multipers 2.3.3b6__cp310-cp310-macosx_11_0_arm64.whl

multipers/gudhi/scc_io.h

@@ -0,0 +1,310 @@
+#ifndef MULTIPERS_SCC_IO_H
+#define MULTIPERS_SCC_IO_H
+
+#include <algorithm>
+#include <cassert>
+#include <cstddef>
+#include <ostream>
+#include <fstream>
+#include <iostream>
+#include <stdexcept>
+#include <string>
+#include <vector>
+#include <limits>
+#include <iomanip>
+#include <cmath>
+
+template <class Slicer>
+inline Slicer read_scc_file(const std::string& inFilePath,
+                            bool isRivetCompatible = false,
+                            bool isReversed = false,
+                            int shiftDimensions = 0) {
+  using Filtration_value = typename Slicer::Filtration_value;
+
+  std::string line;
+  std::ifstream file(inFilePath);
+  Slicer slicer;
+  unsigned int numberOfParameters;
+
+  if (file.is_open()) {
+    auto error = [&file](std::string msg) {
+      file.close();
+      throw std::invalid_argument(msg);
+    };
+    auto is_comment_or_empty_line = [](const std::string& line) -> bool {
+      size_t current = line.find_first_not_of(' ', 0);
+      if (current == std::string::npos) return true;  // is empty line
+      if (line[current] == '#') return true;          // is comment
+      return false;
+    };
+
+    while (getline(file, line, '\n') && is_comment_or_empty_line(line));
+    if (!file) error("Empty file!");
+
+    if (isRivetCompatible && line.compare("firep") != 0) error("Wrong file format. Should start with 'firep'.");
+    if (!isRivetCompatible && line.compare("scc2020") != 0) error("Wrong file format. Should start with 'scc2020'.");
+
+    while (getline(file, line, '\n') && is_comment_or_empty_line(line));
+    if (!file) error("Premature ending of the file. Stops before numbers of parameters.");
+
+    if (isRivetCompatible) {
+      numberOfParameters = 2;
+      getline(file, line, '\n');  // second rivet label
+    } else {
+      std::size_t current = line.find_first_not_of(' ', 0);
+      std::size_t next = line.find_first_of(' ', current);
+      numberOfParameters = std::stoi(line.substr(current, next - current));
+    }
+
+    while (getline(file, line, '\n') && is_comment_or_empty_line(line));
+    if (!file) error("Premature ending of the file. Not a single cell was specified.");
+
+    std::vector<unsigned int> counts;
+    unsigned int numberOfCells = 0;
+    counts.reserve(line.size() + shiftDimensions);
+    std::size_t current = line.find_first_not_of(' ', 0);
+    if (shiftDimensions != 0 && isReversed && current != std::string::npos) {
+      if (shiftDimensions > 0) {
+        counts.resize(shiftDimensions, 0);
+      } else {
+        for (int i = shiftDimensions; i < 0 && current != std::string::npos; ++i) {
+          std::size_t next = line.find_first_of(' ', current);
+          current = line.find_first_not_of(' ', next);
+        }
+      }
+    }
+    while (current != std::string::npos) {
+      std::size_t next = line.find_first_of(' ', current);
+      counts.push_back(std::stoi(line.substr(current, next - current)));
+      numberOfCells += counts.back();
+      current = line.find_first_not_of(' ', next);
+    }
+    if (shiftDimensions != 0 && !isReversed) {
+      counts.resize(counts.size() + shiftDimensions, 0);
+    }
+
+    std::size_t dimIt = 0;
+    while (dimIt < counts.size() && counts[dimIt] == 0) ++dimIt;
+
+    if (dimIt == counts.size()) return slicer;
+
+    std::size_t shift = isReversed ? 0 : counts[dimIt];
+    unsigned int nextShift = isReversed ? 0 : counts.size() == 1 ? 0 : counts[dimIt + 1];
+    unsigned int tmpNextShift = counts[dimIt];
+
+    auto get_boundary = [&isReversed, &numberOfCells](const std::string& line,
+                                                      std::size_t start,
+                                                      std::size_t shift) -> std::vector<unsigned int> {
+      std::vector<unsigned int> res;
+      res.reserve(line.size() - start);
+      std::size_t current = line.find_first_not_of(' ', start);
+      while (current != std::string::npos) {
+        std::size_t next = line.find_first_of(' ', current);
+        unsigned int idx = std::stoi(line.substr(current, next - current)) + shift;
+        res.push_back(isReversed ? idx : numberOfCells - 1 - idx);
+        current = line.find_first_not_of(' ', next);
+      }
+      std::sort(res.begin(), res.end());
+      return res;
+    };
+    auto get_filtration_value = [](const std::string& line, std::size_t end) -> Filtration_value {
+      Filtration_value res(0);
+      res.reserve(end);
+      bool isPlusInf = true;
+      bool isMinusInf = true;
+      std::size_t current = line.find_first_not_of(' ', 0);
+      while (current < end) {
+        std::size_t next = line.find_first_of(' ', current);
+        res.push_back(std::stod(line.substr(current, next - current)));
+        if (isPlusInf && res.back() != Filtration_value::T_inf) isPlusInf = false;
+        if (isMinusInf && res.back() != -Filtration_value::T_inf) isMinusInf = false;
+        current = line.find_first_not_of(' ', next);
+      }
+      if (isPlusInf) res = Filtration_value::inf();
+      if (isMinusInf) res = Filtration_value::minus_inf();
+      return res;
+    };
+
+    std::vector<std::vector<unsigned int> > generator_maps(numberOfCells);
+    std::vector<int> generator_dimensions(numberOfCells);
+    std::vector<typename Slicer::Filtration_value> generator_filtrations(numberOfCells);
+    std::size_t i = 0;
+    // because of possible negative dimension shifts, the document should not always be read to the end
+    // therefore `dimIt < counts.size()` is also a stop condition
+    while (getline(file, line, '\n') && dimIt < counts.size()) {
+      if (!is_comment_or_empty_line(line)) {
+        std::size_t sep = line.find_first_of(';', 0);
+        generator_filtrations[i] = get_filtration_value(line, sep);
+        if (generator_filtrations[i].is_finite() && generator_filtrations[i].num_parameters() != numberOfParameters)
+          error("Wrong format. The number of parameters does not match.");
+        generator_maps[i] = get_boundary(line, sep + 1, shift);
+        generator_dimensions[i] = isReversed ? dimIt : counts.size() - 1 - dimIt;
+
+        --counts[dimIt];
+        while (dimIt < counts.size() && counts[dimIt] == 0) {
+          ++dimIt;
+          if (dimIt != counts.size()) {
+            shift += nextShift;
+            nextShift = isReversed ? tmpNextShift : dimIt < counts.size() - 1 ? counts[dimIt + 1] : 0;
+            tmpNextShift = counts[dimIt];
+          }
+        }
+        ++i;
+      }
+    }
+
+    if (!isReversed) {  // to order by dimension
+      std::reverse(generator_dimensions.begin(), generator_dimensions.end());
+      std::reverse(generator_maps.begin(), generator_maps.end());
+      std::reverse(generator_filtrations.begin(), generator_filtrations.end());
+    }
+
+    slicer = Slicer(generator_maps, generator_dimensions, generator_filtrations);
+
+    file.close();
+  } else {
+    std::cerr << "Unable to open input file: " << inFilePath << std::endl;
+    file.setstate(std::ios::failbit);
+  }
+
+  return slicer;
+};
+
+template <class Slicer>
+inline void write_scc_file(const std::string& outFilePath,
+                           const Slicer& slicer,
+                           int numberOfParameters = -1,
+                           int degree = -1,
+                           bool rivetCompatible = false,
+                           bool IgnoreLastGenerators = false,
+                           bool stripComments = false,
+                           bool reverse = false) {
+  constexpr bool verbose = false;
+  if (numberOfParameters < 0) {
+    numberOfParameters = slicer.num_parameters();
+  }
+  assert(numberOfParameters > 0 && "Invalid number of parameters!");
+
+  std::ofstream file(outFilePath);
+
+  if (rivetCompatible)
+    file << "firep\n";
+  else
+    file << "scc2020\n";
+
+  if (!stripComments && !rivetCompatible)
+    file << "# This file was generated by multipers (https://github.com/DavidLapous/multipers).\n";
+
+  if (!stripComments && !rivetCompatible) file << "# Number of parameters\n";
+
+  if (rivetCompatible) {
+    assert(numberOfParameters == 2 && "Rivet only handles bifiltrations.");
+    file << "Filtration 1\n";
+    file << "Filtration 2\n";
+  } else {
+    file << std::to_string(numberOfParameters) << "\n";
+  }
+
+  if (!stripComments) file << "# Sizes of generating sets\n";
+
+  using Filtration_value = typename Slicer::Filtration_value;
+
+  const auto& boundaries = slicer.get_structure();
+  int maxDim = boundaries.max_dimension();
+  int minDim = maxDim;
+
+  std::vector<std::vector<std::size_t> > indicesByDim(maxDim + 1);
+  std::vector<std::size_t> shiftedIndices(boundaries.size());
+  for (std::size_t i = 0; i < boundaries.size(); ++i) {
+    auto dim = boundaries.dimension(i);
+    minDim = dim < minDim ? dim : minDim;
+    auto& atDim = indicesByDim[reverse ? dim : maxDim - dim];
+    shiftedIndices[i] = atDim.size();
+    atDim.push_back(i);
+  }
+  if (degree < 0) degree = minDim;
+  int minIndex = reverse ? degree - 1 : 0;
+  int maxIndex = reverse ? maxDim : maxDim - degree + 1;
+  if (maxIndex < -1) maxIndex = -1;
+  if (IgnoreLastGenerators) maxIndex--;
+  if (rivetCompatible)
+    minIndex = maxIndex -2;
+
+  if constexpr (verbose) {
+    std::cout << "minDim = " << minDim << " maxDim = " << maxDim << " minIndex = " << minIndex
+              << " maxIndex = " << maxIndex << " degree = " << degree << std::endl;
+  }
+
+  auto print_fil_values = [&](const Filtration_value& fil) {
+    if (fil.is_finite()) {
+      if constexpr (Filtration_value::is_multicritical()) {
+        for (const auto& ifil : fil) {
+          for (auto f : ifil) file << f << " ";
+        }
+      } else {
+        assert(fil.size() == static_cast<unsigned int>(numberOfParameters));
+        for (auto f : fil) file << f << " ";
+      }
+    } else {
+      // assert(fil.size() == 1);
+      for (int p = 0; p < numberOfParameters; ++p) file << fil[0] << " ";
+    }
+  };
+
+  if (minIndex < 0) file << 0 << " ";
+  for (int i = 0; i < minIndex; ++i) file << 0 << " ";
+  for (int i = std::max(minIndex, 0); i <= std::min(maxDim, maxIndex); ++i) {
+    file << indicesByDim[i].size() << " ";
+  }
+  if (!rivetCompatible)
+    for (int i = maxIndex + 1; i <= maxDim; ++i) file << 0 << " ";
+  if (maxIndex > maxDim) file << 0;
+  file << "\n";
+
+  file << std::setprecision(std::numeric_limits<typename Filtration_value::value_type>::digits);
+
+  std::size_t startIndex = reverse ? minIndex + 1 : minIndex;
+  std::size_t endIndex = reverse ? maxIndex : maxIndex - 1;
+  const auto& filtValues = slicer.get_filtrations();
+  int currDim;
+  if (reverse)
+    currDim = minIndex == -1 ? 0 : minIndex;
+  else
+    currDim = maxIndex == maxDim + 1 ? maxDim + 1 : maxDim;
+
+  if (reverse) {
+    if (!stripComments) file << "# Block of dimension " << currDim++ << "\n";
+    if (minIndex >= 0) {
+      for (auto index : indicesByDim[minIndex]) {
+        print_fil_values(filtValues[index]);
+        file << ";\n";
+      }
+    }
+  }
+  for (std::size_t i = startIndex; i <= endIndex; ++i) {
+    if (!stripComments) {
+      file << "# Block of dimension " << currDim << "\n";
+      if (reverse)
+        ++currDim;
+      else
+        --currDim;
+    }
+    for (auto index : indicesByDim[i]) {
+      print_fil_values(filtValues[index]);
+      file << "; ";
+      for (auto b : boundaries[index]) file << shiftedIndices[b] << " ";
+      file << "\n";
+    }
+  }
+  if (!reverse) {
+    if (!stripComments) file << "# Block of dimension " << currDim << "\n";
+    if (maxIndex <= maxDim) {
+      for (auto index : indicesByDim[maxIndex]) {
+        print_fil_values(filtValues[index]);
+        file << ";\n";
+      }
+    }
+  }
+};
+
+#endif  // MULTIPERS_SCC_IO_H