DualTreeKMeansStatistic(TreeType& node) :
neighbor::NeighborSearchStat<neighbor::NearestNeighborSort>(),
upperBound(DBL_MAX),
lowerBound(DBL_MAX),
owner(size_t(-1)),
pruned(size_t(-1)),
staticPruned(false),
staticUpperBoundMovement(0.0),
staticLowerBoundMovement(0.0),
trueParent(node.Parent())
{
// Empirically calculate the centroid.
centroid.zeros(node.Dataset().n_rows);
for (size_t i = 0; i < node.NumPoints(); ++i)
{
// Correct handling of cover tree: don't double-count the point which
// appears in the children.
if (tree::TreeTraits<TreeType>::HasSelfChildren && i == 0 &&
node.NumChildren() > 0)
continue;
centroid += node.Dataset().col(node.Point(i));
}
for (size_t i = 0; i < node.NumChildren(); ++i)
centroid += node.Child(i).NumDescendants() *
node.Child(i).Stat().Centroid();
centroid /= node.NumDescendants();
// Set the true children correctly.
trueChildren.resize(node.NumChildren());
for (size_t i = 0; i < node.NumChildren(); ++i)
trueChildren[i] = &node.Child(i);
}
inline double KDERules<MetricType, KernelType, TreeType>::
Score(const size_t queryIndex, TreeType& referenceNode)
{
double score, maxKernel, minKernel, bound;
const arma::vec& queryPoint = querySet.unsafe_col(queryIndex);
const double minDistance = referenceNode.MinDistance(queryPoint);
bool newCalculations = true;
if (tree::TreeTraits<TreeType>::FirstPointIsCentroid &&
lastQueryIndex == queryIndex &&
traversalInfo.LastReferenceNode() != NULL &&
traversalInfo.LastReferenceNode()->Point(0) == referenceNode.Point(0))
{
// Don't duplicate calculations.
newCalculations = false;
lastQueryIndex = queryIndex;
lastReferenceIndex = referenceNode.Point(0);
}
else
{
// Calculations are new.
maxKernel = kernel.Evaluate(minDistance);
minKernel = kernel.Evaluate(referenceNode.MaxDistance(queryPoint));
bound = maxKernel - minKernel;
}
if (newCalculations &&
bound <= (absError + relError * minKernel) / referenceSet.n_cols)
{
// Estimate values.
double kernelValue;
// Calculate kernel value based on reference node centroid.
if (tree::TreeTraits<TreeType>::FirstPointIsCentroid)
{
kernelValue = EvaluateKernel(queryIndex, referenceNode.Point(0));
}
else
{
kde::KDEStat& referenceStat = referenceNode.Stat();
kernelValue = EvaluateKernel(queryPoint, referenceStat.Centroid());
}
densities(queryIndex) += referenceNode.NumDescendants() * kernelValue;
// Don't explore this tree branch.
score = DBL_MAX;
}
else
{
score = minDistance;
}
++scores;
traversalInfo.LastReferenceNode() = &referenceNode;
traversalInfo.LastScore() = score;
return score;
}
PellegMooreKMeansStatistic(TreeType& node)
{
centroid.zeros(node.Dataset().n_rows);
// Hope it's a depth-first build procedure. Also, this won't work right for
// trees that have self-children or stuff like that.
for (size_t i = 0; i < node.NumChildren(); ++i)
{
centroid += node.Child(i).NumDescendants() *
node.Child(i).Stat().Centroid();
}
for (size_t i = 0; i < node.NumPoints(); ++i)
{
centroid += node.Dataset().col(node.Point(i));
}
if (node.NumDescendants() > 0)
centroid /= node.NumDescendants();
else
centroid.fill(DBL_MAX); // Invalid centroid. What else can we do?
}
void RangeSearchRules<MetricType, TreeType>::AddResult(const size_t queryIndex,
TreeType& referenceNode)
{
// Some types of trees calculate the base case evaluation before Score() is
// called, so if the base case has already been calculated, then we must avoid
// adding that point to the results again.
size_t baseCaseMod = 0;
if (tree::TreeTraits<TreeType>::FirstPointIsCentroid &&
(queryIndex == lastQueryIndex) &&
(referenceNode.Point(0) == lastReferenceIndex))
{
baseCaseMod = 1;
}
// Resize distances and neighbors vectors appropriately. We have to use
// reserve() and not resize(), because we don't know if we will encounter the
// case where the datasets and points are the same (and we skip in that case).
const size_t oldSize = neighbors[queryIndex].size();
neighbors[queryIndex].reserve(oldSize + referenceNode.NumDescendants() -
baseCaseMod);
distances[queryIndex].reserve(oldSize + referenceNode.NumDescendants() -
baseCaseMod);
for (size_t i = baseCaseMod; i < referenceNode.NumDescendants(); ++i)
{
if ((&referenceSet == &querySet) &&
(queryIndex == referenceNode.Descendant(i)))
continue;
const double distance = metric.Evaluate(querySet.unsafe_col(queryIndex),
referenceNode.Dataset().unsafe_col(referenceNode.Descendant(i)));
neighbors[queryIndex].push_back(referenceNode.Descendant(i));
distances[queryIndex].push_back(distance);
}
}
DualTreeKMeansStatistic(TreeType& node) :
closestQueryNode(NULL),
minQueryNodeDistance(DBL_MAX),
maxQueryNodeDistance(DBL_MAX),
clustersPruned(0),
iteration(size_t() - 1)
{
// Empirically calculate the centroid.
centroid.zeros(node.Dataset().n_rows);
for (size_t i = 0; i < node.NumPoints(); ++i)
centroid += node.Dataset().col(node.Point(i));
for (size_t i = 0; i < node.NumChildren(); ++i)
centroid += node.Child(i).NumDescendants() *
node.Child(i).Stat().Centroid();
centroid /= node.NumDescendants();
}
void CheckBound(const TreeType& tree)
{
typedef typename TreeType::ElemType ElemType;
for (size_t i = 0; i < tree.NumDescendants(); i++)
{
arma::Col<ElemType> point = tree.Dataset().col(tree.Descendant(i));
// Check that the point is contained in the bound.
BOOST_REQUIRE_EQUAL(true, tree.Bound().Contains(point));
const arma::Mat<ElemType>& loBound = tree.Bound().LoBound();
const arma::Mat<ElemType>& hiBound = tree.Bound().HiBound();
// Ensure that there is a hyperrectangle that contains the point.
bool success = false;
for (size_t j = 0; j < tree.Bound().NumBounds(); j++)
{
success = true;
for (size_t k = 0; k < loBound.n_rows; k++)
{
if (point[k] < loBound(k, j) - 1e-14 * std::fabs(loBound(k, j)) ||
point[k] > hiBound(k, j) + 1e-14 * std::fabs(hiBound(k, j)))
{
success = false;
break;
}
}
if (success)
break;
}
BOOST_REQUIRE_EQUAL(success, true);
}
if (!tree.IsLeaf())
{
CheckBound(*tree.Left());
CheckBound(*tree.Right());
}
}
double PellegMooreKMeansRules<MetricType, TreeType>::Score(
const size_t /* queryIndex */,
TreeType& referenceNode)
{
// Obtain the parent's blacklist. If this is the root node, we'll start with
// an empty blacklist. This means that after each iteration, we don't need to
// reset any statistics.
if (referenceNode.Parent() == NULL ||
referenceNode.Parent()->Stat().Blacklist().n_elem == 0)
referenceNode.Stat().Blacklist().zeros(centroids.n_cols);
else
referenceNode.Stat().Blacklist() =
referenceNode.Parent()->Stat().Blacklist();
// The query index is a fake index that we won't use, and the reference node
// holds all of the points in the dataset. Our goal is to determine whether
// or not this node is dominated by a single cluster.
const size_t whitelisted = centroids.n_cols -
arma::accu(referenceNode.Stat().Blacklist());
distanceCalculations += whitelisted;
// Which cluster has minimum distance to the node?
size_t closestCluster = centroids.n_cols;
double minMinDistance = DBL_MAX;
for (size_t i = 0; i < centroids.n_cols; ++i)
{
if (referenceNode.Stat().Blacklist()[i] == 0)
{
const double minDistance = referenceNode.MinDistance(centroids.col(i));
if (minDistance < minMinDistance)
{
minMinDistance = minDistance;
closestCluster = i;
}
}
}
// Now, for every other whitelisted cluster, determine if the closest cluster
// owns the point. This calculation is specific to hyperrectangle trees (but,
// this implementation is specific to kd-trees, so that's okay). For
// circular-bound trees, the condition should be simpler and can probably be
// expressed as a comparison between minimum and maximum distances.
size_t newBlacklisted = 0;
for (size_t c = 0; c < centroids.n_cols; ++c)
{
if (referenceNode.Stat().Blacklist()[c] == 1 || c == closestCluster)
continue;
// This algorithm comes from the proof of Lemma 4 in the extended version
// of the Pelleg-Moore paper (the CMU tech report, that is). It has been
// adapted for speed.
arma::vec cornerPoint(centroids.n_rows);
for (size_t d = 0; d < referenceNode.Bound().Dim(); ++d)
{
if (centroids(d, c) > centroids(d, closestCluster))
cornerPoint(d) = referenceNode.Bound()[d].Hi();
else
cornerPoint(d) = referenceNode.Bound()[d].Lo();
}
const double closestDist = metric.Evaluate(cornerPoint,
centroids.col(closestCluster));
const double otherDist = metric.Evaluate(cornerPoint, centroids.col(c));
distanceCalculations += 3; // One for cornerPoint, then two distances.
if (closestDist < otherDist)
{
// The closest cluster dominates the node with respect to the cluster c.
// So we can blacklist c.
referenceNode.Stat().Blacklist()[c] = 1;
++newBlacklisted;
}
}
if (whitelisted - newBlacklisted == 1)
{
// This node is dominated by the closest cluster.
counts[closestCluster] += referenceNode.NumDescendants();
newCentroids.col(closestCluster) += referenceNode.NumDescendants() *
referenceNode.Stat().Centroid();
return DBL_MAX;
}
// Perform the base case here.
for (size_t i = 0; i < referenceNode.NumPoints(); ++i)
{
size_t bestCluster = centroids.n_cols;
double bestDistance = DBL_MAX;
for (size_t c = 0; c < centroids.n_cols; ++c)
{
if (referenceNode.Stat().Blacklist()[c] == 1)
continue;
++distanceCalculations;
// The reference index is the index of the data point.
const double distance = metric.Evaluate(centroids.col(c),
dataset.col(referenceNode.Point(i)));
if (distance < bestDistance)
{
bestDistance = distance;
bestCluster = c;
}
}
// Add to resulting centroid.
newCentroids.col(bestCluster) += dataset.col(referenceNode.Point(i));
++counts(bestCluster);
}
// Otherwise, we're not sure, so we can't prune. Recursion order doesn't make
// a difference, so we'll just return a score of 0.
return 0.0;
}
void CheckTrees(TreeType& tree,
TreeType& xmlTree,
TreeType& textTree,
TreeType& binaryTree)
{
const typename TreeType::Mat* dataset = &tree.Dataset();
// Make sure that the data matrices are the same.
if (tree.Parent() == NULL)
{
CheckMatrices(*dataset,
xmlTree.Dataset(),
textTree.Dataset(),
binaryTree.Dataset());
// Also ensure that the other parents are null too.
BOOST_REQUIRE_EQUAL(xmlTree.Parent(), (TreeType*) NULL);
BOOST_REQUIRE_EQUAL(textTree.Parent(), (TreeType*) NULL);
BOOST_REQUIRE_EQUAL(binaryTree.Parent(), (TreeType*) NULL);
}
// Make sure the number of children is the same.
BOOST_REQUIRE_EQUAL(tree.NumChildren(), xmlTree.NumChildren());
BOOST_REQUIRE_EQUAL(tree.NumChildren(), textTree.NumChildren());
BOOST_REQUIRE_EQUAL(tree.NumChildren(), binaryTree.NumChildren());
// Make sure the number of descendants is the same.
BOOST_REQUIRE_EQUAL(tree.NumDescendants(), xmlTree.NumDescendants());
BOOST_REQUIRE_EQUAL(tree.NumDescendants(), textTree.NumDescendants());
BOOST_REQUIRE_EQUAL(tree.NumDescendants(), binaryTree.NumDescendants());
// Make sure the number of points is the same.
BOOST_REQUIRE_EQUAL(tree.NumPoints(), xmlTree.NumPoints());
BOOST_REQUIRE_EQUAL(tree.NumPoints(), textTree.NumPoints());
BOOST_REQUIRE_EQUAL(tree.NumPoints(), binaryTree.NumPoints());
// Check that each point is the same.
for (size_t i = 0; i < tree.NumPoints(); ++i)
{
BOOST_REQUIRE_EQUAL(tree.Point(i), xmlTree.Point(i));
BOOST_REQUIRE_EQUAL(tree.Point(i), textTree.Point(i));
BOOST_REQUIRE_EQUAL(tree.Point(i), binaryTree.Point(i));
}
// Check that the parent distance is the same.
BOOST_REQUIRE_CLOSE(tree.ParentDistance(), xmlTree.ParentDistance(), 1e-8);
BOOST_REQUIRE_CLOSE(tree.ParentDistance(), textTree.ParentDistance(), 1e-8);
BOOST_REQUIRE_CLOSE(tree.ParentDistance(), binaryTree.ParentDistance(), 1e-8);
// Check that the furthest descendant distance is the same.
BOOST_REQUIRE_CLOSE(tree.FurthestDescendantDistance(),
xmlTree.FurthestDescendantDistance(), 1e-8);
BOOST_REQUIRE_CLOSE(tree.FurthestDescendantDistance(),
textTree.FurthestDescendantDistance(), 1e-8);
BOOST_REQUIRE_CLOSE(tree.FurthestDescendantDistance(),
binaryTree.FurthestDescendantDistance(), 1e-8);
// Check that the minimum bound distance is the same.
BOOST_REQUIRE_CLOSE(tree.MinimumBoundDistance(),
xmlTree.MinimumBoundDistance(), 1e-8);
BOOST_REQUIRE_CLOSE(tree.MinimumBoundDistance(),
textTree.MinimumBoundDistance(), 1e-8);
BOOST_REQUIRE_CLOSE(tree.MinimumBoundDistance(),
binaryTree.MinimumBoundDistance(), 1e-8);
// Recurse into the children.
for (size_t i = 0; i < tree.NumChildren(); ++i)
{
// Check that the child dataset is the same.
BOOST_REQUIRE_EQUAL(&xmlTree.Dataset(), &xmlTree.Child(i).Dataset());
BOOST_REQUIRE_EQUAL(&textTree.Dataset(), &textTree.Child(i).Dataset());
BOOST_REQUIRE_EQUAL(&binaryTree.Dataset(), &binaryTree.Child(i).Dataset());
// Make sure the parent link is right.
BOOST_REQUIRE_EQUAL(xmlTree.Child(i).Parent(), &xmlTree);
BOOST_REQUIRE_EQUAL(textTree.Child(i).Parent(), &textTree);
BOOST_REQUIRE_EQUAL(binaryTree.Child(i).Parent(), &binaryTree);
CheckTrees(tree.Child(i), xmlTree.Child(i), textTree.Child(i),
binaryTree.Child(i));
}
}
inline double KDERules<MetricType, KernelType, TreeType>::
Score(TreeType& queryNode, TreeType& referenceNode)
{
double score, maxKernel, minKernel, bound;
const double minDistance = queryNode.MinDistance(referenceNode);
// Calculations are not duplicated.
bool newCalculations = true;
if (tree::TreeTraits<TreeType>::FirstPointIsCentroid &&
(traversalInfo.LastQueryNode() != NULL) &&
(traversalInfo.LastReferenceNode() != NULL) &&
(traversalInfo.LastQueryNode()->Point(0) == queryNode.Point(0)) &&
(traversalInfo.LastReferenceNode()->Point(0) == referenceNode.Point(0)))
{
// Don't duplicate calculations.
newCalculations = false;
lastQueryIndex = queryNode.Point(0);
lastReferenceIndex = referenceNode.Point(0);
}
else
{
// Calculations are new.
maxKernel = kernel.Evaluate(minDistance);
minKernel = kernel.Evaluate(queryNode.MaxDistance(referenceNode));
bound = maxKernel - minKernel;
}
// If possible, avoid some calculations because of the error tolerance.
if (newCalculations &&
bound <= (absError + relError * minKernel) / referenceSet.n_cols)
{
// Auxiliary variables.
double kernelValue;
kde::KDEStat& referenceStat = referenceNode.Stat();
kde::KDEStat& queryStat = queryNode.Stat();
// If calculating a center is not required.
if (tree::TreeTraits<TreeType>::FirstPointIsCentroid)
{
kernelValue = EvaluateKernel(queryNode.Point(0), referenceNode.Point(0));
}
// Sadly, we have no choice but to calculate the center.
else
{
kernelValue = EvaluateKernel(queryStat.Centroid(),
referenceStat.Centroid());
}
// Sum up estimations.
for (size_t i = 0; i < queryNode.NumDescendants(); ++i)
{
densities(queryNode.Descendant(i)) +=
referenceNode.NumDescendants() * kernelValue;
}
score = DBL_MAX;
}
else
{
score = minDistance;
}
++scores;
traversalInfo.LastQueryNode() = &queryNode;
traversalInfo.LastReferenceNode() = &referenceNode;
traversalInfo.LastScore() = score;
return score;
}
void CheckDistance(TreeType& tree, TreeType* node = NULL)
{
typedef typename TreeType::ElemType ElemType;
if (node == NULL)
{
node = &tree;
while (node->Parent() != NULL)
node = node->Parent();
CheckDistance<TreeType, MetricType>(tree, node);
for (size_t j = 0; j < tree.Dataset().n_cols; j++)
{
const arma::Col<ElemType>& point = tree. Dataset().col(j);
ElemType maxDist = 0;
ElemType minDist = std::numeric_limits<ElemType>::max();
for (size_t i = 0; i < tree.NumDescendants(); i++)
{
ElemType dist = MetricType::Evaluate(
tree.Dataset().col(tree.Descendant(i)),
tree.Dataset().col(j));
if (dist > maxDist)
maxDist = dist;
if (dist < minDist)
minDist = dist;
}
BOOST_REQUIRE_LE(tree.Bound().MinDistance(point), minDist *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
BOOST_REQUIRE_LE(maxDist, tree.Bound().MaxDistance(point) *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
math::RangeType<ElemType> r = tree.Bound().RangeDistance(point);
BOOST_REQUIRE_LE(r.Lo(), minDist *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
BOOST_REQUIRE_LE(maxDist, r.Hi() *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
}
if (!tree.IsLeaf())
{
CheckDistance<TreeType, MetricType>(*tree.Left());
CheckDistance<TreeType, MetricType>(*tree.Right());
}
}
else
{
if (&tree != node)
{
ElemType maxDist = 0;
ElemType minDist = std::numeric_limits<ElemType>::max();
for (size_t i = 0; i < tree.NumDescendants(); i++)
for (size_t j = 0; j < node->NumDescendants(); j++)
{
ElemType dist = MetricType::Evaluate(
tree.Dataset().col(tree.Descendant(i)),
node->Dataset().col(node->Descendant(j)));
if (dist > maxDist)
maxDist = dist;
if (dist < minDist)
minDist = dist;
}
BOOST_REQUIRE_LE(tree.Bound().MinDistance(node->Bound()), minDist *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
BOOST_REQUIRE_LE(maxDist, tree.Bound().MaxDistance(node->Bound()) *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
math::RangeType<ElemType> r = tree.Bound().RangeDistance(node->Bound());
BOOST_REQUIRE_LE(r.Lo(), minDist *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
BOOST_REQUIRE_LE(maxDist, r.Hi() *
(1.0 + 10 * std::numeric_limits<ElemType>::epsilon()));
}
if (!node->IsLeaf())
{
CheckDistance<TreeType, MetricType>(tree, node->Left());
CheckDistance<TreeType, MetricType>(tree, node->Right());
}
}
}
double RangeSearchRules<MetricType, TreeType>::Score(TreeType& queryNode,
TreeType& referenceNode)
{
math::Range distances;
if (tree::TreeTraits<TreeType>::FirstPointIsCentroid)
{
// It is possible that the base case has already been calculated.
double baseCase = 0.0;
bool alreadyDone = false;
if (tree::TreeTraits<TreeType>::HasSelfChildren)
{
TreeType* lastQuery = (TreeType*) referenceNode.Stat().LastDistanceNode();
TreeType* lastRef = (TreeType*) queryNode.Stat().LastDistanceNode();
// Did the query node's last combination do the base case?
if ((lastRef != NULL) && (referenceNode.Point(0) == lastRef->Point(0)))
{
baseCase = queryNode.Stat().LastDistance();
alreadyDone = true;
}
// Did the reference node's last combination do the base case?
if ((lastQuery != NULL) && (queryNode.Point(0) == lastQuery->Point(0)))
{
baseCase = referenceNode.Stat().LastDistance();
alreadyDone = true;
}
// If the query node is a self-child, did the query parent's last
// combination do the base case?
if ((queryNode.Parent() != NULL) &&
(queryNode.Point(0) == queryNode.Parent()->Point(0)))
{
TreeType* lastParentRef = (TreeType*)
queryNode.Parent()->Stat().LastDistanceNode();
if ((lastParentRef != NULL) &&
(referenceNode.Point(0) == lastParentRef->Point(0)))
{
baseCase = queryNode.Parent()->Stat().LastDistance();
alreadyDone = true;
}
}
// If the reference node is a self-child, did the reference parent's last
// combination do the base case?
if ((referenceNode.Parent() != NULL) &&
(referenceNode.Point(0) == referenceNode.Parent()->Point(0)))
{
TreeType* lastQueryRef = (TreeType*)
referenceNode.Parent()->Stat().LastDistanceNode();
if ((lastQueryRef != NULL) &&
(queryNode.Point(0) == lastQueryRef->Point(0)))
{
baseCase = referenceNode.Parent()->Stat().LastDistance();
alreadyDone = true;
}
}
}
if (!alreadyDone)
{
// We must calculate the base case.
baseCase = BaseCase(queryNode.Point(0), referenceNode.Point(0));
}
else
{
// Make sure that if BaseCase() is called, we don't duplicate results.
lastQueryIndex = queryNode.Point(0);
lastReferenceIndex = referenceNode.Point(0);
}
distances.Lo() = baseCase - queryNode.FurthestDescendantDistance()
- referenceNode.FurthestDescendantDistance();
distances.Hi() = baseCase + queryNode.FurthestDescendantDistance()
+ referenceNode.FurthestDescendantDistance();
// Update the last distances performed for the query and reference node.
queryNode.Stat().LastDistanceNode() = (void*) &referenceNode;
queryNode.Stat().LastDistance() = baseCase;
referenceNode.Stat().LastDistanceNode() = (void*) &queryNode;
referenceNode.Stat().LastDistance() = baseCase;
}
else
{
// Just perform the calculation.
distances = referenceNode.RangeDistance(&queryNode);
}
// If the ranges do not overlap, prune this node.
if (!distances.Contains(range))
return DBL_MAX;
// In this case, all of the points in the reference node will be part of all
// the results for each point in the query node.
if ((distances.Lo() >= range.Lo()) && (distances.Hi() <= range.Hi()))
{
for (size_t i = 0; i < queryNode.NumDescendants(); ++i)
AddResult(queryNode.Descendant(i), referenceNode);
return DBL_MAX; // We don't need to go any deeper.
}
// Otherwise the score doesn't matter. Recursion order is irrelevant in range
// search.
return 0.0;
}