int
main(int argc, char **argv) {
char *err;
fprintf(stderr, "(from Teem %s, %s)\n",
airTeemVersion, airTeemReleaseDate);
if (!nrrdSanity()) {
fprintf(stderr, "\n");
fprintf(stderr, "!!! nrrd sanity check FAILED: fix and re-compile\n");
err = biffGet(NRRD);
fprintf(stderr, "%s\n", err);
free(err);
return 1;
} else {
fprintf(stderr, "(nrrdSanity check passed)\n\n");
}
if (2 != argc) {
fprintf(stderr, "usage: demoIO <filename>\n");
return 1;
}
demoIO(argv[1]);
return 0;
}
int
main(int argc, char *argv[]) {
int ret;
char *me, *err;
AIR_UNUSED(argc);
me = argv[0];
if (!nrrdSanity()) {
err = biffGetDone(NRRD);
fprintf(stderr, "%s: nrrdSanity failed:\n%s", me, err);
free(err);
ret = 1;
} else {
fprintf(stderr, "%s: nrrdSanity passed\n", me);
ret = 0;
}
return ret;
}
int
main(int argc, char **argv) {
int i, ret;
char *me, *argv0 = NULL, *err;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for how Teem was built here.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_FALSE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->cleverPluralizeOtherY = AIR_TRUE;
hparm->columns = 78;
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
tendUsage(TEND, hparm);
airMopError(mop);
exit(1);
}
/* else, we see if its --version */
if (!strcmp("--version", argv[1])) {
printf("Teem version %s (%s)\n",
airTeemVersion, airTeemReleaseDate);
exit(0);
}
/* else, we should see if they're asking for a command we know about */
for (i=0; tendCmdList[i]; i++) {
if (!strcmp(argv[1], tendCmdList[i]->name))
break;
if (!strcmp("--help", argv[1])
&& !strcmp("about", tendCmdList[i]->name)) {
break;
}
}
if (tendCmdList[i]) {
/* yes, we have that command */
/* initialize variables used by the various commands */
argv0 = (char *)calloc(strlen(TEND) + strlen(argv[1]) + 2, sizeof(char));
airMopMem(mop, &argv0, airMopAlways);
sprintf(argv0, "%s %s", TEND, argv[1]);
/* run the individual unu program, saving its exit status */
ret = tendCmdList[i]->main(argc-2, argv+2, argv0, hparm);
} else {
fprintf(stderr, "%s: unrecognized command: \"%s\"; type \"%s\" for "
"complete list\n", me, argv[1], me);
ret = 1;
}
airMopDone(mop, ret);
return ret;
}
int
main(int argc, char **argv) {
int i, ret;
char *me, *argv0 = NULL, *err;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for Teem.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_FALSE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->cleverPluralizeOtherY = AIR_TRUE;
hparm->columns = 78;
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
baneGkmsUsage(GKMS, hparm);
airMopError(mop);
exit(1);
}
/* else, we should see if they're asking for a command we know about */
/* baneGkmsCmdList[] is NULL-terminated */
for (i=0; baneGkmsCmdList[i]; i++) {
if (!strcmp(argv[1], baneGkmsCmdList[i]->name))
break;
}
if (baneGkmsCmdList[i]) {
/* yes, we have that command */
/* initialize variables used by the various commands */
argv0 = AIR_CAST(char*, malloc(strlen(GKMS) + strlen(argv[1]) + 2));
airMopMem(mop, &argv0, airMopAlways);
sprintf(argv0, "%s %s", GKMS, argv[1]);
/* run the individual unu program, saving its exit status */
ret = baneGkmsCmdList[i]->main(argc-2, argv+2, argv0, hparm);
if (1 == ret) {
airMopAdd(mop, err=biffGetDone(BANE), airFree, airMopAlways);
fprintf(stderr, "%s: error:\n%s", argv0, err);
} else if (2 == ret) {
/* gkms command has already handled printing error messages */
ret = 1;
}
} else {
int
main(int argc, char **argv) {
int i, ret;
char *me, *argv0 = NULL, *err;
hestParm *hparm;
airArray *mop;
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* if user hasn't tried to set nrrdStateKindNoop by an environment
variable, we set it to false, since its probably what people expect */
if (!getenv("NRRD_STATE_KIND_NOOP")) {
nrrdStateKindNoop = AIR_FALSE;
}
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for how Teem was built here.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
hparm->elideSingleOtherDefault = AIR_TRUE;
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
hparm->columns = unrrduDefNumColumns;
/* if there are no arguments, then we give general usage information */
if (1 >= argc) {
unrrduUsage("unu", hparm);
airMopError(mop);
exit(1);
}
/* else, we should see if they're asking for a command we know about */
for (i=0; unrrduCmdList[i]; i++) {
if (!strcmp(argv[1], unrrduCmdList[i]->name))
break;
}
/* unrrduCmdList[] is NULL-terminated */
if (unrrduCmdList[i]) {
/* yes, we have that command */
/* initialize variables used by the various commands */
argv0 = (char *)calloc(strlen(UNU) + strlen(argv[1]) + 2, sizeof(char));
airMopMem(mop, &argv0, airMopAlways);
sprintf(argv0, "%s %s", UNU, argv[1]);
/* run the individual unu program, saving its exit status */
ret = unrrduCmdList[i]->main(argc-2, argv+2, argv0, hparm);
} else {
fprintf(stderr, "%s: unrecognized command: \"%s\"; type \"%s\" for "
"complete list\n", me, argv[1], me);
ret = 1;
}
airMopDone(mop, ret);
return ret;
}
int
main(int argc, const char *argv[]) {
gageKind *kind;
const char *me;
char *whatS, *err, *outS, *stackReadFormat, *stackSaveFormat;
hestParm *hparm;
hestOpt *hopt = NULL;
NrrdKernelSpec *k00, *k11, *k22, *kSS, *kSSblur;
int what, E=0, renorm, SSuniform, SSoptim, verbose, zeroZ,
orientationFromSpacing, SSnormd;
unsigned int iBaseDim, oBaseDim, axi, numSS, ninSSIdx, seed;
const double *answer;
Nrrd *nin, *nout, **ninSS=NULL;
Nrrd *ngrad=NULL, *nbmat=NULL;
size_t ai, ansLen, idx, xi, yi, zi, six, siy, siz, sox, soy, soz;
double bval=0, gmc, rangeSS[2], wrlSS, idxSS=AIR_NAN,
dsix, dsiy, dsiz, dsox, dsoy, dsoz;
gageContext *ctx;
gagePerVolume *pvl=NULL;
double t0, t1, x, y, z, scale[3], rscl[3], min[3], maxOut[3], maxIn[3];
airArray *mop;
unsigned int hackZi, *skip, skipNum;
double (*ins)(void *v, size_t I, double d);
gageStackBlurParm *sbp;
char hackKeyStr[]="TEEM_VPROBE_HACK_ZI", *hackValStr;
int otype, hackSet;
char stmp[4][AIR_STRLEN_SMALL];
me = argv[0];
/* parse environment variables first, in case they break nrrdDefault*
or nrrdState* variables in a way that nrrdSanity() should see */
nrrdDefaultGetenv();
nrrdStateGetenv();
/* no harm done in making sure we're sane */
if (!nrrdSanity()) {
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s: nrrd sanity check FAILED.\n", me);
fprintf(stderr, "\n");
fprintf(stderr, " This means that either nrrd can't work on this "
"platform, or (more likely)\n");
fprintf(stderr, " there was an error in the compilation options "
"and variable definitions\n");
fprintf(stderr, " for how Teem was built here.\n");
fprintf(stderr, "\n");
fprintf(stderr, " %s\n", err = biffGetDone(NRRD));
fprintf(stderr, "\n");
fprintf(stderr, "******************************************\n");
fprintf(stderr, "******************************************\n");
free(err);
return 1;
}
mop = airMopNew();
hparm = hestParmNew();
airMopAdd(mop, hparm, AIR_CAST(airMopper, hestParmFree), airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
"input volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
"\"kind\" of volume (\"scalar\", \"vector\", "
"\"tensor\", or \"dwi\")",
NULL, NULL, meetHestGageKind);
hestOptAdd(&hopt, "v", "verbosity", airTypeInt, 1, 1, &verbose, "1",
"verbosity level");
hestOptAdd(&hopt, "q", "query", airTypeString, 1, 1, &whatS, NULL,
"the quantity (scalar, vector, or matrix) to learn by probing");
hestOptAdd(&hopt, "s", "sclX sclY sxlZ", airTypeDouble, 3, 3, scale,
"1.0 1.0 1.0",
"scaling factor for resampling on each axis "
"(>1.0 : supersampling)");
hestOptAdd(&hopt, "k00", "kern00", airTypeOther, 1, 1, &k00,
"tent", "kernel for gageKernel00",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k11", "kern11", airTypeOther, 1, 1, &k11,
"cubicd:1,0", "kernel for gageKernel11",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "k22", "kern22", airTypeOther, 1, 1, &k22,
"cubicdd:1,0", "kernel for gageKernel22",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "seed", "N", airTypeUInt, 1, 1, &seed, "42",
"RNG seed; mostly for debugging");
hestOptAdd(&hopt, "zz", "bool", airTypeBool, 1, 1, &zeroZ, "false",
"enable \"zeroZ\" behavior in gage that partially "
"implements working with 3D images as if they are 2D");
hestOptAdd(&hopt, "ssn", "SS #", airTypeUInt, 1, 1, &numSS,
"0", "how many scale-space samples to evaluate, or, "
"0 to turn-off all scale-space behavior");
hestOptAdd(&hopt, "ssr", "scale range", airTypeDouble, 2, 2, rangeSS,
"nan nan", "range of scales in scale-space");
hestOptAdd(&hopt, "ssrf", "SS read format", airTypeString, 1, 1,
&stackReadFormat, "",
"printf-style format (including a \"%u\") for the "
"filenames from which to *read* "
"pre-blurred volumes computed for the stack");
hestOptAdd(&hopt, "sssf", "SS save format", airTypeString, 1, 1,
&stackSaveFormat, "",
"printf-style format (including a \"%u\") for the "
"filenames in which to *save* "
"pre-blurred volumes computed for the stack");
hestOptAdd(&hopt, "ssw", "SS pos", airTypeDouble, 1, 1, &wrlSS, "0",
"\"world\"-space position (true sigma) "
"at which to sample in scale-space");
hestOptAdd(&hopt, "kssb", "kernel", airTypeOther, 1, 1, &kSSblur,
"dgauss:1,5", "blurring kernel, to sample scale space",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "kssr", "kernel", airTypeOther, 1, 1, &kSS,
"hermite", "kernel for reconstructing from scale space samples",
NULL, NULL, nrrdHestKernelSpec);
hestOptAdd(&hopt, "ssu", NULL, airTypeInt, 0, 0, &SSuniform, NULL,
"do uniform samples along sigma, and not (by default) "
"samples according to the effective diffusion scale");
hestOptAdd(&hopt, "sso", NULL, airTypeInt, 0, 0, &SSoptim, NULL,
"if not using \"-ssu\", use pre-computed optimal "
"sigmas when possible");
hestOptAdd(&hopt, "ssnd", NULL, airTypeInt, 0, 0, &SSnormd, NULL,
"normalize derivatives by scale");
hestOptAdd(&hopt, "rn", NULL, airTypeInt, 0, 0, &renorm, NULL,
"renormalize kernel weights at each new sample location. "
"\"Accurate\" kernels don't need this; doing it always "
"makes things go slower");
hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc,
"0.0", "For curvature-based queries, use zero when gradient "
"magnitude is below this");
hestOptAdd(&hopt, "ofs", "ofs", airTypeInt, 0, 0, &orientationFromSpacing,
NULL, "If only per-axis spacing is available, use that to "
"contrive full orientation info");
hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &otype, "float",
"type of output volume", NULL, nrrdType);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output volume");
hestParseOrDie(hopt, argc-1, argv+1, hparm,
me, probeInfo, AIR_TRUE, AIR_TRUE, AIR_TRUE);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestOptFree), airMopAlways);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestParseFree), airMopAlways);
what = airEnumVal(kind->enm, whatS);
if (!what) {
/* 0 indeed always means "unknown" for any gageKind */
fprintf(stderr, "%s: couldn't parse \"%s\" as measure of \"%s\" volume\n",
me, whatS, kind->name);
hestUsage(stderr, hopt, me, hparm);
hestGlossary(stderr, hopt, hparm);
airMopError(mop);
return 1;
}
/* special set-up required for DWI kind */
if (!strcmp(TEN_DWI_GAGE_KIND_NAME, kind->name)) {
if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &bval, &skip, &skipNum, nin)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing DWI info:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (skipNum) {
fprintf(stderr, "%s: sorry, can't do DWI skipping in tenDwiGage", me);
airMopError(mop); return 1;
}
/* this could stand to use some more command-line arguments */
if (tenDwiGageKindSet(kind, 50, 1, bval, 0.001, ngrad, nbmat,
tenEstimate1MethodLLS,
tenEstimate2MethodQSegLLS, seed)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble parsing DWI info:\n%s\n", me, err);
airMopError(mop); return 1;
}
}
/* for setting up pre-blurred scale-space samples */
if (numSS) {
unsigned int vi;
sbp = gageStackBlurParmNew();
airMopAdd(mop, sbp, (airMopper)gageStackBlurParmNix, airMopAlways);
ninSS = AIR_CAST(Nrrd **, calloc(numSS, sizeof(Nrrd *)));
if (!ninSS) {
fprintf(stderr, "%s: couldn't allocate ninSS", me);
airMopError(mop); return 1;
}
for (ninSSIdx=0; ninSSIdx<numSS; ninSSIdx++) {
ninSS[ninSSIdx] = nrrdNew();
airMopAdd(mop, ninSS[ninSSIdx], (airMopper)nrrdNuke, airMopAlways);
}
if (gageStackBlurParmScaleSet(sbp, numSS, rangeSS[0], rangeSS[1],
SSuniform, SSoptim)
|| gageStackBlurParmKernelSet(sbp, kSSblur)
|| gageStackBlurParmRenormalizeSet(sbp, AIR_TRUE)
|| gageStackBlurParmBoundarySet(sbp, nrrdBoundaryBleed, AIR_NAN)
|| gageStackBlurParmVerboseSet(sbp, verbose)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble with stack blur info:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (airStrlen(stackReadFormat)) {
if (nrrdLoadMulti(ninSS, numSS,
stackReadFormat, 0, NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble loading blurrings:\n%s\n", me, err);
airMopError(mop); return 1;
}
if (gageStackBlurCheck(AIR_CAST(const Nrrd *const*, ninSS),
sbp, nin, kind)) {
airMopAdd(mop, err = biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
}
} else {
if (gageStackBlur(ninSS, sbp, nin, kind)) {
