bool ListReaderH5::GetCellKIJ (T *a_) const
{
std::pair<int, int> myPair(0, m_nRows);
VEC_INT_PAIR indices(1, myPair);
CStr str(m_path);
str += "/";
str += CELLIDS;
H5DataSetReader r(m_file, str, indices);
CellIdToIJK g(m_nGridRows, m_nGridCols);
std::vector<int> cellIds(m_nRows, 0);
if (!r.GetData(&cellIds[0], cellIds.size()))
return false;
for (size_t i=0; i<cellIds.size(); i++)
{
a_[i*m_nFields] = (T)g.KFromId(cellIds.at(i));
a_[i*m_nFields+1] = (T)g.IFromId(cellIds.at(i));
a_[i*m_nFields+2] = (T)g.JFromId(cellIds.at(i));
}
return true;
} // ListReaderH5::GetCellKIJ
/* Read the cellIDs into an array */
std::vector<uint64_t> readCellIds(vlsvinterface::Reader& r) {
uint64_t arraySize=0;
uint64_t vectorSize=0;
uint64_t byteSize=0;
vlsv::datatype::type dataType;
std::list<std::pair<std::string,std::string> > attribs;
attribs.push_back(std::pair<std::string,std::string>("name","CellID"));
if( r.getArrayInfo("VARIABLE",attribs, arraySize,vectorSize,dataType,byteSize) == false ) {
std::cerr << "getArrayInfo returned false when trying to read CellID VARIABLE." << std::endl;
exit(1);
}
if(dataType != vlsv::datatype::type::UINT || byteSize != 8 || vectorSize != 1) {
std::cerr << "Datatype of CellID VARIABLE entries is not uint64_t." << std::endl;
exit(1);
}
/* Allocate memory for the cellIds */
std::vector<uint64_t> cellIds(arraySize*vectorSize);
if( r.readArray("VARIABLE",attribs,0,arraySize,(char*) cellIds.data()) == false) {
std::cerr << "readArray faied when trying to read CellID Variable." << std::endl;
exit(1);
}
return cellIds;
}
void
TolerantEditDistance::extractCells() {
if (_groundTruth->size() != _reconstruction->size())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("ground truth and reconstruction have different size") << STACK_TRACE);
if (_groundTruth->height() != _reconstruction->height() || _groundTruth->width() != _reconstruction->width())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("ground truth and reconstruction have different size") << STACK_TRACE);
_depth = _groundTruth->size();
_width = _groundTruth->width();
_height = _groundTruth->height();
LOG_ALL(tedlog) << "extracting cells in " << _width << "x" << _height << "x" << _depth << " volume" << std::endl;
vigra::MultiArray<3, std::pair<float, float> > gtAndRec(vigra::Shape3(_width, _height, _depth));
vigra::MultiArray<3, unsigned int> cellIds(vigra::Shape3(_width, _height, _depth));
// prepare gt and rec image
for (unsigned int z = 0; z < _depth; z++) {
boost::shared_ptr<Image> gt = (*_groundTruth)[z];
boost::shared_ptr<Image> rec = (*_reconstruction)[z];
for (unsigned int x = 0; x < _width; x++)
for (unsigned int y = 0; y < _height; y++) {
float gtLabel = (*gt)(x, y);
float recLabel = (*rec)(x, y);
gtAndRec(x, y, z) = std::make_pair(gtLabel, recLabel);
}
}
// find connected components in gt and rec image
cellIds = 0;
_numCells = vigra::labelMultiArray(gtAndRec, cellIds);
LOG_DEBUG(tedlog) << "found " << _numCells << " cells" << std::endl;
// let tolerance function extract cells from that
_toleranceFunction->extractCells(
_numCells,
cellIds,
*_reconstruction,
*_groundTruth);
LOG_ALL(tedlog)
<< "found "
<< _toleranceFunction->getGroundTruthLabels().size()
<< " ground truth labels and "
<< _toleranceFunction->getReconstructionLabels().size()
<< " reconstruction labels"
<< std::endl;
}
