Hierarchy¶

The Tree class contains the construction of the hierarchy in it’s constructors and class methods.

Tree Structure¶

Functions

std::ostream &operator<<(std::ostream&, std::shared_ptr<Annotation> &annotation)¶

std::ostream &operator<<(std::ostream&, std::shared_ptr<Node> &node)¶

std::shared_ptr<Node> convertUltrametricTreeNodeToNode(std::shared_ptr<UltrametricTreeNode> ultrametricTreeRootNode)¶

struct Annotation¶

#include <tree_structure.hpp>

Public Functions

inline Annotation(double cost_decrease, long long center, std::weak_ptr<Annotation> parent = std::weak_ptr<Annotation>(), std::weak_ptr<Node> tree_node = std::weak_ptr<Node>(), std::weak_ptr<Node> orig_node = std::weak_ptr<Node>(), long long level = 0)¶

inline bool operator<(const Annotation &other) const¶

inline bool operator>(const Annotation &other) const¶

Public Members

double cost_decrease¶

long long center¶

std::weak_ptr<Annotation> parent¶

std::weak_ptr<Node> tree_node¶

std::weak_ptr<Node> orig_node¶

long long level¶

struct Node : public std::enable_shared_from_this<Node>¶

#include <tree_structure.hpp>

Public Functions

inline Node(long long id, double cost, std::vector<std::shared_ptr<Node>> children = {}, std::weak_ptr<Node> parent = std::weak_ptr<Node>(), long long k = -1, unsigned long long size = 0, bool is_cluster = false, long long low = -1, long long high = -1, std::shared_ptr<Annotation> anno = nullptr)¶

inline bool operator<(const Node &other) const¶

inline bool operator>(const Node &other) const¶

std::string to_json(bool fast_index = false)¶

Public Members

long long id¶

double cost¶

std::vector<std::shared_ptr<Node>> children¶

std::weak_ptr<Node> parent = std::weak_ptr<Node>()¶

long long k¶

unsigned long long size¶

bool is_cluster = false¶

long long low¶

long long high¶

std::shared_ptr<Node> orig_node¶

std::shared_ptr<Annotation> anno¶

bool is_merger = false¶

std::vector<double> representative¶

long long k_marking = -1¶

double closest_center = std::numeric_limits<double>::infinity()¶

long long level¶

class Tree¶

#include <tree_structure.hpp>

Public Functions

Tree(std::shared_ptr<Node> root, std::vector<std::vector<double>> &data, UltrametricTreeType tree_type, double hierarchy, const std::unordered_map<std::string, std::string> &config = {})¶

inline double cost_function(double value)¶

std::vector<std::vector<double>> get_distance_matrix()¶

std::string to_json(bool fast_index = false)¶

std::tuple<std::vector<long long>, std::vector<long long>> kcenter_cut(long long k)¶

std::tuple<std::vector<long long>, std::vector<long long>> kcenter_elbow_cut(bool triangle = true)¶

std::tuple<std::vector<long long>, std::vector<long long>> threshold_elbow_cut()¶

std::tuple<std::vector<long long>, std::vector<long long>> threshold_cut(long long k)¶

std::tuple<std::vector<long long>, std::vector<long long>> stability_cut(unsigned long long mcs)¶

std::tuple<std::vector<long long>, std::vector<long long>> normalized_stability_cut(unsigned long long mcs)¶

std::tuple<std::vector<long long>, std::vector<long long>> threshold_q_coverage(long long k, unsigned long long minPts, bool prune_stem = false, bool elbow = false, bool use_full_tree_elbow = false)¶

std::tuple<std::vector<long long>, std::vector<long long>> get_lca_prune_solution(bool triangle = true)¶

unsigned long long get_elbow_k(bool triangle = true)¶

Public Members

std::shared_ptr<Node> root¶

UltrametricTreeType tree_type¶

double hierarchy¶

std::unordered_map<std::string, std::string> config¶

std::vector<long long> index_order¶

std::vector<std::shared_ptr<Node>> sorted_nodes¶

std::vector<std::shared_ptr<Annotation>> k_solutions¶

double max_cost¶

std::vector<double> costs¶

std::vector<double> cost_decreases¶

Private Functions

void setup_fast_index()¶

void compute_sorted_nodes()¶

void compute_sorted_costs()¶

void assign_nodes_their_k_values()¶

std::shared_ptr<Node> create_centroids_hierarchy()¶

void annotate_tree(std::shared_ptr<Node> root, std::vector<std::vector<double>> &data)¶

inline double sq_euclid_dist(std::vector<double> &p1, std::vector<double> &p2)¶

void update_pointers(std::vector<double> &center, std::shared_ptr<Annotation> curr_anno, std::shared_ptr<Node> start_node, long long k)¶

void optimize_annotations(std::shared_ptr<Node> root, std::vector<std::vector<double>> &data)¶

void compute_representatives(std::shared_ptr<Node> fullTree, std::vector<std::vector<double>> &data)¶

std::shared_ptr<Node> convert_to_real_nodes_solution(std::shared_ptr<Node> pruned_solution)¶

long long mark_tree(std::shared_ptr<Node> tree, std::set<long long> centers)¶

std::tuple<std::vector<long long>, std::vector<long long>> k_solution(long long k, std::shared_ptr<Node> curr_solution)¶

void get_k_solution_helper(long long k, std::shared_ptr<Node> fullTree, std::shared_ptr<Node> new_solution)¶

void label_tree(std::vector<long long> &labels, std::shared_ptr<Node> tree, long long label)¶

void extract_labels(std::vector<long long> &labels, std::vector<long long> &centers, std::shared_ptr<Node> solution)¶

void label_clusters_helper_merge(std::shared_ptr<Node> tree, std::vector<long long> &labels, std::vector<long long> &centers, long long k)¶

std::tuple<std::vector<long long>, std::vector<long long>> label_clusters_merge(std::shared_ptr<Node> tree, long long k = -1)¶

void threshold_cut_main(std::vector<std::shared_ptr<Node>> &node_list, long long k, bool force_kcenter_cut = false)¶

void trim_stem(std::vector<std::shared_ptr<Node>> &node_list)¶

long long threshold(long long k = 0, bool stemTrim = false, bool force_kcenter_cut = false)¶

void mark_tree_from_pruned(std::vector<std::shared_ptr<Node>> pruned_nodes)¶

double stability(long long size, double pdist, double fallout_sum)¶

long long split_size(std::shared_ptr<Node> tree, unsigned long long mcs)¶

void bottom_up_cluster(std::shared_ptr<Node> fullTree, unsigned long long min_cluster_size)¶

void bottom_up_cluster_normalized(std::shared_ptr<Node> fullTree, unsigned long long min_cluster_size)¶