echoThreadState *
echoThreadStateNew(void) {
echoThreadState *state;
state = (echoThreadState *)calloc(1, sizeof(echoThreadState));
if (state) {
state->thread = airThreadNew();
state->verbose = 0;
state->threadIdx = -1;
state->depth = -1;
state->njitt = nrrdNew();
state->nperm = nrrdNew();
state->permBuff = NULL;
state->jitt = NULL;
state->chanBuff = NULL;
state->rst = airRandMTStateNew(0);
state->returnPtr = NULL;
}
return state;
}
pullTask *
_pullTaskNew(pullContext *pctx, int threadIdx) {
char me[]="_pullTaskNew", err[BIFF_STRLEN];
pullTask *task;
unsigned int ii, offset;
task = (pullTask *)calloc(1, sizeof(pullTask));
if (!task) {
sprintf(err, "%s: couldn't allocate task", me);
biffAdd(PULL, err); return NULL;
}
task->pctx = pctx;
for (ii=0; ii<pctx->volNum; ii++) {
if (!(task->vol[ii] = _pullVolumeCopy(pctx->vol[ii]))) {
sprintf(err, "%s: trouble copying vol %u/%u", me, ii, pctx->volNum);
biffAdd(PULL, err); return NULL;
}
}
if (0) {
gagePerVolume *pvl;
const double *ans;
double pos[3];
int gret;
for (ii=0; ii<pctx->volNum; ii++) {
pvl = task->vol[ii]->gctx->pvl[0];
fprintf(stderr, "!%s: vol[%u] query:\n", me, ii);
gageQueryPrint(stderr, pvl->kind, pvl->query);
ans = gageAnswerPointer(task->vol[ii]->gctx, pvl, gageSclValue);
ELL_3V_SET(pos, 0.6, 0.6, 0.3);
gret = gageProbeSpace(task->vol[ii]->gctx, pos[0], pos[1], pos[2],
AIR_FALSE, AIR_TRUE);
fprintf(stderr, "!%s: (%d) val(%g,%g,%g) = %g\n", me, gret,
pos[0], pos[1], pos[2], *ans);
ELL_3V_SET(pos, 0.5, 0.0, 0.0);
gret = gageProbeSpace(task->vol[ii]->gctx, pos[0], pos[1], pos[2],
AIR_FALSE, AIR_TRUE);
fprintf(stderr, "!%s: (%d) val(%g,%g,%g) = %g\n", me, gret,
pos[0], pos[1], pos[2], *ans);
}
}
offset = 0;
for (ii=0; ii<=PULL_INFO_MAX; ii++) {
unsigned int volIdx;
if (pctx->ispec[ii]) {
volIdx = pctx->ispec[ii]->volIdx;
task->ans[ii] = gageAnswerPointer(task->vol[volIdx]->gctx,
task->vol[volIdx]->gpvl,
pctx->ispec[ii]->item);
fprintf(stderr, "!%s: task->ans[%u] = %p\n", me, ii, task->ans[ii]);
} else {
task->ans[ii] = NULL;
}
}
if (pctx->threadNum > 1) {
task->thread = airThreadNew();
}
task->threadIdx = threadIdx;
task->rng = airRandMTStateNew(pctx->rngSeed + threadIdx);
task->pointBuffer = pullPointNew(pctx);
pctx->idtagNext = 0; /* because pullPointNew incremented it */
task->neighPoint = AIR_CAST(pullPoint **, calloc(_PULL_NEIGH_MAXNUM,
sizeof(pullPoint*)));
task->returnPtr = NULL;
task->stuckNum = 0;
return task;
}
/*
** parties until the gradients settle down
*/
int
tenGradientBalance(Nrrd *nout, const Nrrd *nin,
tenGradientParm *tgparm) {
static const char me[]="tenGradientBalance";
double len, lastLen, improv;
airRandMTState *rstate;
Nrrd *ncopy;
unsigned int iter, maxIter;
int done;
airArray *mop;
if (!nout || tenGradientCheck(nin, nrrdTypeUnknown, 2) || !tgparm) {
biffAddf(TEN, "%s: got NULL pointer (%p,%p) or invalid nin", me,
AIR_VOIDP(nout), AIR_VOIDP(tgparm));
return 1;
}
if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
biffMovef(TEN, NRRD, "%s: can't initialize output with input", me);
return 1;
}
mop = airMopNew();
ncopy = nrrdNew();
airMopAdd(mop, ncopy, (airMopper)nrrdNuke, airMopAlways);
rstate = airRandMTStateNew(tgparm->seed);
airMopAdd(mop, rstate, (airMopper)airRandMTStateNix, airMopAlways);
/* HEY: factor of 100 is an approximate hack */
maxIter = 100*tgparm->maxIteration;
lastLen = 1.0;
done = AIR_FALSE;
do {
iter = 0;
do {
iter++;
len = party(nout, rstate);
} while (len > lastLen && iter < maxIter);
if (iter >= maxIter) {
if (tgparm->verbose) {
fprintf(stderr, "%s: stopping at max iter %u\n", me, maxIter);
}
if (nrrdCopy(nout, ncopy)) {
biffMovef(TEN, NRRD, "%s: trouble copying", me);
airMopError(mop); return 1;
}
done = AIR_TRUE;
} else {
if (nrrdCopy(ncopy, nout)) {
biffMovef(TEN, NRRD, "%s: trouble copying", me);
airMopError(mop); return 1;
}
improv = lastLen - len;
lastLen = len;
if (tgparm->verbose) {
fprintf(stderr, "%s: (iter %u) improvement: %g (mean length = %g)\n",
me, iter, improv, len);
}
done = (improv <= tgparm->minMeanImprovement
|| len < tgparm->minMean);
}
} while (!done);
airMopOkay(mop);
return 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;
}
