/* *************************************************************** */
void reg_io_writeNRRDfile(Nrrd *image, const char *filename)
{
// Set the encoding to gziped as it is compiled as part of the NiftyReg project
NrrdIoState *nio=nrrdIoStateNew();
if (nrrdEncodingGzip->available()){
nrrdIoStateEncodingSet(nio, nrrdEncodingGzip);
nrrdIoStateSet(nio, nrrdIoStateZlibLevel, 9);
}
else{
fprintf(stderr, "[NiftyReg ERROR] Can not compress the file: \"%s\"\n", filename);
}
char *err;
if (nrrdSave(filename, image, nio)){
err = biffGetDone(NRRD);
fprintf(stderr, "[NiftyReg ERROR] Can not write the file \"%s\":\n%s\n", filename, err);
free(err);
exit(1);
}
return;
}
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;
}
