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703 lines (615 loc) 路 22.4 KB
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//
// Created by Alan Freitas on 2020-07-07.
//
#include <cmath>
#include <sstream>
#include <regex>
#include <random>
#include <matplot/axes_objects/network.h>
#include <matplot/core/axes.h>
#include <matplot/util/common.h>
#include <nodesoup.hpp>
namespace matplot {
network::network(class axes* parent) : axes_object(parent) {}
network::network(class axes* parent, const std::vector<std::pair<size_t,size_t>>& edges, const vector_1d& weights, size_t n_vertices, const std::string& line_spec)
: axes_object(parent), edges_(edges), weights_(weights), n_vertices_(n_vertices), line_spec_(this,line_spec) {
line_spec_.marker_face(true);
}
std::vector<line_spec::style_to_plot> network::styles_to_plot() {
return {line_spec::style_to_plot::plot_line_only, line_spec::style_to_plot::plot_marker_only};
}
std::string network::plot_string() {
maybe_update_line_spec();
maybe_update_graph_layout();
std::string res;
bool first = true;
for (const auto& style: styles_to_plot()) {
if (!first) {
res += ",";
}
const bool we_are_plotting_line = style == line_spec::style_to_plot::plot_line_only;
const bool line_width_is_variable = !line_widths_.empty() && z_data_.empty();
const bool we_are_plotting_marker = style != line_spec::style_to_plot::plot_line_only;
const bool marker_size_is_variable = !marker_sizes_.empty();
const bool color_is_variable = !marker_colors_.empty();
std::string str;
if (we_are_plotting_line && directed_) {
str += " '-' with vectors " + line_spec_.plot_string(line_spec::style_to_plot::plot_line_only, false);
} else if (we_are_plotting_line && line_width_is_variable) {
str += " '-' with filledcurves " + line_spec_.plot_string(line_spec::style_to_plot::plot_line_only, false);
} else {
str = " '-' " + line_spec_.plot_string(style, true);
}
if (marker_size_is_variable && we_are_plotting_marker) {
str = std::regex_replace(str, std::regex(" pointsize \\d*\\.?\\d* "), " pointsize variable ");
}
if (color_is_variable && we_are_plotting_marker) {
str = std::regex_replace(str, std::regex(" linecolor rgb +[^ ]+ "), " linecolor palette ");
}
if (use_y2_) {
str += " xlim x1y2";
}
res += str;
if (first) {
first = false;
}
}
if (show_labels_ || !edge_labels_.empty()) {
res += ", '-' with labels left font \"Helvetica,11\" offset char 1";
}
return res;
}
std::string network::legend_string(const std::string& title) {
if (line_spec_.has_line() && line_spec_.has_non_custom_marker()) {
return " keyentry " + line_spec_.plot_string(line_spec::style_to_plot::plot_line_and_marker) + " title \"" + escape(title) + "\"";
} else if (line_spec_.has_line()) {
return " keyentry " + line_spec_.plot_string(line_spec::style_to_plot::plot_line_only) + " title \"" + escape(title) + "\"";
} else {
return " keyentry " + line_spec_.plot_string(line_spec::style_to_plot::plot_marker_only) + " title \"" + escape(title) + "\"";
}
}
std::string network::data_string() {
std::stringstream ss;
bool plot_z_data = z_data_.size() == x_data_.size();
bool line_width_is_variable = !line_widths_.empty() && z_data_.empty();
// plot edges
if (!directed_) {
// when not directed, each edge is a line
for (size_t i = 0; i < edges_.size(); ++i) {
ss << " " << x_data_[edges_[i].first];
if (!line_width_is_variable) {
ss << " " << y_data_[edges_[i].first];
} else {
ss << " " << y_data_[edges_[i].first] - line_widths_[i] / 2.;
ss << " " << y_data_[edges_[i].first] + line_widths_[i] / 2.;
}
if (plot_z_data) {
ss << " " << z_data_[edges_[i].first];
}
ss << "\n";
ss << " " << x_data_[edges_[i].second];
if (!line_width_is_variable) {
ss << " " << y_data_[edges_[i].second];
} else {
ss << " " << y_data_[edges_[i].second] - line_widths_[i] / 2.;
ss << " " << y_data_[edges_[i].second] + line_widths_[i] / 2.;
}
if (plot_z_data) {
ss << " " << z_data_[edges_[i].second];
}
ss << "\n\n";
}
ss << "e\n";
} else {
// when directed, each edge is a vector
// for each edge, plot two vectors
// - one from start to middle
// - one from middle to end
for (size_t i = 0; i < edges_.size(); ++i) {
double x1 = x_data_[edges_[i].first];
double y1 = y_data_[edges_[i].first];
double x2 = x_data_[edges_[i].second];
double y2 = y_data_[edges_[i].second];
double xmean = 0.5 * (x1 + x2);
double ymean = 0.5 * (y1 + y2);
double u1 = xmean - x1;
double v1 = ymean - y1;
double u2 = x2 - xmean;
double v2 = y2 - ymean;
if (!plot_z_data) {
ss << " " << x1 << " " << y1 << " " << u1 << " " << v1 << "\n";
ss << " " << xmean << " " << ymean << " " << u2 << " " << v2 << "\n";
} else {
double z1 = z_data_[edges_[i].first];
double z2 = z_data_[edges_[i].second];
double zmean = 0.5 * (z1 + z2);
double w1 = zmean - z1;
double w2 = z2 - zmean;
ss << " " << x1 << " " << y1 << " " << z1 << " " << u1 << " " << v1 << " " << w1 << "\n";
ss << " " << xmean << " " << ymean << " " << zmean << " " << u2 << " " << v2 << " " << w2 << "\n";
}
}
ss << "e\n";
}
// plot vertices
const bool marker_size_is_variable = !marker_sizes_.empty();
const bool marker_color_is_variable = !marker_colors_.empty();
for (size_t i = 0; i < x_data_.size(); ++i) {
ss << " " << x_data_[i];
ss << " " << y_data_[i];
if (plot_z_data) {
ss << " " << z_data_[i];
}
if (marker_size_is_variable) {
ss << " " << marker_sizes_[i];
}
if (marker_color_is_variable) {
ss << " " << marker_colors_[i];
}
ss << "\n";
}
ss << "e\n";
// plot labels
if (show_labels_ || !edge_labels_.empty()) {
if (show_labels_) {
for (size_t i = 0; i < x_data_.size(); ++i) {
ss << " " << x_data_[i];
ss << " " << y_data_[i];
if (plot_z_data) {
ss << " " << z_data_[i];
}
if (node_labels().size() > i) {
ss << " " << std::quoted(node_labels_[i]);
} else {
ss << " " << i;
}
ss << "\n";
}
}
// plot edge labels
if (!edge_labels_.empty()) {
for (size_t i = 0; i < edge_labels_.size(); ++i) {
ss << " " << 0.5*(x_data_[edges_[i].first] + x_data_[edges_[i].second]);
ss << " " << 0.5*(y_data_[edges_[i].first] + y_data_[edges_[i].second]);
if (plot_z_data) {
ss << " " << 0.5*(z_data_[edges_[i].first] + z_data_[edges_[i].second]);
}
ss << " " << std::quoted(edge_labels_[i]);
ss << "\n";
}
}
ss << "e\n";
}
return ss.str();
}
void network::maybe_update_line_spec() {
if (line_spec_.has_line() && !line_spec_.user_color()) {
// if user didn't set the color, get color from xlim
auto c = parent_->get_color_and_bump();
line_spec_.color(c);
} else if (line_spec_.has_non_custom_marker() && !line_spec_.user_color() && !line_spec_.marker_user_color()) {
auto c = parent_->get_color_and_bump();
line_spec_.marker_color(c);
}
}
void network::maybe_update_graph_layout() {
const bool layout_ready = !x_data_.empty();
if (!layout_ready) {
switch (layout_algorithm_) {
case layout::random:
process_random_layout();
break;
case layout::force:
process_force_layout();
break;
case layout::automatic: {
size_t n_edges = edges_.size();
size_t n_vert = n_vertices();
if (n_vert < 100 && n_edges < 1000) {
process_kawai_layout();
} else {
process_force_layout();
}
}
case layout::kawai:
process_kawai_layout();
break;
case layout::circle:
process_circle_layout();
break;
default:
break;
}
}
}
/// If the user has not provided a list of nodes
/// we assume this is a list from 0 to max(edge)
void network::infer_n_vertices() {
// look for highest edge index
size_t n_vertices = edges_[0].first;
for (const auto &[edge_index_a, edge_index_b] : edges_) {
if (edge_index_a > n_vertices) {
n_vertices = edge_index_a;
}
if (edge_index_b > n_vertices) {
n_vertices = edge_index_b;
}
}
n_vertices_ = n_vertices + 1;
}
size_t network::n_vertices() {
if (n_vertices_ != 0) {
return n_vertices_;
} else {
infer_n_vertices();
return n_vertices_;
}
}
void network::process_random_layout() {
x_data_.clear();
y_data_.clear();
z_data_.clear();
size_t n = n_vertices();
unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
std::mt19937 g(seed);
int width = parent_->width() * parent_->parent()->width();
int height = parent_->height() * parent_->parent()->height();
std::uniform_real_distribution<double> dx(0,width);
std::uniform_real_distribution<double> dy(0,height);
for (size_t i = 0; i < n; ++i) {
x_data_.emplace_back(dx(g));
y_data_.emplace_back(dy(g));
}
}
void network::process_force_layout() {
x_data_.clear();
y_data_.clear();
z_data_.clear();
size_t n = n_vertices();
nodesoup::adj_list_t g(n);
for (size_t i = 0; i < edges_.size(); ++i) {
g[edges_[i].first].emplace_back(edges_[i].second);
}
std::vector<double> radiuses = nodesoup::size_radiuses(g);
double k = layout_k_;
if (k == -1.0) {
k = 15.0;
}
int width = parent_->width() * parent_->parent()->width();
int height = parent_->height() * parent_->parent()->height();
int iters_count = layout_iterations_;
if (iters_count == -1) {
iters_count = 300;
}
std::vector<nodesoup::Point2D> positions = nodesoup::fruchterman_reingold(g, width, height, iters_count, k);
for (size_t i = 0; i < positions.size(); ++i) {
x_data_.emplace_back(positions[i].x);
y_data_.emplace_back(positions[i].y);
}
}
void network::process_circle_layout() {
int previous_layout_iterations = layout_iterations_;
double previous_layout_k = layout_k_;
layout_iterations_ = 0;
layout_k_ = 15.0;
process_force_layout();
layout_iterations_ = previous_layout_iterations;
layout_k_ = previous_layout_k;
}
void network::process_kawai_layout() {
x_data_.clear();
y_data_.clear();
z_data_.clear();
size_t n = n_vertices();
nodesoup::adj_list_t g(n);
for (size_t i = 0; i < edges_.size(); ++i) {
g[edges_[i].first].emplace_back(edges_[i].second);
}
std::vector<double> radiuses = nodesoup::size_radiuses(g);
double k = layout_k_;
if (k == -1.0) {
k = 300.0;
}
int width = parent_->width() * parent_->parent()->width();
int height = parent_->height() * parent_->parent()->height();
nodesoup::iter_callback_t cback = nullptr;
std::vector<nodesoup::Point2D> positions = nodesoup::kamada_kawai(g, width, height, k, energy_threshold_);
for (size_t i = 0; i < positions.size(); ++i) {
x_data_.emplace_back(positions[i].x);
y_data_.emplace_back(positions[i].y);
}
}
double network::xmax() {
maybe_update_graph_layout();
if (x_data_.empty()) {
if (!y_data_.empty()) {
return y_data_.size()-1;
} else {
return axes_object::xmax();
}
}
auto [xmin_it, xmax_it] = std::minmax_element(x_data_.begin(), x_data_.end());
return *xmax_it + 0.1 * (*xmax_it - *xmin_it);
}
double network::xmin() {
maybe_update_graph_layout();
if (x_data_.empty()) {
if (!y_data_.empty()) {
return 0;
} else {
return axes_object::xmin();
}
}
auto [xmin_it, xmax_it] = std::minmax_element(x_data_.begin(), x_data_.end());
return *xmin_it - 0.1 * (*xmax_it - *xmin_it);
}
double network::ymax() {
maybe_update_graph_layout();
if (y_data_.empty()) {
return axes_object::ymax();
}
auto [ymin_it, ymax_it] = std::minmax_element(y_data_.begin(), y_data_.end());
return *ymax_it + 0.1 * (*ymax_it - *ymin_it);
}
double network::ymin() {
maybe_update_graph_layout();
if (y_data_.empty()) {
return axes_object::ymin();
}
auto [ymin_it, ymax_it] = std::minmax_element(y_data_.begin(), y_data_.end());
return *ymin_it - 0.1 * (*ymax_it - *ymin_it);
}
enum axes_object::axes_category network::axes_category() {
if (z_data_.empty()) {
return axes_object::axes_category::two_dimensional;
} else {
return axes_object::axes_category::three_dimensional;
}
}
class network& network::line_style(const std::string& str) {
line_spec_.parse_string(str);
touch();
return *this;
}
const line_spec &network::line_spec() const {
return line_spec_;
}
line_spec &network::line_spec() {
return line_spec_;
}
class network& network::line_spec(const class line_spec &line_spec) {
line_spec_ = line_spec;
touch();
return *this;
}
const std::vector<double> &network::y_data() const {
return y_data_;
}
class network& network::y_data(const std::vector<double> &y_data) {
y_data_ = y_data;
if (!y_data.empty() && parent_->children().size() == 1) {
parent_->y_axis().limits({ymin(), ymax()});
}
touch();
return *this;
}
const std::vector<double> &network::x_data() const {
return x_data_;
}
class network& network::x_data(const std::vector<double> &x_data) {
x_data_ = x_data;
if (!x_data.empty() && parent_->children().size() == 1) {
parent_->x_axis().limits({xmin(), xmax()});
}
touch();
return *this;
}
const std::vector<double> &network::z_data() const {
return z_data_;
}
class network& network::z_data(const std::vector<double> &z_data) {
z_data_ = z_data;
if (!z_data.empty() && parent_->children().size() == 1) {
auto [zmin,zmax] = minmax(z_data);
parent_->z_axis().limits({zmin, zmax});
}
touch();
return *this;
}
bool network::visible() const {
return visible_;
}
class network& network::visible(bool visible) {
visible_ = visible;
touch();
return *this;
}
float network::line_width() const {
return line_spec().line_width();
}
class network& network::line_width(float line_width) {
line_spec().line_width(line_width);
return *this;
}
enum line_spec::marker_style network::marker_style() const {
return line_spec().marker();
}
enum line_spec::marker_style network::marker() const {
return line_spec().marker();
}
float network::marker_size() const {
return line_spec().marker_size();
}
class network& network::marker_size(float size) {
line_spec().marker_size(size);
return *this;
}
class network& network::marker_size(const std::vector<float>& size_vector) {
marker_sizes_ = size_vector;
touch();
return *this;
}
class network& network::marker_size(const std::vector<double>& size_vector) {
std::vector<float> size_vector_float(size_vector.begin(), size_vector.end());
marker_size(size_vector_float);
return *this;
}
bool network::marker_face() const {
return line_spec().marker_face();
}
class network& network::marker_face(bool marker_face) {
line_spec().marker_face(marker_face);
return *this;
}
const std::array<float, 4>& network::color() const {
return line_spec().color();
}
const std::array<float, 4>& network::marker_color() const {
return line_spec().marker_color();
}
const std::array<float, 4>& network::marker_face_color() const {
return line_spec().marker_face_color();
}
bool network::use_y2() const {
return use_y2_;
}
class network& network::use_y2(bool use_y_2) {
use_y2_ = use_y_2;
touch();
return *this;
}
bool network::show_labels() const {
return show_labels_;
}
class network& network::show_labels(bool v) {
show_labels_ = v;
touch();
return *this;
}
bool network::directed() const {
return directed_;
}
class network& network::directed(bool v) {
if (v != directed_) {
directed_ = v;
touch();
}
return *this;
}
bool network::use_y_2() const {
return use_y2_;
}
class network& network::use_y_2(bool use_y_2) {
use_y2_ = use_y_2;
touch();
return *this;
}
const std::vector<std::string> &network::edge_labels() const {
return edge_labels_;
}
class network& network::edge_labels(const std::vector<std::string> &edge_labels) {
edge_labels_ = edge_labels;
touch();
return *this;
}
const std::vector<std::string> &network::node_labels() const {
return node_labels_;
}
class network& network::node_labels(const std::vector<std::string> &node_labels) {
node_labels_ = node_labels;
touch();
return *this;
}
const std::vector<double> &network::line_widths() const {
return line_widths_;
}
class network& network::line_widths(const std::vector<double> &line_widths) {
line_widths_ = line_widths;
touch();
return *this;
}
const std::vector<std::pair<size_t, size_t>> &network::edges() const {
return edges_;
}
class network& network::edges(const std::vector<std::pair<size_t, size_t>> &edges) {
edges_ = edges;
touch();
return *this;
}
class network& network::n_vertices(size_t n_vertices) {
n_vertices_ = n_vertices;
touch();
return *this;
}
const vector_1d &network::weights() const {
return weights_;
}
class network& network::weights(const vector_1d &weights) {
weights_ = weights;
touch();
return *this;
}
matplot::network::layout network::layout_algorithm() const {
return layout_algorithm_;
}
class network& network::layout_algorithm(matplot::network::layout layout_algorithm) {
if (layout_algorithm_ != layout_algorithm) {
layout_algorithm_ = layout_algorithm;
x_data_.clear();
y_data_.clear();
z_data_.clear();
touch();
}
return *this;
}
double network::layout_k() const {
return layout_k_;
}
class network& network::layout_k(double layout_k) {
if (layout_k_ != layout_k) {
layout_k_ = layout_k;
x_data_.clear();
y_data_.clear();
z_data_.clear();
touch();
}
return *this;
}
int network::layout_iterations() const {
return layout_iterations_;
}
class network& network::layout_iterations(int layout_iterations) {
if (layout_iterations_ != layout_iterations) {
layout_iterations_ = layout_iterations;
x_data_.clear();
y_data_.clear();
z_data_.clear();
touch();
}
return *this;
}
double network::energy_threshold() const {
return energy_threshold_;
}
class network& network::energy_threshold(double energy_threshold) {
if (energy_threshold_ != energy_threshold) {
energy_threshold_ = energy_threshold;
x_data_.clear();
y_data_.clear();
z_data_.clear();
touch();
}
return *this;
}
const std::vector<float> &network::marker_sizes() const {
return marker_sizes_;
}
class network& network::marker_sizes(const std::vector<float> &marker_sizes) {
marker_sizes_ = marker_sizes;
touch();
return *this;
}
const std::vector<double> &network::marker_colors() const {
return marker_colors_;
}
}