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, long long 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::vector<long long> kcenter_cut(long long k)

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

std::vector<long long> threshold_elbow_cut()

std::vector<long long> threshold_cut(long long k)

std::vector<long long> stability_cut(unsigned long long mcs)

std::vector<long long> normalized_stability_cut(unsigned long long mcs)

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::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

long long 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::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> &res, std::shared_ptr<Node> tree, long long label)

void extract_labels(std::vector<long long> &res, std::shared_ptr<Node> solution)

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

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)