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Miscellaenous cleanup

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This commit is contained in:
Dongryeol Lee
2007-10-14 18:11:27 +00:00
parent 8fdcdd5fd0
commit 01f4f2fa3f
2 changed files with 100 additions and 36 deletions
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fastlib/u/dongryel/kde/kde.h
+87 -32
View File
@@ -13,10 +13,14 @@ class NaiveKde {
/** query dataset */
Matrix qset_;
ArrayList<index_t> q_old_from_new_;
/** reference dataset */
Matrix rset_;
ArrayList<index_t> r_old_from_new_;
/** kernel */
TKernel kernel_;
@@ -56,18 +60,21 @@ class NaiveKde {
densities_.SetZero();
}
void Init(Matrix &qset, Matrix &rset) {
void Init(Matrix &qset, ArrayList<index_t> &q_old_from_new,
Matrix &rset, ArrayList<index_t> &r_old_from_new) {
// get datasets
qset_.Alias(qset);
q_old_from_new_.Steal(&q_old_from_new);
rset_.Alias(rset);
r_old_from_new_.Steal(&r_old_from_new);
// get bandwidth
kernel_.Init(fx_param_double_req(NULL, "bandwidth"));
// allocate density storage
densities_.Init(qset.n_cols());
densities_.SetZero();
densities_.SetZero();
}
void PrintDebug() {
@@ -78,7 +85,9 @@ class NaiveKde {
if((fname = fx_param_str(NULL, "naive_kde_output", NULL)) != NULL) {
stream = fopen(fname, "w+");
}
densities_.PrintDebug("Naive KDE results", stream);
for(index_t q = 0; q < qset_.n_cols(); q++) {
fprintf(stream, "%g\n", densities_[q_old_from_new_[q]]);
}
if(stream != stdout) {
fclose(stream);
@@ -197,8 +206,11 @@ class FastKde {
}
void MergeChildBounds(KdeStat &left_stat, KdeStat &right_stat) {
// steal left and right children's tokens
double min_mass_t = min(left_stat.mass_t_, right_stat.mass_t_);
// improve lower and upper bound
mass_l_ = max(mass_l_, min(left_stat.mass_l_, right_stat.mass_l_));
mass_u_ = min(mass_u_, max(left_stat.mass_u_, right_stat.mass_u_));
mass_t_ += min_mass_t;
@@ -244,15 +256,27 @@ class FastKde {
/** query dataset */
Matrix qset_;
/**
* maps new indices of the query dataset to the old indices (of original
* text dataset
*/
ArrayList<index_t> q_old_from_new_;
/** query tree */
Tree *qroot_;
/** reference dataset */
Matrix rset_;
/**
* maps new indices of the reference dataset to the old indices (of original
* text dataset
*/
ArrayList<index_t> r_old_from_new_;
/** reference tree */
Tree *rroot_;
/** reference weights */
Vector rset_weights_;
@@ -288,7 +312,6 @@ class FastKde {
// member functions
void UpdateBounds(Tree *qnode, Tree *rnode,
KdeStat *left_stat, KdeStat *right_stat,
double *dl, double *de, double *du, double *dt) {
// query self statistics
@@ -348,7 +371,7 @@ class FastKde {
// for a leaf node, incorporate the lower and upper bound changes into
// its additional offset
if(left_stat == NULL) {
if(qnode->is_leaf()) {
qstat.more_l_ += dl_ref;
qstat.more_u_ += du_ref;
}
@@ -357,10 +380,10 @@ class FastKde {
// the immediate descendants
else {
left_stat->owed_l_ += dl_ref;
left_stat->owed_u_ += du_ref;
right_stat->owed_l_ += dl_ref;
right_stat->owed_u_ += du_ref;
qnode->left()->stat().owed_l_ += dl_ref;
qnode->left()->stat().owed_u_ += du_ref;
qnode->right()->stat().owed_l_ += dl_ref;
qnode->right()->stat().owed_u_ += du_ref;
}
// zero out lower and upper bounds
@@ -375,9 +398,14 @@ class FastKde {
// compute unnormalized sum
for(index_t q = qnode->begin(); q < qnode->end(); q++) {
// get query point
const double *q_col = qset_.GetColumnPtr(q);
for(index_t r = rnode->begin(); r < rnode->end(); r++) {
// get reference point
const double *r_col = rset_.GetColumnPtr(r);
// pairwise distance and kernel value
double dsqd = la::DistanceSqEuclidean(qset_.n_rows(), q_col, r_col);
double ker_value = kernel_.EvalUnnormOnSq(dsqd);
@@ -387,7 +415,7 @@ class FastKde {
}
}
// tally up the unused error components
// tally up the unused error components due to exhaustive computation
qnode->stat().mass_t_ += rnode->count();
// get a tighter lower and upper bound by looping over each query point
@@ -525,7 +553,7 @@ class FastKde {
return 1;
}
else {
dl_ = du_ = dt_ = 0;
dl_ = de_ = du_ = dt_ = 0;
return 0;
}
}
@@ -550,31 +578,33 @@ class FastKde {
/** canonical fast KDE case */
void FKde(Tree *qnode, Tree *rnode) {
// query node statistics
KdeStat &stat = qnode->stat();
// left child and right child of query node statistics
KdeStat *left_stat = NULL;
KdeStat *right_stat = NULL;
// process density bound changes sent from the ancestor query nodes
// then tighten lower/upper bounds and the error reclaimed based on
// the children
// process density bound changes sent from the ancestor query nodes,
UpdateBounds(qnode, rnode, &stat.owed_l_, NULL, &stat.owed_u_, NULL);
// for non-leaf query node, tighten lower/upper bounds and the
// reclaim tokens unused by the children.
if(!qnode->is_leaf()) {
left_stat = &(qnode->left()->stat());
right_stat = &(qnode->right()->stat());
UpdateBounds(qnode, rnode, left_stat, right_stat, &stat.owed_l_, NULL,
&stat.owed_u_, NULL);
stat.MergeChildBounds(*left_stat, *right_stat);
}
// try finite difference pruning first
if(Prunable(qnode, rnode)) {
UpdateBounds(qnode, rnode, left_stat, right_stat, &dl_, &de_, &du_,
&dt_);
UpdateBounds(qnode, rnode, &dl_, &de_, &du_, &dt_);
return;
}
// if prunable, then prune
// try series-expansion pruning
else if(PrunableEnhanced(qnode, rnode)) {
UpdateBounds(qnode, rnode, left_stat, right_stat, &dl_, NULL, &du_,
&dt_);
UpdateBounds(qnode, rnode, &dl_, NULL, &du_, &dt_);
return;
}
@@ -641,20 +671,35 @@ class FastKde {
*/
void PreProcess(Tree *node) {
// initialize the center of expansions and bandwidth for
// series expansion
node->stat().Init(sqrt(kernel_.bandwidth_sq()), &sea_);
node->bound().CalculateMidpoint
(&(node->stat().farfield_expansion_.get_center()));
node->bound().CalculateMidpoint
(&(node->stat().local_expansion_.get_center()));
// initialize lower bound to 0
node->stat().mass_l_ = 0;
// set the finite difference approximated amounts to 0
node->stat().mass_e_ = 0;
// set the upper bound to the number of reference points
node->stat().mass_u_ = rset_.n_cols();
// set the number of tokens to 0
node->stat().mass_t_ = 0;
// for non-leaf node, recurse
if(!node->is_leaf()) {
node->stat().owed_l_ = node->stat().owed_u_ = 0;
PreProcess(node->left());
PreProcess(node->right());
}
else {
node->stat().more_l_ = node->stat().more_u_ = 0;
}
}
/** post processing step */
@@ -711,10 +756,18 @@ class FastKde {
/** get the reference dataset */
Matrix &get_reference_dataset() { return rset_; }
ArrayList<index_t> &get_reference_old_from_new_mapping() {
return r_old_from_new_;
}
/** get the query dataset */
Matrix &get_query_dataset() { return qset_; }
ArrayList<index_t> &get_query_old_from_new_mapping() {
return q_old_from_new_;
}
/** get the density estimate */
const Vector &get_density_estimates() { return densities_e_; }
@@ -728,7 +781,7 @@ class FastKde {
// initialize the lower and upper bound densities
densities_l_.SetZero();
densities_e_.SetZero();
densities_u_.SetZero();
densities_u_.SetAll(rset_.n_cols());
printf("\nStarting fast KDE...\n");
fx_timer_start(NULL, "fast_kde_compute");
@@ -744,7 +797,7 @@ class FastKde {
order_farfield_ = order_local_ = order_farfield_to_local_ = -1;
FKde(qroot_, rroot_);
// postprocessing step
// postprocessing step for finalizing the sums
PostProcess(qroot_);
// normalize densities
@@ -787,27 +840,27 @@ class FastKde {
// construct query and reference trees
fx_timer_start(NULL, "tree_d");
rroot_ = tree::MakeKdTreeMidpoint<Tree>(rset_, leaflen, NULL);
rroot_ = tree::MakeKdTreeMidpoint<Tree>(rset_, leaflen,
&r_old_from_new_);
if(!strcmp(qfname, rfname)) {
qset_.Alias(rset_);
qroot_ = rroot_;
q_old_from_new_.Copy(r_old_from_new_);
}
else {
Dataset query_dataset;
query_dataset.InitFromFile(qfname);
qset_.Own(&(query_dataset.matrix()));
qroot_ = tree::MakeKdTreeMidpoint<Tree>(qset_, leaflen, NULL);
qroot_ = tree::MakeKdTreeMidpoint<Tree>(qset_, leaflen,
&q_old_from_new_);
}
fx_timer_stop(NULL, "tree_d");
// initialize the density lists
densities_l_.Init(qset_.n_cols());
densities_l_.SetZero();
densities_e_.Init(qset_.n_cols());
densities_e_.SetZero();
densities_u_.Init(qset_.n_cols());
densities_u_.SetAll(rset_.n_cols());
// initialize the kernel
kernel_.Init(fx_param_double_req(NULL, "bandwidth"));
@@ -824,7 +877,9 @@ class FastKde {
if((fname = fx_param_str(NULL, "fast_kde_output", NULL)) != NULL) {
stream = fopen(fname, "w+");
}
densities_e_.PrintDebug("Fast KDE results", stream);
for(index_t q = 0; q < qset_.n_cols(); q++) {
fprintf(stream, "%g\n", densities_e_[q_old_from_new_[q]]);
}
if(stream != stdout) {
fclose(stream);
fastlib/u/dongryel/kde/main.cc
+13 -4
View File
@@ -10,16 +10,25 @@ int main(int argc, char *argv[]) {
FastKde<GaussianKernel, GaussianKernelDerivative> fast_kde;
fast_kde.Init();
fast_kde.Compute(fx_param_double(NULL, "tau", 0.1));
//fast_kde.PrintDebug();
if(fx_param_exists(NULL, "fast_kde_output")) {
fast_kde.PrintDebug();
}
Vector fast_kde_results;
fast_kde_results.Alias(fast_kde.get_density_estimates());
if(do_naive) {
NaiveKde<GaussianKernel> naive_kde;
naive_kde.Init(fast_kde.get_query_dataset(),
fast_kde.get_reference_dataset());
naive_kde.Init(fast_kde.get_query_dataset(),
fast_kde.get_query_old_from_new_mapping(),
fast_kde.get_reference_dataset(),
fast_kde.get_reference_old_from_new_mapping());
naive_kde.Compute();
//naive_kde.PrintDebug();
if(fx_param_exists(NULL, "naive_kde_output")) {
naive_kde.PrintDebug();
}
naive_kde.ComputeMaximumRelativeError(fast_kde_results);
}