi++) {
fprintf(fout, " %s", airSprintSize_t(stmp, size[axi]));
}
fprintf(fout, "\n");
fprintf(fout, "endian: %s\n", airEnumStr(airEndian, airMyEndian()));
fprintf(fout, "encoding: %s\n", airEnumStr(nrrdEncodingType,
nrrdEncodingTypeRaw));
if (!negskip) {
if (pad[0]) {
fprintf(fout, "byte skip: %s\n", airSprintSize_t(stmp, pad[0]));
}
} else {
fprintf(fout, "byte skip: -%s\n", airSprintSize_t(stmp, pad[1]+1));
}
fprintf(fout, "data file: %s\n", outS[0]);
airMopSingleOkay(mop, fout);
/* read it in, make sure it checks out */
fprintf(stderr, "reading data . . . \n");
nin = nrrdNew();
airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nin, outS[1], NULL)) {
airMopAdd(mop, berr=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error reading back in: %s\n", me, berr);
airMopError(mop); return 1;
}
if (printbytes) {
size_t bi, rpb, nn;
char stmp[AIR_STRLEN_SMALL];
nn = nrrdElementSize(nin)*nrrdElementNumber(nin);
rpb = AIR_MIN(printbytes, nn);
dataUC = AIR_CAST(unsigned char *, nin->data);
fprintf(stderr, "FOUND %s bytes at beginning:\n",
airSprintSize_t(stmp, rpb));
for (bi=0; bi<rpb; bi++) {
fprintf(stderr, "%x ", dataUC[bi]);
}
fprintf(stderr, "...\n");
fprintf(stderr, "FOUND %s bytes at end:\n",
airSprintSize_t(stmp, rpb));
fprintf(stderr, "...");
for (bi=nn - rpb; bi<nn; bi++) {
fprintf(stderr, " %x", dataUC[bi]);
}
fprintf(stderr, "\n");
}
fprintf(stderr, "finding new CRC . . . \n");
gotCRC = nrrdCRC32(nin, airEndianBig);
if (refCRC != gotCRC) {
fprintf(stderr, "%s: got CRC %u but wanted %u\n", me, gotCRC, refCRC);
airMopError(mop); return 1;
}
fprintf(stderr, "(all ok)\n");
/* HEY: to test gzip reading, we really want to do a system call to
gzip compress the data, and write a new header to point to the
compressed data, and make sure we can read in that just the same */
airMopOkay(mop);
return 0;
}
int
main(int argc, const char *argv[]) {
const char *me;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char **ninStr, *err, *outS, doneStr[13];
Nrrd *nin0, *nin, *nrgb, *nout, *nhist[2], *npreout, *nhproj[3];
float *rgb;
float *out, *preout, *hist[2], maxSum,
upSample, overSampleScale;
unsigned int size0, sX, sY, sH, ninLen, ti, overSampleNum;
NrrdResampleContext *rsmc;
NrrdKernelSpec *ksp;
me = argv[0];
mop = airMopNew();
hopt = NULL;
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->respFileEnable = AIR_TRUE;
hestOptAdd(&hopt, "i", "images", airTypeString, 1, -1, &ninStr, NULL,
"input image sequence", &ninLen, NULL, NULL);
hestOptAdd(&hopt, "sh", "histo size", airTypeUInt, 1, 1, &sH, "500",
"histogram size");
hestOptAdd(&hopt, "k", "kern", airTypeOther, 1, 1, &ksp,
"tent", "kernel for upsampling images",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "us", "upsampling", airTypeFloat, 1, 1, &upSample,
"1", "amount of upsampling of image");
hestOptAdd(&hopt, "osn", "# oversmp", airTypeUInt, 1, 1, &overSampleNum,
"1", "number of sample per (upsampled) pixel");
hestOptAdd(&hopt, "osc", "scaling", airTypeFloat, 1, 1, &overSampleScale,
"1", "scaling with oversampling");
hestOptAdd(&hopt, "ms", "max sum", airTypeFloat, 1, 1, &maxSum,
"10", "per-hue histogram summation is non-linearly and "
"asymptotically clamped to this maximum");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output filename", NULL);
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, mchistInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (0 == overSampleNum) {
fprintf(stderr, "%s: overSampleNum must be > 0\n", me);
airMopError(mop);
return 1;
}
nin0 = nrrdNew();
airMopAdd(mop, nin0, (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nin0, ninStr[0], NULL)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't load first image:\n%s", me, err);
airMopError(mop);
return 1;
}
if (!( (3 == nin0->axis[0].size || 4 == nin0->axis[0].size)
&& 3 == nin0->dim
&& nrrdTypeUChar == nin0->type )) {
fprintf(stderr, "%s: 1st image not 3D (3-or-4)-by-X-by-Y %s array "
"(got %u-D %s array)\n", me,
airEnumStr(nrrdType, nrrdTypeUChar),
nin0->dim,
airEnumStr(nrrdType, nin0->type));
airMopError(mop);
return 1;
}
rsmc = nrrdResampleContextNew();
airMopAdd(mop, rsmc, (airMopper)nrrdResampleContextNix, airMopAlways);
size0 = AIR_CAST(unsigned int, nin0->axis[0].size);
sX = AIR_CAST(unsigned int, upSample*nin0->axis[1].size);
sY = AIR_CAST(unsigned int, upSample*nin0->axis[2].size);
nrgb = nrrdNew();
airMopAdd(mop, nrgb, (airMopper)nrrdNuke, airMopAlways);
if (nrrdResampleDefaultCenterSet(rsmc, nrrdCenterCell)
|| nrrdResampleInputSet(rsmc, nin0)
|| nrrdResampleKernelSet(rsmc, 1, ksp->kernel, ksp->parm)
|| nrrdResampleKernelSet(rsmc, 2, ksp->kernel, ksp->parm)
|| nrrdResampleSamplesSet(rsmc, 1, sX)
|| nrrdResampleSamplesSet(rsmc, 2, sY)
|| nrrdResampleRangeFullSet(rsmc, 1)
|| nrrdResampleRangeFullSet(rsmc, 2)
|| nrrdResampleTypeOutSet(rsmc, nrrdTypeFloat)
|| nrrdResampleRenormalizeSet(rsmc, AIR_TRUE)
|| nrrdResampleExecute(rsmc, nrgb)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling slice:\n%s", me, err);
airMopError(mop);
return 1;
}
nhist[0] = nrrdNew();
airMopAdd(mop, nhist[0], (airMopper)nrrdNuke, airMopAlways);
nhist[1] = nrrdNew();
airMopAdd(mop, nhist[1], (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nhist[0], nrrdTypeFloat, 2,
AIR_CAST(size_t, sH),
AIR_CAST(size_t, sH))
|| nrrdMaybeAlloc_va(nhist[1], nrrdTypeFloat, 2,
AIR_CAST(size_t, sH),
AIR_CAST(size_t, sH))) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error allocating histos:\n%s", me, err);
airMopError(mop);
return 1;
}
nhist[0]->axis[0].min = nhist[0]->axis[1].min = 0.0;
nhist[0]->axis[0].max = nhist[0]->axis[1].max = 1.0;
nhist[1]->axis[0].min = nhist[1]->axis[1].min = 0.0;
nhist[1]->axis[0].max = nhist[1]->axis[1].max = 1.0;
nhproj[0] = nrrdNew();
airMopAdd(mop, nhproj[0], (airMopper)nrrdNix, airMopAlways);
nhproj[1] = nrrdNew();
airMopAdd(mop, nhproj[1], (airMopper)nrrdNix, airMopAlways);
nhproj[2] = nrrdNew();
airMopAdd(mop, nhproj[2], (airMopper)nrrdNix, airMopAlways);
printf("working ... ");
hist[0] = AIR_CAST(float *, nhist[0]->data);
hist[1] = AIR_CAST(float *, nhist[1]->data);
nin = nrrdNew();
airMopAdd(mop, nin, (airMopper)nrrdNuke, airMopAlways);
npreout = nrrdNew();
airMopAdd(mop, npreout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(npreout, nrrdTypeFloat, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, sH),
AIR_CAST(size_t, ninLen))) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error allocating pre-output:\n%s", me, err);
airMopError(mop);
return 1;
}
preout = AIR_CAST(float *, npreout->data);
for (ti=0; ti<ninLen; ti++) {
printf("%s", airDoneStr(0, ti, ninLen, doneStr)); fflush(stdout);
if (nrrdLoad(nin, ninStr[ti], NULL)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't load image[%u]:\n%s", me, ti, err);
airMopError(mop);
return 1;
}
if (!nrrdSameSize(nin0, nin, AIR_TRUE)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: nin[%u] not like nin[0]:\n%s", me, ti, err);
airMopError(mop);
return 1;
}
if (nrrdResampleInputSet(rsmc, nin)
|| nrrdResampleExecute(rsmc, nrgb)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble resampling nin[%u]:\n%s", me, ti, err);
airMopError(mop);
return 1;
}
if (nrrdWrap_va(nhproj[0], preout + 0*sH, nrrdTypeFloat, 1, AIR_CAST(size_t, sH)) ||
nrrdWrap_va(nhproj[1], preout + 1*sH, nrrdTypeFloat, 1, AIR_CAST(size_t, sH)) ||
nrrdWrap_va(nhproj[2], preout + 2*sH, nrrdTypeFloat, 1, AIR_CAST(size_t, sH))) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble wrapping output[%u]:\n%s", me, ti, err);
airMopError(mop);
return 1;
}
rgb = AIR_CAST(float *, nrgb->data);
imageProc(nhproj, nhist, sH,
rgb, size0, sX*sY,
overSampleNum, overSampleScale);
preout += 3*sH;
}
printf("%s\n", airDoneStr(0, ti, ninLen, doneStr)); fflush(stdout);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 3,
AIR_CAST(size_t, 3),
AIR_CAST(size_t, sH),
AIR_CAST(size_t, ninLen))) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error allocating output:\n%s", me, err);
airMopError(mop);
return 1;
}
out = AIR_CAST(float *, nout->data);
preout = AIR_CAST(float *, npreout->data);
for (ti=0; ti<ninLen; ti++) {
unsigned int hi;
float hh, vv, ss, scl;
for (hi=0; hi<sH; hi++) {
hh = AIR_AFFINE(0, hi, sH, 0, 1);
if (!preout[hi + 2*sH]) {
ELL_3V_SET(out + 3*hi, 0, 0, 0);
} else {
ss = preout[hi + 2*sH];
scl = ss/(maxSum + ss);
vv = scl*preout[hi + 1*sH];
dyeHSVtoRGB(out + 0 + 3*hi, out + 1 + 3*hi, out + 2 + 3*hi,
hh, preout[hi + 0*sH], vv);
}
}
out += 3*sH;
preout += 3*sH;
}
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error saving output:\n%s", me, err);
airMopError(mop);
return 1;
}
airMopOkay(mop);
return 0;
}
int
main(int argc, char *argv[]) {
char *me, *outS;
hestOpt *hopt;
hestParm *hparm;
airArray *mop;
char *err, done[13];
Nrrd *nin, *nblur, *nout;
NrrdKernelSpec *kb0, *kb1, *k00, *k11, *k22;
NrrdResampleContext *rsmc;
int E;
unsigned int sx, sy, sz, xi, yi, zi, ai;
gageContext *ctx;
gagePerVolume *pvl;
const double *gvec, *gmag, *evec0, *eval;
double (*ins)(void *v, size_t I, double d);
double (*lup)(const void *v, size_t I);
double dotmax, dotpow, gmmax, evalshift, gmpow, _dotmax, _gmmax, scl, clamp;
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 volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "kb0", "kernel", airTypeOther, 1, 1, &kb0,
"guass:3,5", "kernel to use for pre-process blurring",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "kb1", "kernel", airTypeOther, 1, 1, &kb1,
"cubic:1.5,1,0", "kernel to use for pos-process blurring",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &k00,
"cubic:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &k11,
"cubicd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "k00", NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "dotmax", "dot", airTypeDouble, 1, 1, &dotmax, "5",
"max effective value of dot(gvec, evec0)");
hestOptAdd(&hopt, "evs", "shift", airTypeDouble, 1, 1, &evalshift, "0",
"negative shift to avoid changing mostly flat regions");
hestOptAdd(&hopt, "clamp", "clamp", airTypeDouble, 1, 1, &clamp, "nan",
"if it exists, data value can't be forced below this");
hestOptAdd(&hopt, "dotpow", "pow", airTypeDouble, 1, 1, &dotpow, "1",
"exponent for dot");
hestOptAdd(&hopt, "gmmax", "dot", airTypeDouble, 1, 1, &gmmax, "2",
"max effective value of gmag");
hestOptAdd(&hopt, "gmpow", "pow", airTypeDouble, 1, 1, &gmpow, "1",
"exponent for gmag");
hestOptAdd(&hopt, "scl", "scale", airTypeDouble, 1, 1, &scl, "0.1",
"how much to scale hack to decrease input value");
hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
"fixed volume output");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, vhInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!( 3 == nin->dim
&& nrrdTypeBlock != nin->type )) {
fprintf(stderr, "%s: need a 3-D scalar nrrd (not %u-D %s)", me,
nin->dim, airEnumStr(nrrdType, nin->type));
airMopError(mop); return 1;
}
nblur = nrrdNew();
airMopAdd(mop, nblur, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nblur, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
fprintf(stderr, "%s: pre-blurring ... ", me);
fflush(stderr);
rsmc = nrrdResampleContextNew();
airMopAdd(mop, rsmc, (airMopper)nrrdResampleContextNix, airMopAlways);
E = AIR_FALSE;
if (!E) E |= nrrdResampleDefaultCenterSet(rsmc, nrrdCenterCell);
if (!E) E |= nrrdResampleNrrdSet(rsmc, nin);
for (ai=0; ai<3; ai++) {
if (!E) E |= nrrdResampleKernelSet(rsmc, ai, kb0->kernel, kb0->parm);
if (!E) E |= nrrdResampleSamplesSet(rsmc, ai, nin->axis[ai].size);
if (!E) E |= nrrdResampleRangeFullSet(rsmc, ai);
}
if (!E) E |= nrrdResampleBoundarySet(rsmc, nrrdBoundaryBleed);
if (!E) E |= nrrdResampleTypeOutSet(rsmc, nrrdTypeDefault);
if (!E) E |= nrrdResampleRenormalizeSet(rsmc, AIR_TRUE);
if (!E) E |= nrrdResampleExecute(rsmc, nblur);
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
fprintf(stderr, "done.\n");
ctx = gageContextNew();
airMopAdd(mop, ctx, (airMopper)gageContextNix, airMopAlways);
gageParmSet(ctx, gageParmRenormalize, AIR_TRUE);
gageParmSet(ctx, gageParmCheckIntegrals, AIR_TRUE);
E = 0;
if (!E) E |= !(pvl = gagePerVolumeNew(ctx, nblur, gageKindScl));
if (!E) E |= gagePerVolumeAttach(ctx, pvl);
if (!E) E |= gageKernelSet(ctx, gageKernel00, k00->kernel, k00->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel11, k11->kernel, k11->parm);
if (!E) E |= gageKernelSet(ctx, gageKernel22, k22->kernel, k22->parm);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradVec);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclGradMag);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclHessEvec0);
if (!E) E |= gageQueryItemOn(ctx, pvl, gageSclHessEval);
if (!E) E |= gageUpdate(ctx);
if (E) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
gvec = gageAnswerPointer(ctx, pvl, gageSclGradVec);
gmag = gageAnswerPointer(ctx, pvl, gageSclGradMag);
evec0 = gageAnswerPointer(ctx, pvl, gageSclHessEvec0);
eval = gageAnswerPointer(ctx, pvl, gageSclHessEval);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdCopy(nout, nin)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: couldn't allocate output:\n%s", me, err);
airMopError(mop); return 1;
}
if (!(nout->type == nin->type && nblur->type == nin->type)) {
fprintf(stderr, "%s: whoa, types (%s %s %s) not all equal\n", me,
airEnumStr(nrrdType, nin->type),
airEnumStr(nrrdType, nblur->type),
airEnumStr(nrrdType, nout->type));
}
ins = nrrdDInsert[nout->type];
lup = nrrdDLookup[nout->type];
sx = nin->axis[0].size;
sy = nin->axis[1].size;
sz = nin->axis[2].size;
gageProbe(ctx, 0, 0, 0);
_dotmax = ELL_3V_DOT(gvec, evec0);
_gmmax = *gmag;
fprintf(stderr, "%s: hacking ", me);
fflush(stderr);
for (zi=0; zi<sz; zi++) {
fprintf(stderr, "%s", airDoneStr(0, zi, sz-1, done));
fflush(stderr);
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
size_t si;
double dot, evl, gm, shift, in, out, mode;
gageProbe(ctx, xi, yi, zi);
si = xi + sx*(yi + sy*zi);
dot = ELL_3V_DOT(gvec, evec0);
_dotmax = AIR_MAX(_dotmax, dot);
dot = AIR_ABS(dot);
dot = 1 - AIR_MIN(dot, dotmax)/dotmax;
dot = pow(dot, dotpow);
evl = AIR_MAX(0, eval[0] - evalshift);
mode = airMode3_d(eval);
evl *= AIR_AFFINE(-1, mode, 1, 0, 1);
_gmmax = AIR_MAX(_gmmax, *gmag);
gm = 1 - AIR_MIN(*gmag, gmmax)/gmmax;
gm = pow(gm, gmpow);
shift = scl*gm*evl*dot;
if (AIR_EXISTS(clamp)) {
in = lup(nin->data, si);
out = in - shift;
out = AIR_MAX(out, clamp);
shift = AIR_MAX(0, in - out);
}
ins(nout->data, si, shift);
}
}
}
fprintf(stderr, "\n");
fprintf(stderr, "%s: max dot seen: %g\n", me, _dotmax);
fprintf(stderr, "%s: max gm seen: %g\n", me, _gmmax);
fprintf(stderr, "%s: post-blurring ... ", me);
fflush(stderr);
E = AIR_FALSE;
if (!E) E |= nrrdResampleNrrdSet(rsmc, nout);
for (ai=0; ai<3; ai++) {
if (!E) E |= nrrdResampleKernelSet(rsmc, ai, kb1->kernel, kb1->parm);
if (!E) E |= nrrdResampleSamplesSet(rsmc, ai, nout->axis[ai].size);
if (!E) E |= nrrdResampleRangeFullSet(rsmc, ai);
}
if (!E) E |= nrrdResampleExecute(rsmc, nblur);
if (E) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: error resampling nrrd:\n%s", me, err);
airMopError(mop);
return 1;
}
fprintf(stderr, "done.\n");
for (zi=0; zi<sz; zi++) {
for (yi=0; yi<sy; yi++) {
for (xi=0; xi<sx; xi++) {
size_t si;
double in, shift;
si = xi + sx*(yi + sy*zi);
in = lup(nin->data, si);
shift = lup(nblur->data, si);
ins(nout->data, si, in - shift);
}
}
}
if (nrrdSave(outS, nout, 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);
}
int
main(int argc, char *argv[]) {
char *me, *err;
hestOpt *hopt=NULL;
airArray *mop;
char *outTenS, *outCovarS, *outRmvS;
int seed, E;
unsigned int NN;
Nrrd *_ninTen, *ninTen, *ngrad, *_ninB0, *ninB0, *nmask,
*noutCovar, *noutTen, *noutRmv, *ntbuff;
float sigma, bval;
size_t sizeX, sizeY, sizeZ;
tenEstimateContext *tec;
int axmap[NRRD_DIM_MAX], randrot;
mop = airMopNew();
me = argv[0];
hestOptAdd(&hopt, "i", "ten", airTypeOther, 1, 1, &_ninTen, NULL,
"input tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "n", "#sim", airTypeUInt, 1, 1, &NN, "100",
"number of simulations to run");
hestOptAdd(&hopt, "seed", "seed", airTypeInt, 1, 1, &seed, "42",
"seed value for RNG which creates noise");
hestOptAdd(&hopt, "r", "reference field", airTypeOther, 1, 1, &_ninB0, NULL,
"reference anatomical scan, with no diffusion weighting",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "rr", NULL, airTypeOther, 0, 0, &randrot, NULL,
"randomize gradient set orientation");
hestOptAdd(&hopt, "g", "grad list", airTypeOther, 1, 1, &ngrad, "",
"gradient list, one row per diffusion-weighted image",
NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "b", "b", airTypeFloat, 1, 1, &bval, "1000",
"b value for simulated scan");
hestOptAdd(&hopt, "sigma", "sigma", airTypeFloat, 1, 1, &sigma, "0.0",
"Rician noise parameter");
hestOptAdd(&hopt, "ot", "filename", airTypeString, 1, 1, &outTenS,
"tout.nrrd", "file to write output tensor nrrd to");
hestOptAdd(&hopt, "oc", "filename", airTypeString, 1, 1, &outCovarS,
"cout.nrrd", "file to write output covariance nrrd to");
hestOptAdd(&hopt, "or", "filename", airTypeString, 1, 1, &outRmvS,
"rout.nrrd", "file to write output R_i means, variances to");
hestParseOrDie(hopt, argc-1, argv+1, NULL,
me, info, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (tenGradientCheck(ngrad, nrrdTypeDefault, 7)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: problem with gradient list:\n%s\n", me, err);
airMopError(mop);
return 1;
}
if (tenTensorCheck(_ninTen, nrrdTypeDefault, AIR_TRUE, AIR_TRUE)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: didn't like input:\n%s\n", me, err);
airMopError(mop);
return 1;
}
sizeX = _ninTen->axis[1].size;
sizeY = _ninTen->axis[2].size;
sizeZ = _ninTen->axis[3].size;
if (!(3 == _ninB0->dim &&
sizeX == _ninB0->axis[0].size &&
sizeY == _ninB0->axis[1].size &&
sizeZ == _ninB0->axis[2].size)) {
fprintf(stderr, "%s: given B0 (%u-D) volume not 3-D " _AIR_SIZE_T_CNV
"x" _AIR_SIZE_T_CNV "x" _AIR_SIZE_T_CNV, me, _ninB0->dim,
sizeX, sizeY, sizeZ);
airMopError(mop);
return 1;
}
ninTen = nrrdNew();
airMopAdd(mop, ninTen, (airMopper)nrrdNuke, airMopOnError);
nmask = nrrdNew();
airMopAdd(mop, nmask, (airMopper)nrrdNuke, airMopOnError);
ninB0 = nrrdNew();
airMopAdd(mop, ninB0, (airMopper)nrrdNuke, airMopOnError);
noutCovar = nrrdNew();
airMopAdd(mop, noutCovar, (airMopper)nrrdNuke, airMopOnError);
noutTen = nrrdNew();
airMopAdd(mop, noutTen, (airMopper)nrrdNuke, airMopOnError);
noutRmv = nrrdNew();
airMopAdd(mop, noutRmv, (airMopper)nrrdNuke, airMopOnError);
ntbuff = nrrdNew();
airMopAdd(mop, ntbuff, (airMopper)nrrdNuke, airMopOnError);
if (nrrdConvert(ninTen, _ninTen, nrrdTypeDouble)
|| nrrdSlice(nmask, ninTen, 0, 0)
|| nrrdConvert(ninB0, _ninB0, nrrdTypeDouble)
|| nrrdMaybeAlloc_va(noutTen, nrrdTypeDouble, 4,
AIR_CAST(size_t, 7), sizeX, sizeY, sizeZ)
|| nrrdMaybeAlloc_va(noutCovar, nrrdTypeDouble, 4,
AIR_CAST(size_t, 21), sizeX, sizeY, sizeZ)
|| nrrdMaybeAlloc_va(noutRmv, nrrdTypeDouble, 4,
AIR_CAST(size_t, 6), sizeX, sizeY, sizeZ)
|| nrrdMaybeAlloc_va(ntbuff, nrrdTypeDouble, 2,
AIR_CAST(size_t, 7), NN)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble setting up tec:\n%s\n", me, err);
airMopError(mop);
return 1;
}
tec = tenEstimateContextNew();
airMopAdd(mop, tec, (airMopper)tenEstimateContextNix, airMopAlways);
E = 0;
if (!E) E |= tenEstimateMethodSet(tec, tenEstimate1MethodLLS);
if (!E) E |= tenEstimateValueMinSet(tec, 0.000000001);
if (!E) E |= tenEstimateGradientsSet(tec, ngrad, bval, AIR_TRUE);
if (!E) E |= tenEstimateThresholdSet(tec, 0, 0);
if (!E) E |= tenEstimateUpdate(tec);
if (E) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble setting up tec:\n%s\n", me, err);
airMopError(mop);
return 1;
}
airSrandMT(seed);
fprintf(stderr, "!%s: randrot = %d\n", me, randrot);
if (1) {
unsigned int II;
unsigned int nsamp;
double *inTen, *outTen, *outCovar, *outRmv,
*dwibuff, (*lup)(const void *, size_t);
char doneStr[AIR_STRLEN_SMALL];
dwibuff = AIR_CAST(double *, calloc(ngrad->axis[1].size, sizeof(double)));
airMopAdd(mop, dwibuff, airFree, airMopAlways);
nsamp = sizeX*sizeY*sizeZ;
inTen = AIR_CAST(double *, ninTen->data);
lup = nrrdDLookup[nrrdTypeDouble];
outTen = AIR_CAST(double *, noutTen->data);
outCovar = AIR_CAST(double *, noutCovar->data);
outRmv = AIR_CAST(double *, noutRmv->data);
fprintf(stderr, "!%s: simulating ... ", me);
fflush(stderr);
for (II=0; II<nsamp; II++) {
if (!(II % sizeX)) {
fprintf(stderr, "%s", airDoneStr(0, II, nsamp, doneStr));
fflush(stderr);
}
if (csimDo(outTen, outCovar, outRmv + 0, outRmv + 3, ntbuff,
tec, dwibuff, sigma,
bval, lup(ninB0->data, II), NN, randrot, inTen)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop);
return 1;
}
inTen += 7;
outTen += 7;
outCovar += 21;
outRmv += 6;
}
fprintf(stderr, "%s\n", airDoneStr(0, II, nsamp, doneStr));
}
