Merge pull request #1005 from MClemot/ripsPersistenceDiagram

Rips persistence diagram

core/base/ripsPersistenceDiagram/CMakeLists.txt

@@ -0,0 +1,10 @@
+ttk_add_base_library(ripsPersistenceDiagram
+  SOURCES
+    RipsPersistenceDiagram.cpp
+    ripserpy.cpp
+  HEADERS
+    RipsPersistenceDiagram.h
+    ripser.h
+  DEPENDS
+    common
+)

core/base/ripsPersistenceDiagram/RipsPersistenceDiagram.cpp

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+#include <RipsPersistenceDiagram.h>
+
+ttk::RipsPersistenceDiagram::RipsPersistenceDiagram() {
+  // inherited from Debug: prefix will be printed at the beginning of every msg
+  this->setDebugMsgPrefix("RipsPersistenceDiagram");
+}
+
+int ttk::RipsPersistenceDiagram::execute(
+  const std::vector<std::vector<double>> &points,
+  std::vector<std::vector<ripser::pers_pair_t>> &ph) const {
+
+  ripser::ripser(points, SimplexMaximumDiameter, SimplexMaximumDimension,
+                 InputIsDistanceMatrix, ph);
+
+  return 0;
+}

core/base/ripsPersistenceDiagram/RipsPersistenceDiagram.h

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+/// \ingroup base
+/// \class ttk::RipsPersistenceDiagram
+/// \author Mattéo Clémot <matteo.clemot@univ-lyon1.fr>
+/// \date January 2024.
+///
+/// \brief TTK base class that computes the persistence diagram of a Rips
+/// complex.
+///
+/// This module defines the %RipsPersistenceDiagram class that takes a point
+/// cloud or a distance matrix and computes the persistence diagram of its Rips
+/// complex.
+///
+/// \sa ttk::Triangulation
+/// \sa ttkRipsPersistenceDiagram.cpp %for a usage example.
+
+#pragma once
+
+// ttk common includes
+#include <Debug.h>
+
+#include <ripser.h>
+
+namespace ttk {
+
+  /**
+   * The RipsPersistenceDiagram class provides a method to call the code Ripser
+   * in order to compute the persistence diagram of the Rips complex of the
+   * input.
+   */
+  class RipsPersistenceDiagram : virtual public Debug {
+
+  public:
+    RipsPersistenceDiagram();
+
+    /**
+     * @brief Main entry point
+     *
+     * @param[in] points Input point cloud in any dimension or input distance
+     * matrix
+     * @param[out] ph Computed Rips persistence diagram
+     */
+    int execute(const std::vector<std::vector<double>> &points,
+                std::vector<std::vector<ripser::pers_pair_t>> &ph) const;
+
+  protected:
+    /** Max dimension of computed persistence diagram */
+    int SimplexMaximumDimension{1};
+    /** Rips threshold */
+    double SimplexMaximumDiameter{1.0};
+    /** is input a distance matrix */
+    int InputIsDistanceMatrix{0};
+
+  }; // RipsPersistenceDiagram class
+
+} // namespace ttk

core/base/ripsPersistenceDiagram/ripser.h

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+/// \ingroup base
+/// \author Mattéo Clémot <matteo.clemot@univ-lyon1.fr>
+/// \date January 2024.
+
+#pragma once
+
+#include <algorithm>
+#include <cassert>
+#include <chrono>
+#include <cmath>
+#include <fstream>
+#include <iostream>
+#include <numeric>
+#include <queue>
+#include <sstream>
+#include <unordered_map>
+
+namespace ripser {
+
+  using value_t = double;
+  using index_t = int64_t;
+  using coefficient_t = uint16_t;
+
+  using simplex_t = std::vector<index_t>;
+  using simplex_diam_t = std::pair<simplex_t, value_t>;
+  using pers_pair_t = std::pair<simplex_diam_t, simplex_diam_t>;
+
+  void ripser(std::vector<std::vector<value_t>> points,
+              value_t threshold,
+              index_t dim_max,
+              bool distanceMatrix,
+              std::vector<std::vector<pers_pair_t>> &ph);
+
+} // namespace ripser