read_binary.h

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// SPDX-FileCopyrightText: © 2025 PRISMS Center at the University of Michigan
// SPDX-License-Identifier: GNU Lesser General Public Version 2.1
 
#pragma once
 
#include <deal.II/base/exceptions.h>
#include <deal.II/base/point.h>
#include <deal.II/lac/vector.h>
 
#include <prismspf/core/types.h>
 
#include <prismspf/field_input/read_field_base.h>
 
#include <prismspf/utilities/utilities.h>
 
#include "prismspf/core/conditional_ostreams.h"
 
#include <bit>
#include <fstream>
#include <iostream>
#include <ranges>
#include <string>
#include <utility>
 
PRISMS_PF_BEGIN_NAMESPACE
 
template <unsigned int dim, typename number>
class ReadBinary : public ReadFieldBase<dim, number>
{
public:
  ReadBinary(const InitialConditionFile       &_ic_file,
             const SpatialDiscretization<dim> &_spatial_discretization);
 
  void
  print_file() override;
 
  static void
  write_file(const std::vector<number> &data, const InitialConditionFile &ic_file);
 
  number
  get_scalar_value(const dealii::Point<dim> &point,
                   const std::string        &scalar_name) override;
 
  dealii::Vector<number>
  get_vector_value(const dealii::Point<dim> &point,
                   const std::string        &vector_name) override;
 
private:
  void
  check_file_size();
 
  dealii::Vector<number>
  get_value(const dealii::types::global_dof_index index, const unsigned int n_components);
 
  dealii::Vector<number>
  interpolate(const dealii::Point<dim> &point, const unsigned int n_components);
 
  dealii::types::global_dof_index n_points = 1;
 
  dealii::types::global_dof_index n_values = 0;
 
  std::vector<number> data;
};
 
template <unsigned int dim, typename number>
inline ReadBinary<dim, number>::ReadBinary(
  const InitialConditionFile       &_ic_file,
  const SpatialDiscretization<dim> &_spatial_discretization)
  : ReadFieldBase<dim, number>(_ic_file, _spatial_discretization)
{
  // Make sure the dataset format is correct
  AssertThrow(this->ic_file.dataset_format == DataFormatType::FlatBinary,
              dealii::ExcMessage("Dataset format must be FlatBinary"));
 
  // Check that only one field is being read in
  AssertThrow(this->ic_file.file_variable_names.size() == 1 &&
                this->ic_file.simulation_variable_names.size() == 1,
              dealii::ExcMessage("Only one field can be read in from a binary file"));
 
  // Make sure we have a rectangular domain
  AssertThrow(_spatial_discretization.type == TriangulationType::Rectangular,
              dealii::ExcMessage(
                "Only rectangular domains are supported for binary input files"));
 
  // Compute the total number of points in the binary file
  for (unsigned int d : std::views::iota(0U, dim))
    {
      n_points *= this->ic_file.n_data_points[d];
    }
 
  // Check that the binary matches an expected size
  check_file_size();
 
  // Read in the binary file
  std::ifstream data_file(this->ic_file.filename, std::ios::binary);
  AssertThrow(data_file,
              dealii::ExcMessage("Could not open binary file: " +
                                 this->ic_file.filename));
 
  // Reserve space in the data vector
  data.reserve(n_values);
 
  // Read in the data
  for (dealii::types::global_dof_index i : std::views::iota(0U, n_values))
    {
      std::array<char, sizeof(number)> buffer;
      data_file.read(buffer.data(), sizeof(number));
      data.push_back(std::bit_cast<number>(buffer));
    }
  data_file.close();
}
 
template <unsigned int dim, typename number>
inline void
ReadBinary<dim, number>::check_file_size()
{
  // Grab the file size of the binary file in bytes
  auto file_size = std::filesystem::file_size(this->ic_file.filename);
 
  // Compute the expected size of the binary file. This is simply the number of points
  // multiplied by the size of each point in bytes.
  auto expected_size_scalar = static_cast<std::uintmax_t>(n_points * sizeof(number));
  auto expected_size_vector = static_cast<std::uintmax_t>(dim * expected_size_scalar);
 
  // Make sure expected size is not zero
  AssertThrow(
    expected_size_scalar != 0 && expected_size_vector != 0,
    dealii::ExcMessage(
      "Expected input array size is zero, check that the number of data points "
      "in each used direction is set correctly in the input file for your binary file. "
      "You likely have the number of data points set to zero in all directions."));
  // Make sure the size matches for either a scalar or vector
  AssertThrow(file_size == expected_size_scalar || file_size == expected_size_vector,
              dealii::ExcMessage(
                "Expected binary file size (" + std::to_string(expected_size_scalar) +
                " bytes for scalar or " + std::to_string(expected_size_vector) +
                " bytes for vector) does not match actual file size (" +
                std::to_string(file_size) + " bytes)."));
 
  // Set the number of values
  n_values = file_size == expected_size_scalar ? n_points : dim * n_points;
}
 
template <unsigned int dim, typename number>
inline void
ReadBinary<dim, number>::write_file(const std::vector<number>  &data,
                                    const InitialConditionFile &ic_file)
{
  // Try to open the file
  std::ofstream data_file(ic_file.filename, std::ios::binary);
  AssertThrow(data_file,
              dealii::ExcMessage("Could not open binary file: " + ic_file.filename));
 
  // Write the data
  for (dealii::types::global_dof_index j : std::views::iota(0U, data.size()))
    {
      auto buffer = std::bit_cast<std::array<char, sizeof(number)>>(data[j]);
      data_file.write(buffer.data(), sizeof(number));
    }
  data_file.close();
}
 
template <unsigned int dim, typename number>
inline dealii::Vector<number>
ReadBinary<dim, number>::get_value(const dealii::types::global_dof_index index,
                                   const unsigned int                    n_components)
{
  // Create vector to hold the value with the correct number of components
  dealii::Vector<number> value(n_components);
 
  // Check that the number of components matches what we expect from the number of values
  Assert(n_values % n_components == 0,
         dealii::ExcMessage("The number of components requested in the get_value call "
                            "does not match the number of values in the binary file."));
 
  // Fill the value vector
  for (unsigned int component : std::views::iota(0U, n_components))
    {
      Assert(((n_components * index) + component) < data.size(),
             dealii::ExcMessage("Index out of bounds in ReadBinary::get_vals"));
      value[component] = data[(n_components * index) + component];
    }
 
  return value;
}
 
template <unsigned int dim, typename number>
inline dealii::Vector<number>
ReadBinary<dim, number>::interpolate(const dealii::Point<dim> &point,
                                     const unsigned int        n_components)
{
  Assert(n_components == 1 || n_components == dim,
         dealii::ExcMessage(
           "Number of components for interpolation must be 1 (scalar) or dim (vector)"));
 
  // Create a vector to hold the interpolated value
  dealii::Vector<number> value(n_components);
 
  // Get the spatial discretization
  const auto &spatial_discretization = this->spatial_discretization;
 
  // Compute the spacing in each direction
  std::array<number, dim> spacing;
  for (unsigned int d : std::views::iota(0U, dim))
    {
      spacing[d] = spatial_discretization.rectangular_mesh.size[d] /
                   static_cast<number>(this->ic_file.n_data_points[d]);
    }
 
  // Compute the indices of the lower corner of the cell containing the point
  std::array<dealii::types::global_dof_index, dim> lower_indices;
  for (unsigned int d : std::views::iota(0U, dim))
    {
      lower_indices[d] =
        static_cast<dealii::types::global_dof_index>(std::floor(point[d] / spacing[d]));
      // Make sure we don't go out of bounds
      if (lower_indices[d] >= this->ic_file.n_data_points[d] - 1)
        {
          lower_indices[d] = this->ic_file.n_data_points[d] - 2;
        }
    }
 
  // Compute the weights for interpolation in each direction
  std::array<number, dim> weights;
  for (unsigned int d : std::views::iota(0U, dim))
    {
      weights[d] = (point[d] - lower_indices[d] * spacing[d]) / spacing[d];
    }
 
  // Perform multilinear interpolation based on the dimension
  if constexpr (dim == 1)
    {
      // Here is the map of the nodes in 1D:
      // 0 — 1
 
      // Grab the index of the lower left corner of the cell
      // cppcheck-suppress-begin containerOutOfBounds
      auto lower_index = lower_indices[0];
      // cppcheck-suppress-end containerOutOfBounds
 
      // Get the indices of the two points in 1D
      auto node_index_0 = lower_index;
      auto node_index_1 = lower_index + 1;
 
      // Get the values at these points
      auto value_0 = get_value(node_index_0, n_components);
      auto value_1 = get_value(node_index_1, n_components);
 
      // Interpolate
      for (unsigned int c : std::views::iota(0U, n_components))
        {
          // cppcheck-suppress-begin containerOutOfBounds
          value[c] = (1.0 - weights[0]) * value_0[c] + weights[0] * value_1[c];
          // cppcheck-suppress-end containerOutOfBounds
        }
    }
  else if constexpr (dim == 2)
    {
      // Here is the map of the nodes in 2D:
      // 01 — 11
      // |     |
      // 00 — 10
 
      // Grab the row length in the x-direction (0th direction)
      auto row_length_0 = this->ic_file.n_data_points[0];
 
      // Grab the index of the lower left corner of the cell
      // cppcheck-suppress-begin containerOutOfBounds
      auto lower_index = lower_indices[0] + (lower_indices[1] * row_length_0);
      // cppcheck-suppress-end containerOutOfBounds
 
      // Get the indices of the four points in 2D
      auto node_index_00 = lower_index;
      auto node_index_10 = lower_index + 1;
 
      auto node_index_01 = lower_index + row_length_0;
      auto node_index_11 = lower_index + row_length_0 + 1;
 
      // Get the values at these points
      auto value_00 = get_value(node_index_00, n_components);
      auto value_10 = get_value(node_index_10, n_components);
 
      auto value_01 = get_value(node_index_01, n_components);
      auto value_11 = get_value(node_index_11, n_components);
 
      // Interpolate
      for (unsigned int c : std::views::iota(0U, n_components))
        {
          // cppcheck-suppress-begin containerOutOfBounds
          value[c] = (1.0 - weights[0]) * (1.0 - weights[1]) * value_00[c] +
                     weights[0] * (1.0 - weights[1]) * value_10[c] +
                     (1.0 - weights[0]) * weights[1] * value_01[c] +
                     weights[0] * weights[1] * value_11[c];
          // cppcheck-suppress-end containerOutOfBounds
        }
    }
  else if constexpr (dim == 3)
    {
      // Here is the map of the nodes in 3D:
      //
      //   011 ———— 111
      //   / |      / |
      //  /  001   /  |
      // 010 ——— 110 101
      // |  /      |  /
      // | /       | /
      // 000 ———— 100
 
      // Grab the row length in the x-direction (0th direction)
      auto row_length_0 = this->ic_file.n_data_points[0];
      // Grab the row length in the y-direction (1st direction)
      auto row_length_1 = this->ic_file.n_data_points[1];
 
      // Grab the index of the lower left corner of the cell
      // cppcheck-suppress-begin containerOutOfBounds
      auto lower_index = lower_indices[0] + (lower_indices[1] * row_length_0) +
                         (lower_indices[2] * row_length_0 * row_length_1);
      // cppcheck-suppress-end containerOutOfBounds
 
      // Get the indices of the eight points in 3D
      auto node_index_000 = lower_index;
      auto node_index_100 = lower_index + 1;
 
      auto node_index_010 = lower_index + row_length_0;
      auto node_index_110 = lower_index + row_length_0 + 1;
 
      auto node_index_001 = lower_index + (row_length_0 * row_length_1);
      auto node_index_101 = lower_index + (row_length_0 * row_length_1) + 1;
 
      auto node_index_011 = lower_index + (row_length_0 * row_length_1) + row_length_0;
      auto node_index_111 =
        lower_index + (row_length_0 * row_length_1) + row_length_0 + 1;
 
      // Get the values at these points
      auto value_000 = get_value(node_index_000, n_components);
      auto value_100 = get_value(node_index_100, n_components);
 
      auto value_010 = get_value(node_index_010, n_components);
      auto value_110 = get_value(node_index_110, n_components);
 
      auto value_001 = get_value(node_index_001, n_components);
      auto value_101 = get_value(node_index_101, n_components);
 
      auto value_011 = get_value(node_index_011, n_components);
      auto value_111 = get_value(node_index_111, n_components);
 
      // Interpolate
      for (unsigned int c : std::views::iota(0U, n_components))
        {
          // cppcheck-suppress-begin containerOutOfBounds
          value[c] =
            (1.0 - weights[0]) * (1.0 - weights[1]) * (1.0 - weights[2]) * value_000[c] +
            weights[0] * (1.0 - weights[1]) * (1.0 - weights[2]) * value_100[c] +
            (1.0 - weights[0]) * weights[1] * (1.0 - weights[2]) * value_010[c] +
            weights[0] * weights[1] * (1.0 - weights[2]) * value_110[c] +
            (1.0 - weights[0]) * (1.0 - weights[1]) * weights[2] * value_001[c] +
            weights[0] * (1.0 - weights[1]) * weights[2] * value_101[c] +
            (1.0 - weights[0]) * weights[1] * weights[2] * value_011[c] +
            weights[0] * weights[1] * weights[2] * value_111[c];
          // cppcheck-suppress-end containerOutOfBounds
        }
    }
 
  return value;
}
 
template <unsigned int dim, typename number>
inline number
ReadBinary<dim, number>::get_scalar_value(const dealii::Point<dim>           &point,
                                          [[maybe_unused]] const std::string &scalar_name)
{
  Assert(n_values == n_points,
         dealii::ExcMessage("The number of points should match the number of values in a "
                            "binary file for a scalar field. Make sure the file size is "
                            "correct and you are trying to access a scalar field."));
  return interpolate(point, 1)[0];
}
 
template <unsigned int dim, typename number>
inline dealii::Vector<number>
ReadBinary<dim, number>::get_vector_value(const dealii::Point<dim>           &point,
                                          [[maybe_unused]] const std::string &vector_name)
{
  Assert((n_values / dim) == n_points,
         dealii::ExcMessage("The number of points should match the number of values "
                            "divided by the dimension in a binary file for a vector "
                            "field. Make sure the file size is correct and you are "
                            "trying to access a vector field."));
 
  return interpolate(point, dim);
}
 
template <unsigned int dim, typename number>
inline void
ReadBinary<dim, number>::print_file()
{
  for (dealii::types::global_dof_index i : std::views::iota(0U, n_values))
    {
      Assert(i < data.size(),
             dealii::ExcMessage("Index out of bounds in ReadBinary::print_file"));
      ConditionalOStreams::pout_summary() << this->data.at(i) << "\n";
    }
  ConditionalOStreams::pout_summary() << std::flush;
}
 
PRISMS_PF_END_NAMESPACE