std::map<Crag::Node, Crag::Node>
CragStackCombiner::copyNodes(const Crag& source, Crag& target) {
std::map<Crag::Node, Crag::Node> nodeMap;
for (Crag::NodeIt i(source); i != lemon::INVALID; ++i) {
Crag::Node n = target.addNode();
ExplicitVolume<unsigned char> volume = source.getVolume(i);
if (!volume.getBoundingBox().isZero())
target.getVolume(n) = volume;
nodeMap[i] = n;
}
for (Crag::EdgeIt e(source); e != lemon::INVALID; ++e) {
Crag::Node u = nodeMap[source.u(e)];
Crag::Node v = nodeMap[source.v(e)];
target.addAdjacencyEdge(u, v);
}
for (Crag::SubsetArcIt a(source); a != lemon::INVALID; ++a) {
Crag::Node s = nodeMap[source.toRag(source.getSubsetGraph().source(a))];
Crag::Node t = nodeMap[source.toRag(source.getSubsetGraph().target(a))];
target.addSubsetArc(s, t);
}
return nodeMap;
}
std::vector<std::pair<Crag::Node, Crag::Node>>
CragStackCombiner::findLinks(const Crag& a, const Crag& b) {
UTIL_TIME_METHOD;
HausdorffDistance hausdorff(a, b, 100);
std::vector<std::pair<Crag::Node, Crag::Node>> links;
for (Crag::NodeIt i(a); i != lemon::INVALID; ++i) {
LOG_DEBUG(cragstackcombinerlog) << "checking for links of node " << a.id(i) << std::endl;
for (Crag::NodeIt j(b); j != lemon::INVALID; ++j) {
if (_requireBbOverlap) {
util::box<float, 2> bb_i = a.getVolume(i).getBoundingBox().project<2>();
util::box<float, 2> bb_j = b.getVolume(j).getBoundingBox().project<2>();
if (!bb_i.intersects(bb_j))
continue;
}
double i_j, j_i;
hausdorff.distance(i, j, i_j, j_i);
double distance = std::min(i_j, j_i);
if (distance <= _maxDistance)
links.push_back(std::make_pair(i, j));
}
}
return links;
}
void
PlanarAdjacencyAnnotator::annotate(Crag& crag) {
if (optionCragType.as<std::string>() == "empty")
return;
UTIL_TIME_METHOD;
util::box<float, 3> cragBB = crag.getBoundingBox();
util::point<float, 3> resolution;
for (Crag::NodeIt n(crag); n != lemon::INVALID; ++n) {
if (!crag.isLeafNode(n))
continue;
resolution = crag.getVolume(n).getResolution();
break;
}
// no nodes?
if (resolution.isZero())
return;
// create a vigra multi-array large enough to hold all volumes
vigra::MultiArray<3, int> ids(
vigra::Shape3(
cragBB.width() /resolution.x(),
cragBB.height()/resolution.y(),
cragBB.depth() /resolution.z()),
std::numeric_limits<int>::max());
for (Crag::NodeIt n(crag); n != lemon::INVALID; ++n) {
if (!crag.isLeafNode(n))
continue;
const util::point<float, 3>& volumeOffset = crag.getVolume(n).getOffset();
const util::box<unsigned int, 3>& volumeDiscreteBB = crag.getVolume(n).getDiscreteBoundingBox();
util::point<unsigned int, 3> begin = (volumeOffset - cragBB.min())/resolution;
util::point<unsigned int, 3> end = begin +
util::point<unsigned int, 3>(
volumeDiscreteBB.width(),
volumeDiscreteBB.height(),
volumeDiscreteBB.depth());
vigra::combineTwoMultiArrays(
crag.getVolume(n).data(),
ids.subarray(
vigra::Shape3(
begin.x(),
begin.y(),
begin.z()),
vigra::Shape3(
end.x(),
end.y(),
end.z())),
ids.subarray(
vigra::Shape3(
begin.x(),
begin.y(),
begin.z()),
vigra::Shape3(
end.x(),
end.y(),
end.z())),
vigra::functor::ifThenElse(
vigra::functor::Arg1() == vigra::functor::Param(1),
vigra::functor::Param(crag.id(n)),
vigra::functor::Arg2()
));
}
//vigra::exportImage(
//ids.bind<2>(0),
//vigra::ImageExportInfo("debug/ids.tif"));
typedef vigra::GridGraph<3> GridGraphType;
typedef vigra::AdjacencyListGraph RagType;
GridGraphType grid(
ids.shape(),
_neighborhood == Direct ? vigra::DirectNeighborhood : vigra::IndirectNeighborhood);
RagType rag;
RagType::EdgeMap<std::vector<GridGraphType::Edge>> affiliatedEdges;
vigra::makeRegionAdjacencyGraph(
grid,
ids,
rag,
affiliatedEdges,
std::numeric_limits<int>::max());
unsigned int numAdded = 0;
crag.setGridGraph(grid);
for (RagType::EdgeIt e(rag); e != lemon::INVALID; ++e) {
int u = rag.id(rag.u(*e));
int v = rag.id(rag.v(*e));
Crag::Edge newEdge = crag.addAdjacencyEdge(
crag.nodeFromId(u),
crag.nodeFromId(v));
crag.setAffiliatedEdges(
newEdge,
affiliatedEdges[*e]);
numAdded++;
LOG_ALL(planaradjacencyannotatorlog)
<< "adding leaf node adjacency between "
<< u << " and " << v << std::endl;
}
LOG_USER(planaradjacencyannotatorlog)
<< "added " << numAdded << " leaf node adjacency edges"
<< std::endl;
if (optionCragType.as<std::string>() == "full")
propagateLeafAdjacencies(crag);
}