std::list<Chunk> Chunk::autoSplice ( uint32_t acquisitionNumberStride )const
{
if ( !isValid() ) {
LOG( Runtime, error ) << "Cannot splice invalid Chunk (missing properties are " << this->getMissing() << ")";
return std::list<Chunk>();
}
util::fvector3 offset;
const util::fvector3 voxelSize = propertyValue( "voxelSize" ).castTo<util::fvector3>();
util::fvector3 voxelGap;
if( hasProperty( "voxelGap" ) )
voxelGap = propertyValue( "voxelGap" ).castTo<util::fvector3>();
const util::fvector3 distance = voxelSize + voxelGap;
size_t atDim = getRelevantDims() - 1;
LOG_IF( atDim < data::timeDim && distance[atDim] == 0, Runtime, error ) << "The voxel distance (voxelSize + voxelGap) at the splicing direction (" << atDim << ") is zero. This will likely cause errors in the Images structure.";
switch( atDim ) { // init offset with the given direction
case rowDim :
offset = this->propertyValue( "rowVec" ).castTo<util::fvector3>();
break;
case columnDim:
offset = this->propertyValue( "columnVec" ).castTo<util::fvector3>();
break;
case sliceDim:
if( this->hasProperty( "sliceVec" ) ) {
offset = this->propertyValue( "sliceVec" ).castTo<util::fvector3>();
} else {
const util::fvector3 &row = this->propertyValue( "rowVec" ).castTo<util::fvector3>();
const util::fvector3 &column = this->propertyValue( "columnVec" ).castTo<util::fvector3>();
assert( util::fuzzyEqual<float>( row.sqlen(), 1 ) );
assert( util::fuzzyEqual<float>( column.sqlen(), 1 ) );
offset[0] = row[1] * column[2] - row[2] * column[1];
offset[1] = row[2] * column[0] - row[0] * column[2];
offset[2] = row[0] * column[1] - row[1] * column[0];
}
break;
case timeDim :
LOG_IF( acquisitionNumberStride == 0, Debug, error ) << "Splicing at timeDim without acquisitionNumberStride will very likely make the next reIndex() fail";
}
// prepare some attributes
const util::fvector3 indexOriginOffset = atDim < data::timeDim ? offset * distance[atDim] : util::fvector3();
LOG( Debug, info ) << "Splicing chunk at dimenstion " << atDim + 1 << " with indexOrigin stride " << indexOriginOffset << " and acquisitionNumberStride " << acquisitionNumberStride;
std::list<Chunk> ret = splice( ( dimensions )atDim ); // do low level splice - get the chunklist
std::list<Chunk>::iterator it = ret.begin();
it++;// skip the first one
for( size_t cnt = 1; it != ret.end(); it++, cnt++ ) { // adapt some metadata in them
util::fvector3 &orig = it->propertyValue( "indexOrigin" ).castTo<util::fvector3>();
if( orig == ret.front().getPropertyAs<util::fvector3>( "indexOrigin" ) ) { // fix pos if its the same as for the first
LOG( Debug, verbose_info ) << "Origin was " << orig << " will be moved by " << indexOriginOffset << "*" << cnt;
orig = orig + indexOriginOffset * ( float )cnt;
}
uint32_t &acq = it->propertyValue( "acquisitionNumber" ).castTo<uint32_t>();//@todo acquisitionTime needs to be fixed as well
if( acq == ret.front().getPropertyAs<uint32_t>( "acquisitionNumber" ) ) {
LOG( Debug, verbose_info ) << "acquisitionNumber was " << acq << " will be moved by " << acquisitionNumberStride << "*" << cnt;
acq += acquisitionNumberStride * cnt; //@todo this might cause trouble if we try to insert this chunks into an image
}
}
return ret;
}
std::list<Chunk> Chunk::autoSplice ( uint32_t acquisitionNumberStride )const
{
if ( !isValid() ) {
LOG( Runtime, error ) << "Cannot splice invalid Chunk (missing properties are " << this->getMissing() << ")";
return std::list<Chunk>();
}
util::fvector4 offset;
const util::fvector4 voxelSize = propertyValue( "voxelSize" ).castTo<util::fvector4>();
util::fvector4 voxelGap;
if( hasProperty( "voxelGap" ) )
voxelGap = propertyValue( "voxelGap" ).castTo<util::fvector4>();
const util::fvector4 distance = voxelSize + voxelGap;
size_t atDim = getRelevantDims() - 1;
switch( atDim ) { // init offset with the given direction
case rowDim :
offset = this->propertyValue( "rowVec" ).castTo<util::fvector4>();
break;
case columnDim:
offset = this->propertyValue( "columnVec" ).castTo<util::fvector4>();
break;
case sliceDim:
if( this->hasProperty( "sliceVec" ) ) {
offset = this->propertyValue( "sliceVec" ).castTo<util::fvector4>();
} else {
const util::fvector4 row = this->propertyValue( "rowVec" ).castTo<util::fvector4>();
const util::fvector4 column = this->propertyValue( "columnVec" ).castTo<util::fvector4>();
assert( util::fuzzyEqual<float>( row.sqlen(), 1 ) );
assert( util::fuzzyEqual<float>( column.sqlen(), 1 ) );
offset[0] = row[1] * column[2] - row[2] * column[1];
offset[1] = row[2] * column[0] - row[0] * column[2];
offset[2] = row[0] * column[1] - row[1] * column[0];
}
break;
case timeDim :
offset = util::fvector4( 0, 0, 0, 1 );
}
// prepare some attributes
assert( util::fuzzyEqual<float>( offset.sqlen(), 1 ) ); // it should be norm here
const util::fvector4 indexOriginOffset = offset * distance[atDim];
LOG( Debug, info ) << "Splicing chunk at dimenstion " << atDim + 1 << " with indexOrigin stride " << indexOriginOffset << " and acquisitionNumberStride " << acquisitionNumberStride;
std::list<Chunk> ret = splice( ( dimensions )atDim ); // do low level splice - get the chunklist
std::list<Chunk>::iterator it = ret.begin();
it++;// skip the first one
for( size_t cnt = 1; it != ret.end(); it++, cnt++ ) { // adapt some metadata in them
util::fvector4 &orig = it->propertyValue( "indexOrigin" ).castTo<util::fvector4>();
if( orig == ret.front().getPropertyAs<util::fvector4>( "indexOrigin" ) ) { // fix pos if its the same as for the first
LOG( Debug, verbose_info ) << "Origin was " << orig << " will be moved by " << indexOriginOffset << "*" << cnt;
orig = orig + indexOriginOffset * ( float )cnt;
}
uint32_t &acq = it->propertyValue( "acquisitionNumber" ).castTo<uint32_t>();
if( acq == ret.front().getPropertyAs<uint32_t>( "acquisitionNumber" ) ) {
LOG( Debug, verbose_info ) << "acquisitionNumber was " << acq << " will be moved by " << acquisitionNumberStride << "*" << cnt;
acq += acquisitionNumberStride * cnt; //@todo this might cause trouble if we try to insert this chunks into an image
}
}
return ret;
}
