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+/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ * Author(s): Pawel Dlotko
+ *
+ * Copyright (C) 2016 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef READ_PERSISTENCE_FROM_FILE_H_
+#define READ_PERSISTENCE_FROM_FILE_H_
+
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <algorithm>
+#include <string>
+#include <utility>
+#include <limits> // for std::numeric_limits<>
+
+namespace Gudhi {
+namespace Persistence_representations {
+
+/**
+ * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments).
+ * It reads the fist line which is not a comment and assume that there are some numerical entries over there. The
+ *program assume
+ * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4).
+ * If there are two numerical entries per line, then the function assume that they are birth/death coordinates.
+ * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death
+ *coordinates.
+ * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed
+ *over which
+ * persistence was computed, dimension and birth/death coordinates.
+ * The 'inf' string can appear only as a last element of a line.
+ * The procedure returns vector of persistence pairs.
+**/
+std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file(
+ std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {
+ bool dbg = false;
+
+ std::string line;
+ std::vector<std::pair<double, double> > barcode_initial =
+ read_persistence_intervals_in_dimension(filename, static_cast<int>(dimension));
+ std::vector<std::pair<double, double> > final_barcode;
+ final_barcode.reserve(barcode_initial.size());
+
+ if (dbg) {
+ std::cerr << "Here are the intervals that we read from the file : \n";
+ for (size_t i = 0; i != barcode_initial.size(); ++i) {
+ std::cout << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl;
+ }
+ getchar();
+ }
+
+ for (size_t i = 0; i != barcode_initial.size(); ++i) {
+ if (dbg) {
+ std::cout << "COnsidering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second
+ << std::endl;
+ }
+
+ if (barcode_initial[i].first > barcode_initial[i].second) {
+ // note that in this case barcode_initial[i].second != std::numeric_limits<double>::infinity()
+ if (dbg) std::cout << "Swap and enter \n";
+ // swap them to make sure that birth < death
+ final_barcode.push_back(std::pair<double, double>(barcode_initial[i].second, barcode_initial[i].first));
+ continue;
+ } else {
+ if (barcode_initial[i].second != std::numeric_limits<double>::infinity()) {
+ if (dbg) std::cout << "Simply enters\n";
+ // in this case, due to the previous conditions we know that barcode_initial[i].first <
+ // barcode_initial[i].second, so we put them as they are
+ final_barcode.push_back(std::pair<double, double>(barcode_initial[i].first, barcode_initial[i].second));
+ }
+ }
+
+ if ((barcode_initial[i].second == std::numeric_limits<double>::infinity()) &&
+ (what_to_substitute_for_infinite_bar != -1)) {
+ if (barcode_initial[i].first < what_to_substitute_for_infinite_bar) {
+ // if only birth < death.
+ final_barcode.push_back(
+ std::pair<double, double>(barcode_initial[i].first, what_to_substitute_for_infinite_bar));
+ }
+ } else {
+ // if the variable what_to_substitute_for_infinite_bar is not set, then we ignore all the infinite bars.
+ }
+ }
+
+ if (dbg) {
+ std::cerr << "Here are the final bars that we are sending further : \n";
+ for (size_t i = 0; i != final_barcode.size(); ++i) {
+ std::cout << final_barcode[i].first << " " << final_barcode[i].second << std::endl;
+ }
+ std::cerr << "final_barcode.size() : " << final_barcode.size() << std::endl;
+ getchar();
+ }
+
+ return final_barcode;
+} // read_persistence_intervals_in_one_dimension_from_file
+
+} // namespace Persistence_representations
+} // namespace Gudhi
+
+#endif // READ_PERSISTENCE_FROM_FILE_H_