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Separated out the naive algorithm into a separate file. Now algorithms are templatized for different primitive types

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This commit is contained in:
Dongryeol Lee
2008-03-09 00:32:12 +00:00
parent 46f9df9c89
commit 2ddadcc3f2
6 changed files with 199 additions and 130 deletions
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fastlib2/mlpack/range_search/build.py
+3 -1
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@@ -2,7 +2,9 @@
librule(
name = "ortho_range_search",
sources = [],
headers = ["ortho_range_search.h",
headers = ["data_aux.h",
"naive_ortho_range_search.h",
"ortho_range_search.h",
"range_reader.h"],
deplibs = ["fastlib:fastlib_int"]
)
fastlib2/mlpack/range_search/data_aux.h
+41
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@@ -0,0 +1,41 @@
#ifndef DATA_AUX_H
#define DATA_AUX_H
#include "fastlib/fastlib.h"
namespace data_aux {
/**
* Loads a matrix from a file.
*
* This supports any type the Dataset class supports with the
* InitFromFile function: CSV and ARFF.
*
* @code
* Matrix A;
* data::Load("foo.csv", &A);
* @endcode
*
* @param fname the file name to load
* @param matrix a pointer to an uninitialized matrix to load
*/
template<typename T>
static success_t Load(const char *fname, GenMatrix<T> *matrix) {
Matrix tmp_matrix;
success_t result = data::Load(fname, &tmp_matrix);
// Allocate the matrix that is to be returned and copy all
// entries.
matrix->Init(tmp_matrix.n_rows(), tmp_matrix.n_cols());
for(index_t c = 0; c < tmp_matrix.n_cols(); c++) {
for(index_t r = 0; r < tmp_matrix.n_rows(); r++) {
matrix->set(r, c, STATIC_CAST(T, tmp_matrix.get(r, c)));
}
}
return result;
}
};
#endif
fastlib2/mlpack/range_search/naive_ortho_range_search.h
+129
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@@ -0,0 +1,129 @@
/** @file naive_ortho_range_search.h
*
* This file contains an implementation of a naive algorithm for
* orthogonal range search.
*
* @author Dongryeol Lee (dongryel)
*/
#ifndef NAIVE_ORTHO_RANGE_SEARCH_H
#define NAIVE_ORTHO_RANGE_SEARCH_H
#include "range_reader.h"
#include "fastlib/fastlib.h"
/** @brief Naive orthogonal range search class.
*
* @code
* NaiveOrthoRangeSearch search;
* search.Init(dataset);
* search.Compute(low_coord_limits, high_coord_limits);
*
* ArrayList<bool> naive_search_results;
*
* // Make sure that the vector is uninitialized before passing.
* search.get_results(&naive_search_results);
* @endcode
*/
template<typename T>
class NaiveOrthoRangeSearch {
// This class object cannot be copied!
FORBID_ACCIDENTAL_COPIES(NaiveOrthoRangeSearch);
private:
/** @brief The i-th position of this array tells whether the i-th
* point is in the specified orthogonal range.
*/
ArrayList<bool> in_range_;
/** @brief The dataset.
*/
GenMatrix<T> data_;
public:
////////// Constructor/Destructor //////////
/** @brief Constructor which does not do anything.
*/
NaiveOrthoRangeSearch() {}
/** @brief Destructor which does not do anything.
*/
~NaiveOrthoRangeSearch() {}
////////// Getters/Setters //////////
/** @brief Retrieve the result of the search.
*
* @param results An uninitialized vector which will have the boolean
* results representing the search results.
*/
void get_results(ArrayList<bool> *results) const {
results->Init(in_range_.size());
for(index_t i = 0; i < in_range_.size(); i++) {
(*results)[i] = in_range_[i];
}
}
////////// User-level Functions //////////
/** @brief Initialize the computation object.
*
* @param data The data used for orthogonal range search.
*/
void Init(const GenMatrix<T> &data) {
// copy the incoming data
data_.Copy(data);
// re-initialize boolean flag
in_range_.Init(data_.n_cols());
for(index_t i = 0; i < data_.n_cols(); i++) {
in_range_[i] = false;
}
}
/** @brief The main computation of naive orthogonal range search.
*
* @param low_coord_limits The lower coordinate range of the search window.
* @param high_coord_limits The upper coordinate range of the search
* window.
*/
void Compute(const GenVector<T> &low_coord_limits,
const GenVector<T> &high_coord_limits) {
// Start the search.
fx_timer_start(NULL, "naive_search");
for(index_t i = 0; i < data_.n_cols(); i++) {
GenVector<T> pt;
bool flag = true;
data_.MakeColumnVector(i, &pt);
// Determine which one of the two cases we have: EXCLUDE, SUBSUME
// first the EXCLUDE case: when dist is above the upper bound distance
// of this dimension, or dist is below the lower bound distance of
// this dimension
for(index_t d = 0; d < data_.n_rows(); d++) {
if(pt[d] < low_coord_limits[d] || pt[d] > high_coord_limits[d]) {
flag = false;
break;
}
}
in_range_[i] = flag;
}
fx_timer_stop(NULL, "naive_search");
// Search is now finished.
}
};
#endif
fastlib2/mlpack/range_search/ortho_range_search.h
+15 -121
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@@ -1,7 +1,7 @@
/** @file ortho_range_search.h
*
* This file contains an implementation of a tree-based and a naive
* algorithm for orthogonal range search.
* This file contains an implementation of a tree-based algorithm for
* orthogonal range search.
*
* @author Dongryeol Lee (dongryel)
*/
@@ -11,115 +11,6 @@
#include "range_reader.h"
#include "fastlib/fastlib.h"
/** @brief Naive orthogonal range search class.
*
* @code
* NaiveOrthoRangeSearch search;
* search.Init(dataset);
* search.Compute(low_coord_limits, high_coord_limits);
*
* Vector naive_search_results;
*
* // Make sure that the vector is uninitialized before passing.
* search.get_results(&naive_search_results);
* @endcode
*/
class NaiveOrthoRangeSearch {
// This class object cannot be copied!
FORBID_ACCIDENTAL_COPIES(NaiveOrthoRangeSearch);
private:
/** @brief The i-th position of this array tells whether the i-th
* point is in the specified orthogonal range.
*/
ArrayList<bool> in_range_;
/** @brief The dataset.
*/
Matrix data_;
public:
////////// Constructor/Destructor //////////
/** @brief Constructor which does not do anything.
*/
NaiveOrthoRangeSearch() {}
/** @brief Destructor which does not do anything.
*/
~NaiveOrthoRangeSearch() {}
////////// Getters/Setters //////////
/** @brief Retrieve the result of the search.
*
* @param results An uninitialized vector which will have the boolean
* results representing the search results.
*/
void get_results(ArrayList<bool> *results) const {
results->Init(in_range_.size());
for(index_t i = 0; i < in_range_.size(); i++) {
(*results)[i] = in_range_[i];
}
}
////////// User-level Functions //////////
/** @brief Initialize the computation object.
*
* @param data The data used for orthogonal range search.
*/
void Init(Matrix &data) {
// copy the incoming data
data_.Copy(data);
// re-initialize boolean flag
in_range_.Init(data_.n_cols());
for(index_t i = 0; i < data_.n_cols(); i++) {
in_range_[i] = false;
}
}
/** @brief The main computation of naive orthogonal range search.
*
* @param low_coord_limits The lower coordinate range of the search window.
* @param high_coord_limits The upper coordinate range of the search
* window.
*/
void Compute(Vector &low_coord_limits, Vector &high_coord_limits) {
// Start the search.
fx_timer_start(NULL, "naive_search");
for(index_t i = 0; i < data_.n_cols(); i++) {
Vector pt;
bool flag = true;
data_.MakeColumnVector(i, &pt);
// Determine which one of the two cases we have: EXCLUDE, SUBSUME
// first the EXCLUDE case: when dist is above the upper bound distance
// of this dimension, or dist is below the lower bound distance of
// this dimension
for(index_t d = 0; d < data_.n_rows(); d++) {
if(pt[d] < low_coord_limits[d] || pt[d] > high_coord_limits[d]) {
flag = false;
break;
}
}
in_range_[i] = flag;
}
fx_timer_stop(NULL, "naive_search");
// Search is now finished.
}
};
/** @brief Faster orthogonal range search class using a tree.
*
@@ -134,6 +25,7 @@ class NaiveOrthoRangeSearch {
* search.get_results(&search_results);
* @endcode
*/
template<typename T>
class OrthoRangeSearch {
// This class object cannot be copied!
@@ -188,7 +80,8 @@ class OrthoRangeSearch {
* @param high_coord_limits The upper coordinate range of the search
* window.
*/
void Compute(Vector &low_coord_limits, Vector &high_coord_limits) {
void Compute(const GenVector<T> &low_coord_limits,
const GenVector<T> &high_coord_limits) {
fx_timer_start(NULL, "tree_range_search");
ortho_range_search(root_, 0, low_coord_limits, high_coord_limits);
@@ -258,7 +151,8 @@ class OrthoRangeSearch {
* If not NULL, the tree is loaded from the
* file whose name is given as the argument.
*/
void Init(Matrix &dataset, bool make_copy, const char *load_tree_file_name) {
void Init(GenMatrix<T> &dataset, bool make_copy,
const char *load_tree_file_name) {
int leaflen = fx_param_int(NULL, "leaflen", 20);
@@ -295,7 +189,7 @@ class OrthoRangeSearch {
private:
/** @brief This defines the type of the tree used in this algorithm. */
typedef BinarySpaceTree<DHrectBound<2>, Matrix> Tree;
typedef BinarySpaceTree<DHrectBound<2>, GenMatrix<T> > Tree;
/** @brief Flag determining a prune */
enum PruneStatus {SUBSUME, INCONCLUSIVE, EXCLUDE};
@@ -303,7 +197,7 @@ class OrthoRangeSearch {
////////// Private Member Variables //////////
/** @brief Pointer to the dataset */
Matrix data_;
GenMatrix<T> data_;
/** @brief Buffer for loading up old_from_new mapping. */
ArrayList<index_t> *old_from_new_buffer_;
@@ -367,11 +261,11 @@ class OrthoRangeSearch {
printf("Tree has been loaded...\n");
// apply permutation to the dataset
Matrix tmp_data;
GenMatrix<T> tmp_data;
tmp_data.Init(data_.n_rows(), data_.n_cols());
for(index_t i = 0; i < data_.n_cols(); i++) {
Vector source, dest;
GenVector<T> source, dest;
data_.MakeColumnVector(i, &source);
tmp_data.MakeColumnVector(new_from_old_[i], &dest);
dest.CopyValues(source);
@@ -388,8 +282,8 @@ class OrthoRangeSearch {
* @param high_coord_limits The upper coordinate limits of the search.
*/
void ortho_slow_range_search(Tree *node, int start_dim,
const Vector &low_coord_limits,
const Vector &high_coord_limits) {
const GenVector<T> &low_coord_limits,
const GenVector<T> &high_coord_limits) {
PruneStatus prune_flag;
for(index_t row = node->begin(); row < node->end(); row++) {
@@ -427,8 +321,8 @@ class OrthoRangeSearch {
* window.
*/
void ortho_range_search(Tree *node, int start_dim,
const Vector &low_coord_limits,
const Vector &high_coord_limits) {
const GenVector<T> &low_coord_limits,
const GenVector<T> &high_coord_limits) {
PruneStatus prune_flag = SUBSUME;
fastlib2/mlpack/range_search/ortho_range_search_main.cc
+7 -5
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@@ -4,6 +4,8 @@
*
* @author Dongryeol Lee (dongryel)
*/
#include "data_aux.h"
#include "naive_ortho_range_search.h"
#include "ortho_range_search.h"
/** Main function which reads parameters and runs the orthogonal
@@ -67,14 +69,14 @@ int main(int argc, char *argv[]) {
const char* dataset_file_name = fx_param_str(NULL, "data", "data.ds");
// column-oriented dataset matrix.
Matrix dataset;
GenMatrix<double> dataset;
// data::Load inits a matrix with the contents of a .csv or .arff.
data::Load(dataset_file_name, &dataset);
data_aux::Load(dataset_file_name, &dataset);
// Read the search range from the file.
const char *range_data_file_name = fx_param_str(NULL, "range", "range.ds");
Vector low_coord_limits, high_coord_limits;
GenVector<double> low_coord_limits, high_coord_limits;
RangeReader::ReadRangeData(&low_coord_limits, &high_coord_limits,
dataset, range_data_file_name);
@@ -92,7 +94,7 @@ int main(int argc, char *argv[]) {
}
// Declare fast tree-based orthogonal range search algorithm object.
OrthoRangeSearch fast_search;
OrthoRangeSearch<double> fast_search;
fast_search.Init(dataset, fx_param_exists(NULL, "do_naive"),
load_tree_file_name);
fast_search.Compute(low_coord_limits, high_coord_limits);
@@ -108,7 +110,7 @@ int main(int argc, char *argv[]) {
// if naive option is specified, do naive algorithm
if(do_naive) {
NaiveOrthoRangeSearch search;
NaiveOrthoRangeSearch<double> search;
search.Init(dataset);
search.Compute(low_coord_limits, high_coord_limits);
ArrayList<bool> naive_search_results;
fastlib2/mlpack/range_search/range_reader.h
+4 -3
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@@ -39,9 +39,10 @@ class RangeReader {
* rows of the text file to read in).
* @param range_data_file_name The file to read the range data from.
*/
static void ReadRangeData(Vector *low_coord_limits,
Vector *high_coord_limits,
Matrix &dataset,
template<typename T>
static void ReadRangeData(GenVector<T> *low_coord_limits,
GenVector<T> *high_coord_limits,
GenMatrix<T> &dataset,
const char *range_data_file_name) {
TextTokenizer tokenizer;