int
main() {
airArray *mop, *submop;
char *err;
int typi;
unsigned int supi, probePass, cti /* context copy index */,
pvlIdx[NRRD_TYPE_MAX+1], sx, sy, sz, subnum;
size_t sizes[3] = {42,61,50} /* one of these must be even */,
ii, nn;
Nrrd *norigScl, *nucharScl, *nunquant, *nqdiff,
*nconvScl[NRRD_TYPE_MAX+1];
unsigned char *ucharScl;
gageContext *gctx[2][KERN_SIZE_MAX+1];
gagePerVolume *gpvl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1];
const double *vansScl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1],
*gansScl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1],
*hansScl[2][NRRD_TYPE_MAX+1][KERN_SIZE_MAX+1];
double *origScl, omin, omax, dsx, dsy, dsz,
spcOrig[NRRD_SPACE_DIM_MAX] = {0.0, 0.0, 0.0},
spcVec[3][NRRD_SPACE_DIM_MAX] = {
{1.1, 0.0, 0.0},
{0.0, 2.2, 0.0},
{0.0, 0.0, 3.3}};
mop = airMopNew();
#define NRRD_NEW(name, mop) \
(name) = nrrdNew(); \
airMopAdd((mop), (name), (airMopper)nrrdNuke, airMopAlways)
/* --------------------------------------------------------------- */
/* Creating initial volume */
NRRD_NEW(norigScl, mop);
if (nrrdMaybeAlloc_nva(norigScl, nrrdTypeDouble, 3, sizes)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "trouble allocating:\n%s", err);
airMopError(mop); return 1;
}
origScl = AIR_CAST(double *, norigScl->data);
nn = nrrdElementNumber(norigScl);
airSrandMT(42*42);
for (ii=0; ii<nn/2; ii++) {
airNormalRand(origScl + 2*ii + 0, origScl + 2*ii + 1);
}
/* learn real range */
omin = omax = origScl[0];
for (ii=1; ii<nn; ii++) {
omin = AIR_MIN(omin, origScl[ii]);
omax = AIR_MAX(omax, origScl[ii]);
}
ELL_3V_SET(spcOrig, 0.0, 0.0, 0.0);
if (nrrdSpaceSet(norigScl, nrrdSpaceRightAnteriorSuperior)
|| nrrdSpaceOriginSet(norigScl, spcOrig)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "trouble setting space:\n%s", err);
airMopError(mop); return 1;
}
nrrdAxisInfoSet_nva(norigScl, nrrdAxisInfoSpaceDirection, spcVec);
dsx = AIR_CAST(double, sizes[0]);
dsy = AIR_CAST(double, sizes[1]);
dsz = AIR_CAST(double, sizes[2]);
sx = AIR_CAST(unsigned int, sizes[0]);
sy = AIR_CAST(unsigned int, sizes[1]);
sz = AIR_CAST(unsigned int, sizes[2]);
subnum = AIR_CAST(unsigned int, PROBE_NUM*0.9);
/* --------------------------------------------------------------- */
/* Quantizing to 8-bits and checking */
submop = airMopNew();
NRRD_NEW(nucharScl, mop);
NRRD_NEW(nunquant, submop);
NRRD_NEW(nqdiff, submop);
if (nrrdQuantize(nucharScl, norigScl, NULL, 8)
|| nrrdUnquantize(nunquant, nucharScl, nrrdTypeDouble)
|| nrrdArithBinaryOp(nqdiff, nrrdBinaryOpSubtract,
norigScl, nunquant)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "trouble quantizing and back:\n%s", err);
airMopError(submop); airMopError(mop); return 1;
}
if (!( nucharScl->oldMin == omin
&& nucharScl->oldMax == omax )) {
fprintf(stderr, "quantization range [%g,%g] != real range [%g,%g]\n",
nucharScl->oldMin, nucharScl->oldMax, omin, omax);
airMopError(submop); airMopError(mop); return 1;
}
{
double *qdiff, *unquant;
/* empirically determined tolerance, which had to be increased in
order to work under valgrind (!)- perhaps because of a
difference in the use of 80-bit registers */
double epsilon=0.50000000000004;
qdiff = AIR_CAST(double *, nqdiff->data);
unquant = AIR_CAST(double *, nunquant->data);
for (ii=0; ii<nn; ii++) {
double dd;
/* with infinite precision, the max difference between original and
quantized values should be exactly half the width (in value)
of 1/256 of value range ==> dd = 0.5 */
dd = qdiff[ii]*256/(omax - omin);
if (AIR_ABS(dd) > epsilon) {
unsigned int ui;
ui = AIR_CAST(unsigned int, ii);
fprintf(stderr, "|orig[%u]=%.17g - unquant=%.17g|*256/%.17g "
"= %.17g > %.17g!\n", ui, origScl[ii], unquant[ii],
omax - omin, AIR_ABS(dd), epsilon);
airMopError(submop); airMopError(mop); return 1;
}
}
}
int
tend_helixMain(int argc, char **argv, char *me, hestParm *hparm) {
int pret;
hestOpt *hopt = NULL;
char *perr, *err;
airArray *mop;
int size[3], nit;
Nrrd *nout;
double R, r, S, bnd, angle, ev[3], ip[3], iq[4], mp[3], mq[4], tmp[9],
orig[3], i2w[9], rot[9], mf[9], spd[4][3], bge;
char *outS;
hestOptAdd(&hopt, "s", "size", airTypeInt, 3, 3, size, NULL,
"sizes along fast, medium, and slow axes of the sampled volume, "
"often called \"X\", \"Y\", and \"Z\". It is best to use "
"slightly different sizes here, to expose errors in interpreting "
"axis ordering (e.g. \"-s 39 40 41\")");
hestOptAdd(&hopt, "ip", "image orientation", airTypeDouble, 3, 3, ip,
"0 0 0",
"quaternion quotient space orientation of image");
hestOptAdd(&hopt, "mp", "measurement orientation", airTypeDouble, 3, 3, mp,
"0 0 0",
"quaternion quotient space orientation of measurement frame");
hestOptAdd(&hopt, "b", "boundary", airTypeDouble, 1, 1, &bnd, "10",
"parameter governing how fuzzy the boundary between high and "
"low anisotropy is. Use \"-b 0\" for no fuzziness");
hestOptAdd(&hopt, "r", "little radius", airTypeDouble, 1, 1, &r, "30",
"(minor) radius of cylinder tracing helix");
hestOptAdd(&hopt, "R", "big radius", airTypeDouble, 1, 1, &R, "50",
"(major) radius of helical turns");
hestOptAdd(&hopt, "S", "spacing", airTypeDouble, 1, 1, &S, "100",
"spacing between turns of helix (along its axis)");
hestOptAdd(&hopt, "a", "angle", airTypeDouble, 1, 1, &angle, "60",
"maximal angle of twist of tensors along path. There is no "
"twist at helical core of path, and twist increases linearly "
"with radius around this path. Positive twist angle with "
"positive spacing resulting in a right-handed twist around a "
"right-handed helix. ");
hestOptAdd(&hopt, "nit", NULL, airTypeInt, 0, 0, &nit, NULL,
"changes behavior of twist angle as function of distance from "
"center of helical core: instead of increasing linearly as "
"describe above, be at a constant angle");
hestOptAdd(&hopt, "ev", "eigenvalues", airTypeDouble, 3, 3, ev,
"0.006 0.002 0.001",
"eigenvalues of tensors (in order) along direction of coil, "
"circumferential around coil, and radial around coil. ");
hestOptAdd(&hopt, "bg", "background", airTypeDouble, 1, 1, &bge, "0.5",
"eigenvalue of isotropic background");
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output file");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_helixInfoL);
JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7),
AIR_CAST(size_t, size[0]),
AIR_CAST(size_t, size[1]),
AIR_CAST(size_t, size[2]))) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble allocating output:\n%s\n", me, err);
airMopError(mop); return 1;
}
ELL_4V_SET(iq, 1.0, ip[0], ip[1], ip[2]);
ell_q_to_3m_d(rot, iq);
ELL_3V_SET(orig,
-2*R + 2*R/size[0],
-2*R + 2*R/size[1],
-2*R + 2*R/size[2]);
ELL_3M_ZERO_SET(i2w);
ELL_3M_DIAG_SET(i2w, 4*R/size[0], 4*R/size[1], 4*R/size[2]);
ELL_3MV_MUL(tmp, rot, orig);
ELL_3V_COPY(orig, tmp);
ELL_3M_MUL(tmp, rot, i2w);
ELL_3M_COPY(i2w, tmp);
ELL_4V_SET(mq, 1.0, mp[0], mp[1], mp[2]);
ell_q_to_3m_d(mf, mq);
tend_helixDoit(nout, bnd,
orig, i2w, mf,
r, R, S, angle*AIR_PI/180, !nit, ev, bge);
nrrdSpaceSet(nout, nrrdSpaceRightAnteriorSuperior);
nrrdSpaceOriginSet(nout, orig);
ELL_3V_SET(spd[0], AIR_NAN, AIR_NAN, AIR_NAN);
ELL_3MV_COL0_GET(spd[1], i2w);
ELL_3MV_COL1_GET(spd[2], i2w);
ELL_3MV_COL2_GET(spd[3], i2w);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoSpaceDirection,
spd[0], spd[1], spd[2], spd[3]);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoCenter,
nrrdCenterUnknown, nrrdCenterCell,
nrrdCenterCell, nrrdCenterCell);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoKind,
nrrdKind3DMaskedSymMatrix, nrrdKindSpace,
nrrdKindSpace, nrrdKindSpace);
nout->measurementFrame[0][0] = mf[0];
nout->measurementFrame[1][0] = mf[1];
nout->measurementFrame[2][0] = mf[2];
nout->measurementFrame[0][1] = mf[3];
nout->measurementFrame[1][1] = mf[4];
nout->measurementFrame[2][1] = mf[5];
nout->measurementFrame[0][2] = mf[6];
nout->measurementFrame[1][2] = mf[7];
nout->measurementFrame[2][2] = mf[8];
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
}
int NrrdWriter(HxUniformScalarField3* field, const char* filename, int encoding)
{
// Identify data type
int nrrdType = nrrdTypeUnknown;
switch ( field->primType() )
{
case McPrimType::mc_uint8: nrrdType = nrrdTypeUChar; break;
case McPrimType::mc_int8: nrrdType = nrrdTypeChar; break;
case McPrimType::mc_uint16: nrrdType = nrrdTypeUShort; break;
case McPrimType::mc_int16: nrrdType = nrrdTypeShort; break;
case McPrimType::mc_int32: nrrdType = nrrdTypeInt; break;
case McPrimType::mc_float: nrrdType = nrrdTypeFloat; break;
case McPrimType::mc_double: nrrdType = nrrdTypeDouble; break;
default: break;
}
if(nrrdType == nrrdTypeUnknown)
{
theMsg->printf("ERROR: unsupported output type: %s for nrrd",field->primType().getName());
return 0;
}
void* data = field->lattice.dataPtr();
Nrrd *nrrd = nrrdNew();
NrrdIoState *nios = nrrdIoStateNew();
if ( encoding == nrrdEncodingTypeGzip) {
if (nrrdEncodingGzip->available() )
{
nrrdIoStateEncodingSet( nios, nrrdEncodingGzip );
nrrdIoStateSet( nios, nrrdIoStateZlibLevel, 9 );
}
else theMsg->printf("WARNING: Nrrd library does not support Gzip compression encoding.\n Make sure Teem_ZLIB is on in CMAKE when building Nrrd library.\n");
} else if ( encoding == nrrdEncodingTypeBzip2) {
if (nrrdEncodingBzip2->available() )
{
nrrdIoStateEncodingSet( nios, nrrdEncodingBzip2 );
// nrrdIoStateSet( nios, nrrdIoStateBzip2BlockSize, 9 );
}
else theMsg->printf("WARNING: Nrrd library does not support Bzip2 compression encoding.\n Make sure Teem_BZIP2 is on in CMAKE when building Nrrd library.\n");
} else if ( encoding == nrrdEncodingTypeAscii) {
nrrdIoStateEncodingSet( nios, nrrdEncodingAscii );
} else {
theMsg->printf("ERROR: Unimplemented nrrd encoding type: %d\n",encoding);
return 0;
}
try
{
if ( nrrdWrap_va( nrrd, data, nrrdType, (size_t)3,
(size_t)field->lattice.dimsInt()[0],
(size_t)field->lattice.dimsInt()[1],
(size_t)field->lattice.dimsInt()[2] ) )
{
throw( biffGetDone(NRRD) );
}
nrrdSpaceDimensionSet( nrrd, 3 );
// TODO: Would be nice to set space units. How does Amira store this?
// if ( writeVolume->MetaKeyExists(CMTK_META_SPACE_UNITS_STRING) )
// {
// nrrd->spaceUnits[0] = strdup( writeVolume->m_MetaInformation[CMTK_META_SPACE_UNITS_STRING].c_str() );
// nrrd->spaceUnits[1] = strdup( writeVolume->m_MetaInformation[CMTK_META_SPACE_UNITS_STRING].c_str() );
// nrrd->spaceUnits[2] = strdup( writeVolume->m_MetaInformation[CMTK_META_SPACE_UNITS_STRING].c_str() );
// }
int kind[NRRD_DIM_MAX] = { nrrdKindDomain, nrrdKindDomain, nrrdKindDomain };
nrrdAxisInfoSet_nva( nrrd, nrrdAxisInfoKind, kind );
// TODO: Would be nice to write some kind of space if this exists
// Fetch bounding box information and voxel size
float* bbox = field->bbox();
McVec3f voxelSize = field->getVoxelSize();
// Just deal with space directions orthogonal to data axes
// TODO: Fetch transformation and use that
double spaceDir[NRRD_DIM_MAX][NRRD_SPACE_DIM_MAX];
for ( int i = 0; i < 3; ++i )
{
for ( int j = 0; j < 3; ++j )
{
if (i == j) spaceDir[i][j] = (double) voxelSize[i];
else spaceDir[i][j] = 0.0; // Can't assume that memory is zeroed
}
}
nrrdAxisInfoSet_nva( nrrd, nrrdAxisInfoSpaceDirection, spaceDir );
double origin[NRRD_DIM_MAX] = { bbox[0], bbox[2], bbox[4] };
if ( nrrdSpaceOriginSet( nrrd, origin ) )
{
throw( biffGetDone(NRRD) );
}
nrrdAxisInfoSet_va( nrrd, nrrdAxisInfoLabel, "x", "y", "z" );
if ( nrrdSave( filename, nrrd, nios ) )
{
throw( biffGetDone(NRRD) );
}
}
catch ( char* err )
{
theMsg->printf("ERROR: hxNrrdIO library returned error '%s'\n", err);
free( err );
return 0;
}
nrrdIoStateNix( nios );
nrrdNix(nrrd);
return 1;
}
