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;
}
void
CragStackCombiner::combine(const std::vector<Crag>& crags, Crag& crag) {
LOG_USER(cragstackcombinerlog)
<< "combining CRAGs, "
<< (_requireBbOverlap ? "" : " do not ")
<< "require bounding box overlap"
<< std::endl;
std::map<Crag::Node, Crag::Node> prevNodeMap;
std::map<Crag::Node, Crag::Node> nextNodeMap;
for (unsigned int z = 1; z < crags.size(); z++) {
LOG_USER(cragstackcombinerlog) << "linking CRAG " << (z-1) << " and " << z << std::endl;
if (z == 1)
prevNodeMap = copyNodes(crags[0], crag);
else
prevNodeMap = nextNodeMap;
nextNodeMap = copyNodes(crags[z], crag);
std::vector<std::pair<Crag::Node, Crag::Node>> links = findLinks(crags[z-1], crags[z]);
for (const auto& pair : links)
crag.addAdjacencyEdge(
prevNodeMap[pair.first],
nextNodeMap[pair.second]);
}
}
std::set<Crag::CragNode>
AdjacencyAnnotator::recurseAdjacencies(Crag& crag, Crag::CragNode n) {
LOG_ALL(adjacencyannotatorlog) << "recursing into node " << crag.id(n) << std::endl;
// get all leaf subnodes
std::set<Crag::CragNode> subnodes;
for (Crag::CragArc a : crag.inArcs(n)) {
std::set<Crag::CragNode> a_subnodes = recurseAdjacencies(crag, a.source());
for (Crag::CragNode s : a_subnodes)
subnodes.insert(s);
}
// for each leaf subnode adjacent to a non-subnode, add an adjacency edge to
// the non-subnode
std::set<Crag::CragNode> neighbors;
LOG_ALL(adjacencyannotatorlog) << "subnodes of " << crag.id(n) << " are:" << std::endl;
for (Crag::CragNode s : subnodes) {
LOG_ALL(adjacencyannotatorlog) << "\t" << crag.id(s) << std::endl;
for (Crag::CragEdge e : crag.adjEdges(s)) {
Crag::CragNode neighbor = e.opposite(s);
// not a subnode
if (!subnodes.count(neighbor))
neighbors.insert(neighbor);
}
}
for (Crag::CragNode neighbor : neighbors) {
LOG_ALL(adjacencyannotatorlog)
<< "adding propagated edge between "
<< crag.id(n) << " and " << crag.id(neighbor)
<< std::endl;
crag.addAdjacencyEdge(n, neighbor);
}
_numAdded += neighbors.size();
subnodes.insert(n);
LOG_ALL(adjacencyannotatorlog) << "leaving node " << crag.id(n) << std::endl;
return subnodes;
}
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);
}
void closed_set_solver() {
/**
* Subsets:
* n7
* / \
* / \
* / \
* n5 n6
* / \ / \
* n1 n2 n3 n4
*
* Adjacencies:
* n7
*
*
* d
* n5--------n6
* \ /
*
* e \ / f
*
* / \
* n1---n2----n3---n4
* a b c
*/
Crag crag;
Crag::CragNode n1 = crag.addNode();
Crag::CragNode n2 = crag.addNode();
Crag::CragNode n3 = crag.addNode();
Crag::CragNode n4 = crag.addNode();
Crag::CragNode n5 = crag.addNode();
Crag::CragNode n6 = crag.addNode();
Crag::CragNode n7 = crag.addNode();
crag.addSubsetArc(n1, n5);
crag.addSubsetArc(n2, n5);
crag.addSubsetArc(n3, n6);
crag.addSubsetArc(n4, n6);
crag.addSubsetArc(n5, n7);
crag.addSubsetArc(n6, n7);
Crag::CragEdge a = crag.addAdjacencyEdge(n1, n2);
Crag::CragEdge b = crag.addAdjacencyEdge(n2, n3);
Crag::CragEdge c = crag.addAdjacencyEdge(n3, n4);
Crag::CragEdge d = crag.addAdjacencyEdge(n5, n6);
Crag::CragEdge e = crag.addAdjacencyEdge(n5, n3);
Crag::CragEdge f = crag.addAdjacencyEdge(n2, n6);
ClosedSetSolver solver(crag);
CragSolution x(crag);
ClosedSetSolver::Status status;
{
Costs costs(crag);
costs.node[n7] = -1;
solver.setCosts(costs);
status = solver.solve(x);
BOOST_CHECK_EQUAL(status, ClosedSetSolver::SolutionFound);
// everything should be turned on
for (Crag::CragNode n : crag.nodes())
BOOST_CHECK(x.selected(n));
for (Crag::CragEdge e : crag.edges())
BOOST_CHECK(x.selected(e));
}
{
Costs costs(crag);
costs.node[n7] = 1;
costs.edge[d] = -1;
solver.setCosts(costs);
status = solver.solve(x);
BOOST_CHECK_EQUAL(status, ClosedSetSolver::SolutionFound);
// everything except n7 should be turned on
for (Crag::CragNode n : crag.nodes())
BOOST_CHECK(n != n7 ? x.selected(n) : !x.selected(n));
for (Crag::CragEdge e : crag.edges())
BOOST_CHECK(x.selected(e));
}
}
void crag_iterators() {
Crag crag;
int numNodes = 10;
for (int i = 0; i < numNodes; i++)
crag.addNode();
int numEdges = 0;
for (int i = 0; i < numNodes; i++)
for (int j = 0; j < numNodes; j++)
if (rand() > RAND_MAX/2) {
crag.addAdjacencyEdge(
crag.nodeFromId(i),
crag.nodeFromId(j));
numEdges++;
}
int numArcs = 0;
for (int i = 0; i < numNodes; i += 5) {
for (int j = i; j < i + 4; j++) {
crag.addSubsetArc(
crag.nodeFromId(j),
crag.nodeFromId(j+1));
numArcs++;
}
}
BOOST_CHECK_EQUAL(crag.nodes().size(), numNodes);
BOOST_CHECK_EQUAL(crag.edges().size(), numEdges);
BOOST_CHECK_EQUAL(crag.arcs().size(), numArcs);
numNodes = 0;
{
//UTIL_TIME_SCOPE("crag node old-school iterator");
//for (int j = 0; j < 1e8; j++)
for (Crag::CragNodeIterator i = crag.nodes().begin(); i != crag.nodes().end(); i++)
numNodes++;
}
{
//UTIL_TIME_SCOPE("crag node iterator");
//for (int j = 0; j < 1e8; j++)
for (Crag::CragNode n : crag.nodes()) {
dontWarnMeAboutUnusedVar(n);
numNodes++;
}
}
{
//UTIL_TIME_SCOPE("lemon node iterator");
//for (int j = 0; j < 1e8; j++)
for (Crag::NodeIt n(crag); n != lemon::INVALID; ++n)
numNodes -= 2;
}
BOOST_CHECK_EQUAL(numNodes, 0);
numEdges = 0;
for (Crag::CragEdge e : crag.edges()) {
dontWarnMeAboutUnusedVar(e);
numEdges++;
}
for (Crag::EdgeIt e(crag); e != lemon::INVALID; ++e)
numEdges--;
BOOST_CHECK_EQUAL(numEdges, 0);
numArcs = 0;
for (Crag::CragArc a : crag.arcs()) {
dontWarnMeAboutUnusedVar(a);
numArcs++;
}
for (Crag::SubsetArcIt a(crag); a != lemon::INVALID; ++a)
numArcs--;
BOOST_CHECK_EQUAL(numArcs, 0);
for (Crag::CragNode n : crag.nodes()) {
int numAdjEdges = 0;
for (Crag::IncEdgeIt e(crag, n); e != lemon::INVALID; ++e)
numAdjEdges++;
BOOST_CHECK_EQUAL(crag.adjEdges(n).size(), numAdjEdges);
for (Crag::CragEdge e : crag.adjEdges(n)) {
dontWarnMeAboutUnusedVar(e);
numAdjEdges--;
}
BOOST_CHECK_EQUAL(numAdjEdges, 0);
int numInArcs = 0;
for (Crag::SubsetInArcIt a(crag, crag.toSubset(n)); a != lemon::INVALID; ++a)
numInArcs++;
BOOST_CHECK_EQUAL(numInArcs, crag.inArcs(n).size());
for (Crag::CragArc a : crag.inArcs(n)) {
dontWarnMeAboutUnusedVar(a);
numInArcs--;
}
BOOST_CHECK_EQUAL(numInArcs, 0);
int numOutArcs = 0;
for (Crag::SubsetOutArcIt a(crag, crag.toSubset(n)); a != lemon::INVALID; ++a)
numOutArcs++;
BOOST_CHECK_EQUAL(numOutArcs, crag.outArcs(n).size());
for (Crag::CragArc a : crag.outArcs(n)) {
dontWarnMeAboutUnusedVar(a);
numOutArcs--;
}
BOOST_CHECK_EQUAL(numOutArcs, 0);
Crag::CragEdgeIterator cei = crag.edges().begin();
Crag::EdgeIt ei(crag);
while (ei != lemon::INVALID) {
BOOST_CHECK((Crag::RagType::Node)((*cei).u()) == crag.getAdjacencyGraph().u(ei));
BOOST_CHECK((Crag::RagType::Node)((*cei).v()) == crag.getAdjacencyGraph().v(ei));
++cei;
++ei;
}
Crag::CragArcIterator cai = crag.arcs().begin();
Crag::SubsetArcIt ai(crag);
while (ai != lemon::INVALID) {
BOOST_CHECK(crag.toSubset((*cai).source()) == crag.getSubsetGraph().source(ai));
BOOST_CHECK(crag.toSubset((*cai).target()) == crag.getSubsetGraph().target(ai));
++cai;
++ai;
}
}
}
