20161997379

Committed 12 Dec 2025 09:14AM UTC coverage: 82.163% (-0.003%) from 82.166%

Build # 20161997379

Build Type

Pull #3678

github

Committed by

web-flow

Commit Message

Merge d9c140b9f into 1b5033dab

Pull Request Pull Request #3678: using id_map in model.plot for more efficient plotting

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75.07

/src/plot.cpp

#include "openmc/plot.h"

#include <algorithm>
#define _USE_MATH_DEFINES // to make M_PI declared in Intel and MSVC compilers
#include <cmath>
#include <cstdio>
#include <fstream>
#include <sstream>

#include "xtensor/xmanipulation.hpp"
#include "xtensor/xview.hpp"
#include <fmt/core.h>
#include <fmt/ostream.h>
#ifdef USE_LIBPNG
#include <png.h>
#endif

#include "openmc/constants.h"
#include "openmc/container_util.h"
#include "openmc/dagmc.h"
#include "openmc/error.h"
#include "openmc/file_utils.h"
#include "openmc/geometry.h"
#include "openmc/hdf5_interface.h"
#include "openmc/material.h"
#include "openmc/mesh.h"
#include "openmc/message_passing.h"
#include "openmc/openmp_interface.h"
#include "openmc/output.h"
#include "openmc/particle.h"
#include "openmc/progress_bar.h"
#include "openmc/random_lcg.h"
#include "openmc/settings.h"
#include "openmc/simulation.h"
#include "openmc/string_utils.h"

namespace openmc {

//==============================================================================
// Constants
//==============================================================================

constexpr int PLOT_LEVEL_LOWEST {-1}; //!< lower bound on plot universe level
constexpr int32_t NOT_FOUND {-2};
constexpr int32_t OVERLAP {-3};

IdData::IdData(size_t h_res, size_t v_res) : data_({v_res, h_res, 3}, NOT_FOUND)
{}

void IdData::set_value(size_t y, size_t x, const GeometryState& p, int level)
{
  // set cell data
  if (p.n_coord() <= level) {
    data_(y, x, 0) = NOT_FOUND;
    data_(y, x, 1) = NOT_FOUND;
  } else {
    data_(y, x, 0) = model::cells.at(p.coord(level).cell())->id_;
    data_(y, x, 1) = level == p.n_coord() - 1
                       ? p.cell_instance()
                       : cell_instance_at_level(p, level);
  }

  // set material data
  Cell* c = model::cells.at(p.lowest_coord().cell()).get();
  if (p.material() == MATERIAL_VOID) {
    data_(y, x, 2) = MATERIAL_VOID;
    return;
  } else if (c->type_ == Fill::MATERIAL) {
    Material* m = model::materials.at(p.material()).get();
    data_(y, x, 2) = m->id_;
  }
}

void IdData::set_overlap(size_t y, size_t x)
{
  xt::view(data_, y, x, xt::all()) = OVERLAP;
}

PropertyData::PropertyData(size_t h_res, size_t v_res)
  : data_({v_res, h_res, 2}, NOT_FOUND)
{}

void PropertyData::set_value(
  size_t y, size_t x, const GeometryState& p, int level)
{
  Cell* c = model::cells.at(p.lowest_coord().cell()).get();
  data_(y, x, 0) = (p.sqrtkT() * p.sqrtkT()) / K_BOLTZMANN;
  if (c->type_ != Fill::UNIVERSE && p.material() != MATERIAL_VOID) {
    Material* m = model::materials.at(p.material()).get();
    data_(y, x, 1) = m->density_gpcc_;
  }
}

void PropertyData::set_overlap(size_t y, size_t x)
{
  data_(y, x) = OVERLAP;
}

//==============================================================================
// Global variables
//==============================================================================

namespace model {

std::unordered_map<int, int> plot_map;
vector<std::unique_ptr<PlottableInterface>> plots;
uint64_t plotter_seed = 1;

} // namespace model

//==============================================================================
// RUN_PLOT controls the logic for making one or many plots
//==============================================================================

extern "C" int openmc_plot_geometry()
{

  for (auto& pl : model::plots) {
    write_message(5, "Processing plot {}: {}...", pl->id(), pl->path_plot());
    pl->create_output();
  }

  return 0;
}

void Plot::create_output() const
{
  if (PlotType::slice == type_) {
    // create 2D image
    create_image();
  } else if (PlotType::voxel == type_) {
    // create voxel file for 3D viewing
    create_voxel();
  }
}

void Plot::print_info() const
{
  // Plot type
  if (PlotType::slice == type_) {
    fmt::print("Plot Type: Slice\n");
  } else if (PlotType::voxel == type_) {
    fmt::print("Plot Type: Voxel\n");
  }

  // Plot parameters
  fmt::print("Origin: {} {} {}\n", origin_[0], origin_[1], origin_[2]);

  if (PlotType::slice == type_) {
    fmt::print("Width: {:4} {:4}\n", width_[0], width_[1]);
  } else if (PlotType::voxel == type_) {
    fmt::print("Width: {:4} {:4} {:4}\n", width_[0], width_[1], width_[2]);
  }

  if (PlotColorBy::cells == color_by_) {
    fmt::print("Coloring: Cells\n");
  } else if (PlotColorBy::mats == color_by_) {
    fmt::print("Coloring: Materials\n");
  }

  if (PlotType::slice == type_) {
    switch (basis_) {
    case PlotBasis::xy:
      fmt::print("Basis: XY\n");
      break;
    case PlotBasis::xz:
      fmt::print("Basis: XZ\n");
      break;
    case PlotBasis::yz:
      fmt::print("Basis: YZ\n");
      break;
    }
    fmt::print("Pixels: {} {}\n", pixels_[0], pixels_[1]);
  } else if (PlotType::voxel == type_) {
    fmt::print("Voxels: {} {} {}\n", pixels_[0], pixels_[1], pixels_[2]);
  }
}

void read_plots_xml()
{
  // Check if plots.xml exists; this is only necessary when the plot runmode is
  // initiated. Otherwise, we want to read plots.xml because it may be called
  // later via the API. In that case, its ok for a plots.xml to not exist
  std::string filename = settings::path_input + "plots.xml";
  if (!file_exists(filename) && settings::run_mode == RunMode::PLOTTING) {
    fatal_error(fmt::format("Plots XML file '{}' does not exist!", filename));
  }

  write_message("Reading plot XML file...", 5);

  // Parse plots.xml file
  pugi::xml_document doc;
  doc.load_file(filename.c_str());

  pugi::xml_node root = doc.document_element();

  read_plots_xml(root);
}

void read_plots_xml(pugi::xml_node root)
{
  for (auto node : root.children("plot")) {
    std::string id_string = get_node_value(node, "id", true);
    int id = std::stoi(id_string);
    if (check_for_node(node, "type")) {
      std::string type_str = get_node_value(node, "type", true);
      if (type_str == "slice") {
        model::plots.emplace_back(
          std::make_unique<Plot>(node, Plot::PlotType::slice));
      } else if (type_str == "voxel") {
        model::plots.emplace_back(
          std::make_unique<Plot>(node, Plot::PlotType::voxel));
      } else if (type_str == "wireframe_raytrace") {
        model::plots.emplace_back(
          std::make_unique<WireframeRayTracePlot>(node));
      } else if (type_str == "solid_raytrace") {
        model::plots.emplace_back(std::make_unique<SolidRayTracePlot>(node));
      } else {
        fatal_error(
          fmt::format("Unsupported plot type '{}' in plot {}", type_str, id));
      }
      model::plot_map[model::plots.back()->id()] = model::plots.size() - 1;
    } else {
      fatal_error(fmt::format("Must specify plot type in plot {}", id));
    }
  }
}

void free_memory_plot()
{
  model::plots.clear();
  model::plot_map.clear();
}

// creates an image based on user input from a plots.xml <plot>
// specification in the PNG/PPM format
void Plot::create_image() const
{

  size_t width = pixels_[0];
  size_t height = pixels_[1];

  ImageData data({width, height}, not_found_);

  // generate ids for the plot
  auto ids = get_map<IdData>();

  // assign colors
  for (size_t y = 0; y < height; y++) {
    for (size_t x = 0; x < width; x++) {
      int idx = color_by_ == PlotColorBy::cells ? 0 : 2;
      auto id = ids.data_(y, x, idx);
      // no setting needed if not found
      if (id == NOT_FOUND) {
        continue;
      }
      if (id == OVERLAP) {
        data(x, y) = overlap_color_;
        continue;
      }
      if (PlotColorBy::cells == color_by_) {
        data(x, y) = colors_[model::cell_map[id]];
      } else if (PlotColorBy::mats == color_by_) {
        if (id == MATERIAL_VOID) {
          data(x, y) = WHITE;
          continue;
        }
        data(x, y) = colors_[model::material_map[id]];
      } // color_by if-else
    }
  }

  // draw mesh lines if present
  if (index_meshlines_mesh_ >= 0) {
    draw_mesh_lines(data);
  }

// create image file
#ifdef USE_LIBPNG
  output_png(path_plot(), data);
#else
  output_ppm(path_plot(), data);
#endif
}

void PlottableInterface::set_id(pugi::xml_node plot_node)
{
  // Copy data into plots
  if (check_for_node(plot_node, "id")) {
    id_ = std::stoi(get_node_value(plot_node, "id"));
  } else {
    fatal_error("Must specify plot id in plots XML file.");
  }

  // Check to make sure 'id' hasn't been used
  if (model::plot_map.find(id_) != model::plot_map.end()) {
    fatal_error(
      fmt::format("Two or more plots use the same unique ID: {}", id_));
  }
}

// Checks if png or ppm is already present
bool file_extension_present(
  const std::string& filename, const std::string& extension)
{
  std::string file_extension_if_present =
    filename.substr(filename.find_last_of(".") + 1);
  if (file_extension_if_present == extension)
    return true;
  return false;
}

void Plot::set_output_path(pugi::xml_node plot_node)
{
  // Set output file path
  std::string filename;

  if (check_for_node(plot_node, "filename")) {
    filename = get_node_value(plot_node, "filename");
  } else {
    filename = fmt::format("plot_{}", id());
  }
  const std::string dir_if_present =
    filename.substr(0, filename.find_last_of("/") + 1);
  if (dir_if_present.size() > 0 && !dir_exists(dir_if_present)) {
    fatal_error(fmt::format("Directory '{}' does not exist!", dir_if_present));
  }
  // add appropriate file extension to name
  switch (type_) {
  case PlotType::slice:
#ifdef USE_LIBPNG
    if (!file_extension_present(filename, "png"))
      filename.append(".png");
#else
    if (!file_extension_present(filename, "ppm"))
      filename.append(".ppm");
#endif
    break;
  case PlotType::voxel:
    if (!file_extension_present(filename, "h5"))
      filename.append(".h5");
    break;
  }

  path_plot_ = filename;

  // Copy plot pixel size
  vector<int> pxls = get_node_array<int>(plot_node, "pixels");
  if (PlotType::slice == type_) {
    if (pxls.size() == 2) {
      pixels_[0] = pxls[0];
      pixels_[1] = pxls[1];
    } else {
      fatal_error(
        fmt::format("<pixels> must be length 2 in slice plot {}", id()));
    }
  } else if (PlotType::voxel == type_) {
    if (pxls.size() == 3) {
      pixels_[0] = pxls[0];
      pixels_[1] = pxls[1];
      pixels_[2] = pxls[2];
    } else {
      fatal_error(
        fmt::format("<pixels> must be length 3 in voxel plot {}", id()));
    }
  }
}

void PlottableInterface::set_bg_color(pugi::xml_node plot_node)
{
  // Copy plot background color
  if (check_for_node(plot_node, "background")) {
    vector<int> bg_rgb = get_node_array<int>(plot_node, "background");
    if (bg_rgb.size() == 3) {
      not_found_ = bg_rgb;
    } else {
      fatal_error(fmt::format("Bad background RGB in plot {}", id()));
    }
  }
}

void Plot::set_basis(pugi::xml_node plot_node)
{
  // Copy plot basis
  if (PlotType::slice == type_) {
    std::string pl_basis = "xy";
    if (check_for_node(plot_node, "basis")) {
      pl_basis = get_node_value(plot_node, "basis", true);
    }
    if ("xy" == pl_basis) {
      basis_ = PlotBasis::xy;
    } else if ("xz" == pl_basis) {
      basis_ = PlotBasis::xz;
    } else if ("yz" == pl_basis) {
      basis_ = PlotBasis::yz;
    } else {
      fatal_error(
        fmt::format("Unsupported plot basis '{}' in plot {}", pl_basis, id()));
    }
  }
}

void Plot::set_origin(pugi::xml_node plot_node)
{
  // Copy plotting origin
  auto pl_origin = get_node_array<double>(plot_node, "origin");
  if (pl_origin.size() == 3) {
    origin_ = pl_origin;
  } else {
    fatal_error(fmt::format("Origin must be length 3 in plot {}", id()));
  }
}

void Plot::set_width(pugi::xml_node plot_node)
{
  // Copy plotting width
  vector<double> pl_width = get_node_array<double>(plot_node, "width");
  if (PlotType::slice == type_) {
    if (pl_width.size() == 2) {
      width_.x = pl_width[0];
      width_.y = pl_width[1];
    } else {
      fatal_error(
        fmt::format("<width> must be length 2 in slice plot {}", id()));
    }
  } else if (PlotType::voxel == type_) {
    if (pl_width.size() == 3) {
      pl_width = get_node_array<double>(plot_node, "width");
      width_ = pl_width;
    } else {
      fatal_error(
        fmt::format("<width> must be length 3 in voxel plot {}", id()));
    }
  }
}

void PlottableInterface::set_universe(pugi::xml_node plot_node)
{
  // Copy plot universe level
  if (check_for_node(plot_node, "level")) {
    level_ = std::stoi(get_node_value(plot_node, "level"));
    if (level_ < 0) {
      fatal_error(fmt::format("Bad universe level in plot {}", id()));
    }
  } else {
    level_ = PLOT_LEVEL_LOWEST;
  }
}

void PlottableInterface::set_default_colors(pugi::xml_node plot_node)
{
  // Copy plot color type and initialize all colors randomly
  std::string pl_color_by = "cell";
  if (check_for_node(plot_node, "color_by")) {
    pl_color_by = get_node_value(plot_node, "color_by", true);
  }
  if ("cell" == pl_color_by) {
    color_by_ = PlotColorBy::cells;
    colors_.resize(model::cells.size());
  } else if ("material" == pl_color_by) {
    color_by_ = PlotColorBy::mats;
    colors_.resize(model::materials.size());
  } else {
    fatal_error(fmt::format(
      "Unsupported plot color type '{}' in plot {}", pl_color_by, id()));
  }

  for (auto& c : colors_) {
    c = random_color();
    // make sure we don't interfere with some default colors
    while (c == RED || c == WHITE) {
      c = random_color();
    }
  }
}

void PlottableInterface::set_user_colors(pugi::xml_node plot_node)
{
  for (auto cn : plot_node.children("color")) {
    // Make sure 3 values are specified for RGB
    vector<int> user_rgb = get_node_array<int>(cn, "rgb");
    if (user_rgb.size() != 3) {
      fatal_error(fmt::format("Bad RGB in plot {}", id()));
    }
    // Ensure that there is an id for this color specification
    int col_id;
    if (check_for_node(cn, "id")) {
      col_id = std::stoi(get_node_value(cn, "id"));
    } else {
      fatal_error(fmt::format(
        "Must specify id for color specification in plot {}", id()));
    }
    // Add RGB
    if (PlotColorBy::cells == color_by_) {
      if (model::cell_map.find(col_id) != model::cell_map.end()) {
        col_id = model::cell_map[col_id];
        colors_[col_id] = user_rgb;
      } else {
        warning(fmt::format(
          "Could not find cell {} specified in plot {}", col_id, id()));
      }
    } else if (PlotColorBy::mats == color_by_) {
      if (model::material_map.find(col_id) != model::material_map.end()) {
        col_id = model::material_map[col_id];
        colors_[col_id] = user_rgb;
      } else {
        warning(fmt::format(
          "Could not find material {} specified in plot {}", col_id, id()));
      }
    }
  } // color node loop
}

void Plot::set_meshlines(pugi::xml_node plot_node)
{
  // Deal with meshlines
  pugi::xpath_node_set mesh_line_nodes = plot_node.select_nodes("meshlines");

  if (!mesh_line_nodes.empty()) {
    if (PlotType::voxel == type_) {
      warning(fmt::format("Meshlines ignored in voxel plot {}", id()));
    }

    if (mesh_line_nodes.size() == 1) {
      // Get first meshline node
      pugi::xml_node meshlines_node = mesh_line_nodes[0].node();

      // Check mesh type
      std::string meshtype;
      if (check_for_node(meshlines_node, "meshtype")) {
        meshtype = get_node_value(meshlines_node, "meshtype");
      } else {
        fatal_error(fmt::format(
          "Must specify a meshtype for meshlines specification in plot {}",
          id()));
      }

      // Ensure that there is a linewidth for this meshlines specification
      std::string meshline_width;
      if (check_for_node(meshlines_node, "linewidth")) {
        meshline_width = get_node_value(meshlines_node, "linewidth");
        meshlines_width_ = std::stoi(meshline_width);
      } else {
        fatal_error(fmt::format(
          "Must specify a linewidth for meshlines specification in plot {}",
          id()));
      }

      // Check for color
      if (check_for_node(meshlines_node, "color")) {
        // Check and make sure 3 values are specified for RGB
        vector<int> ml_rgb = get_node_array<int>(meshlines_node, "color");
        if (ml_rgb.size() != 3) {
          fatal_error(
            fmt::format("Bad RGB for meshlines color in plot {}", id()));
        }
        meshlines_color_ = ml_rgb;
      }

      // Set mesh based on type
      if ("ufs" == meshtype) {
        if (!simulation::ufs_mesh) {
          fatal_error(
            fmt::format("No UFS mesh for meshlines on plot {}", id()));
        } else {
          for (int i = 0; i < model::meshes.size(); ++i) {
            if (const auto* m =
                  dynamic_cast<const RegularMesh*>(model::meshes[i].get())) {
              if (m == simulation::ufs_mesh) {
                index_meshlines_mesh_ = i;
              }
            }
          }
          if (index_meshlines_mesh_ == -1)
            fatal_error("Could not find the UFS mesh for meshlines plot");
        }
      } else if ("entropy" == meshtype) {
        if (!simulation::entropy_mesh) {
          fatal_error(
            fmt::format("No entropy mesh for meshlines on plot {}", id()));
        } else {
          for (int i = 0; i < model::meshes.size(); ++i) {
            if (const auto* m =
                  dynamic_cast<const RegularMesh*>(model::meshes[i].get())) {
              if (m == simulation::entropy_mesh) {
                index_meshlines_mesh_ = i;
              }
            }
          }
          if (index_meshlines_mesh_ == -1)
            fatal_error("Could not find the entropy mesh for meshlines plot");
        }
      } else if ("tally" == meshtype) {
        // Ensure that there is a mesh id if the type is tally
        int tally_mesh_id;
        if (check_for_node(meshlines_node, "id")) {
          tally_mesh_id = std::stoi(get_node_value(meshlines_node, "id"));
        } else {
          std::stringstream err_msg;
          fatal_error(fmt::format("Must specify a mesh id for meshlines tally "
                                  "mesh specification in plot {}",
            id()));
        }
        // find the tally index
        int idx;
        int err = openmc_get_mesh_index(tally_mesh_id, &idx);
        if (err != 0) {
          fatal_error(fmt::format("Could not find mesh {} specified in "
                                  "meshlines for plot {}",
            tally_mesh_id, id()));
        }
        index_meshlines_mesh_ = idx;
      } else {
        fatal_error(fmt::format("Invalid type for meshlines on plot {}", id()));
      }
    } else {
      fatal_error(fmt::format("Mutliple meshlines specified in plot {}", id()));
    }
  }
}

void PlottableInterface::set_mask(pugi::xml_node plot_node)
{
  // Deal with masks
  pugi::xpath_node_set mask_nodes = plot_node.select_nodes("mask");

  if (!mask_nodes.empty()) {
    if (mask_nodes.size() == 1) {
      // Get pointer to mask
      pugi::xml_node mask_node = mask_nodes[0].node();

      // Determine how many components there are and allocate
      vector<int> iarray = get_node_array<int>(mask_node, "components");
      if (iarray.size() == 0) {
        fatal_error(
          fmt::format("Missing <components> in mask of plot {}", id()));
      }

      // First we need to change the user-specified identifiers to indices
      // in the cell and material arrays
      for (auto& col_id : iarray) {
        if (PlotColorBy::cells == color_by_) {
          if (model::cell_map.find(col_id) != model::cell_map.end()) {
            col_id = model::cell_map[col_id];
          } else {
            fatal_error(fmt::format("Could not find cell {} specified in the "
                                    "mask in plot {}",
              col_id, id()));
          }
        } else if (PlotColorBy::mats == color_by_) {
          if (model::material_map.find(col_id) != model::material_map.end()) {
            col_id = model::material_map[col_id];
          } else {
            fatal_error(fmt::format("Could not find material {} specified in "
                                    "the mask in plot {}",
              col_id, id()));
          }
        }
      }

      // Alter colors based on mask information
      for (int j = 0; j < colors_.size(); j++) {
        if (contains(iarray, j)) {
          if (check_for_node(mask_node, "background")) {
            vector<int> bg_rgb = get_node_array<int>(mask_node, "background");
            colors_[j] = bg_rgb;
          } else {
            colors_[j] = WHITE;
          }
        }
      }

    } else {
      fatal_error(fmt::format("Mutliple masks specified in plot {}", id()));
    }
  }
}

void PlottableInterface::set_overlap_color(pugi::xml_node plot_node)
{
  color_overlaps_ = false;
  if (check_for_node(plot_node, "show_overlaps")) {
    color_overlaps_ = get_node_value_bool(plot_node, "show_overlaps");
    // check for custom overlap color
    if (check_for_node(plot_node, "overlap_color")) {
      if (!color_overlaps_) {
        warning(fmt::format(
          "Overlap color specified in plot {} but overlaps won't be shown.",
          id()));
      }
      vector<int> olap_clr = get_node_array<int>(plot_node, "overlap_color");
      if (olap_clr.size() == 3) {
        overlap_color_ = olap_clr;
      } else {
        fatal_error(fmt::format("Bad overlap RGB in plot {}", id()));
      }
    }
  }

  // make sure we allocate the vector for counting overlap checks if
  // they're going to be plotted
  if (color_overlaps_ && settings::run_mode == RunMode::PLOTTING) {
    settings::check_overlaps = true;
    model::overlap_check_count.resize(model::cells.size(), 0);
  }
}

PlottableInterface::PlottableInterface(pugi::xml_node plot_node)
{
  set_id(plot_node);
  set_bg_color(plot_node);
  set_universe(plot_node);
  set_default_colors(plot_node);
  set_user_colors(plot_node);
  set_mask(plot_node);
  set_overlap_color(plot_node);
}

Plot::Plot(pugi::xml_node plot_node, PlotType type)
  : PlottableInterface(plot_node), type_(type), index_meshlines_mesh_ {-1}
{
  set_output_path(plot_node);
  set_basis(plot_node);
  set_origin(plot_node);
  set_width(plot_node);
  set_meshlines(plot_node);
  slice_level_ = level_; // Copy level employed in SlicePlotBase::get_map
  slice_color_overlaps_ = color_overlaps_;
}

//==============================================================================
// OUTPUT_PPM writes out a previously generated image to a PPM file
//==============================================================================

void output_ppm(const std::string& filename, const ImageData& data)
{
  // Open PPM file for writing
  std::string fname = filename;
  fname = strtrim(fname);
  std::ofstream of;

  of.open(fname);

  // Write header
  of << "P6\n";
  of << data.shape()[0] << " " << data.shape()[1] << "\n";
  of << "255\n";
  of.close();

  of.open(fname, std::ios::binary | std::ios::app);
  // Write color for each pixel
  for (int y = 0; y < data.shape()[1]; y++) {
    for (int x = 0; x < data.shape()[0]; x++) {
      RGBColor rgb = data(x, y);
      of << rgb.red << rgb.green << rgb.blue;
    }
  }
  of << "\n";
}

//==============================================================================
// OUTPUT_PNG writes out a previously generated image to a PNG file
//==============================================================================

#ifdef USE_LIBPNG
void output_png(const std::string& filename, const ImageData& data)
{
  // Open PNG file for writing
  std::string fname = filename;
  fname = strtrim(fname);
  auto fp = std::fopen(fname.c_str(), "wb");

  // Initialize write and info structures
  auto png_ptr =
    png_create_write_struct(PNG_LIBPNG_VER_STRING, nullptr, nullptr, nullptr);
  auto info_ptr = png_create_info_struct(png_ptr);

  // Setup exception handling
  if (setjmp(png_jmpbuf(png_ptr)))
    fatal_error("Error during png creation");

  png_init_io(png_ptr, fp);

  // Write header (8 bit colour depth)
  int width = data.shape()[0];
  int height = data.shape()[1];
  png_set_IHDR(png_ptr, info_ptr, width, height, 8, PNG_COLOR_TYPE_RGB,
    PNG_INTERLACE_NONE, PNG_COMPRESSION_TYPE_BASE, PNG_FILTER_TYPE_BASE);
  png_write_info(png_ptr, info_ptr);

  // Allocate memory for one row (3 bytes per pixel - RGB)
  std::vector<png_byte> row(3 * width);

  // Write color for each pixel
  for (int y = 0; y < height; y++) {
    for (int x = 0; x < width; x++) {
      RGBColor rgb = data(x, y);
      row[3 * x] = rgb.red;
      row[3 * x + 1] = rgb.green;
      row[3 * x + 2] = rgb.blue;
    }
    png_write_row(png_ptr, row.data());
  }

  // End write
  png_write_end(png_ptr, nullptr);

  // Clean up data structures
  std::fclose(fp);
  png_free_data(png_ptr, info_ptr, PNG_FREE_ALL, -1);
  png_destroy_write_struct(&png_ptr, &info_ptr);
}
#endif

//==============================================================================
// DRAW_MESH_LINES draws mesh line boundaries on an image
//==============================================================================

void Plot::draw_mesh_lines(ImageData& data) const
{
  RGBColor rgb;
  rgb = meshlines_color_;

  int ax1, ax2;
  switch (basis_) {
  case PlotBasis::xy:
    ax1 = 0;
    ax2 = 1;
    break;
  case PlotBasis::xz:
    ax1 = 0;
    ax2 = 2;
    break;
  case PlotBasis::yz:
    ax1 = 1;
    ax2 = 2;
    break;
  default:
    UNREACHABLE();
  }

  Position ll_plot {origin_};
  Position ur_plot {origin_};

  ll_plot[ax1] -= width_[0] / 2.;
  ll_plot[ax2] -= width_[1] / 2.;
  ur_plot[ax1] += width_[0] / 2.;
  ur_plot[ax2] += width_[1] / 2.;

  Position width = ur_plot - ll_plot;

  // Find the (axis-aligned) lines of the mesh that intersect this plot.
  auto axis_lines =
    model::meshes[index_meshlines_mesh_]->plot(ll_plot, ur_plot);

  // Find the bounds along the second axis (accounting for low-D meshes).
  int ax2_min, ax2_max;
  if (axis_lines.second.size() > 0) {
    double frac = (axis_lines.second.back() - ll_plot[ax2]) / width[ax2];
    ax2_min = (1.0 - frac) * pixels_[1];
    if (ax2_min < 0)
      ax2_min = 0;
    frac = (axis_lines.second.front() - ll_plot[ax2]) / width[ax2];
    ax2_max = (1.0 - frac) * pixels_[1];
    if (ax2_max > pixels_[1])
      ax2_max = pixels_[1];
  } else {
    ax2_min = 0;
    ax2_max = pixels_[1];
  }

  // Iterate across the first axis and draw lines.
  for (auto ax1_val : axis_lines.first) {
    double frac = (ax1_val - ll_plot[ax1]) / width[ax1];
    int ax1_ind = frac * pixels_[0];
    for (int ax2_ind = ax2_min; ax2_ind < ax2_max; ++ax2_ind) {
      for (int plus = 0; plus <= meshlines_width_; plus++) {
        if (ax1_ind + plus >= 0 && ax1_ind + plus < pixels_[0])
          data(ax1_ind + plus, ax2_ind) = rgb;
        if (ax1_ind - plus >= 0 && ax1_ind - plus < pixels_[0])
          data(ax1_ind - plus, ax2_ind) = rgb;
      }
    }
  }

  // Find the bounds along the first axis.
  int ax1_min, ax1_max;
  if (axis_lines.first.size() > 0) {
    double frac = (axis_lines.first.front() - ll_plot[ax1]) / width[ax1];
    ax1_min = frac * pixels_[0];
    if (ax1_min < 0)
      ax1_min = 0;
    frac = (axis_lines.first.back() - ll_plot[ax1]) / width[ax1];
    ax1_max = frac * pixels_[0];
    if (ax1_max > pixels_[0])
      ax1_max = pixels_[0];
  } else {
    ax1_min = 0;
    ax1_max = pixels_[0];
  }

  // Iterate across the second axis and draw lines.
  for (auto ax2_val : axis_lines.second) {
    double frac = (ax2_val - ll_plot[ax2]) / width[ax2];
    int ax2_ind = (1.0 - frac) * pixels_[1];
    for (int ax1_ind = ax1_min; ax1_ind < ax1_max; ++ax1_ind) {
      for (int plus = 0; plus <= meshlines_width_; plus++) {
        if (ax2_ind + plus >= 0 && ax2_ind + plus < pixels_[1])
          data(ax1_ind, ax2_ind + plus) = rgb;
        if (ax2_ind - plus >= 0 && ax2_ind - plus < pixels_[1])
          data(ax1_ind, ax2_ind - plus) = rgb;
      }
    }
  }
}

/* outputs a binary file that can be input into silomesh for 3D geometry
 * visualization.  It works the same way as create_image by dragging a particle
 * across the geometry for the specified number of voxels. The first 3 int's in
 * the binary are the number of x, y, and z voxels.  The next 3 double's are
 * the widths of the voxels in the x, y, and z directions. The next 3 double's
 * are the x, y, and z coordinates of the lower left point. Finally the binary
 * is filled with entries of four int's each. Each 'row' in the binary contains
 * four int's: 3 for x,y,z position and 1 for cell or material id.  For 1
 * million voxels this produces a file of approximately 15MB.
 */
void Plot::create_voxel() const
{
  // compute voxel widths in each direction
  array<double, 3> vox;
  vox[0] = width_[0] / static_cast<double>(pixels_[0]);
  vox[1] = width_[1] / static_cast<double>(pixels_[1]);
  vox[2] = width_[2] / static_cast<double>(pixels_[2]);

  // initial particle position
  Position ll = origin_ - width_ / 2.;

  // Open binary plot file for writing
  std::ofstream of;
  std::string fname = std::string(path_plot_);
  fname = strtrim(fname);
  hid_t file_id = file_open(fname, 'w');

  // write header info
  write_attribute(file_id, "filetype", "voxel");
  write_attribute(file_id, "version", VERSION_VOXEL);
  write_attribute(file_id, "openmc_version", VERSION);

#ifdef GIT_SHA1
  write_attribute(file_id, "git_sha1", GIT_SHA1);
#endif

  // Write current date and time
  write_attribute(file_id, "date_and_time", time_stamp().c_str());
  array<int, 3> pixels;
  std::copy(pixels_.begin(), pixels_.end(), pixels.begin());
  write_attribute(file_id, "num_voxels", pixels);
  write_attribute(file_id, "voxel_width", vox);
  write_attribute(file_id, "lower_left", ll);

  // Create dataset for voxel data -- note that the dimensions are reversed
  // since we want the order in the file to be z, y, x
  hsize_t dims[3];
  dims[0] = pixels_[2];
  dims[1] = pixels_[1];
  dims[2] = pixels_[0];
  hid_t dspace, dset, memspace;
  voxel_init(file_id, &(dims[0]), &dspace, &dset, &memspace);

  SlicePlotBase pltbase;
  pltbase.width_ = width_;
  pltbase.origin_ = origin_;
  pltbase.basis_ = PlotBasis::xy;
  pltbase.pixels_ = pixels_;
  pltbase.slice_color_overlaps_ = color_overlaps_;

  ProgressBar pb;
  for (int z = 0; z < pixels_[2]; z++) {
    // update z coordinate
    pltbase.origin_.z = ll.z + z * vox[2];

    // generate ids using plotbase
    IdData ids = pltbase.get_map<IdData>();

    // select only cell/material ID data and flip the y-axis
    int idx = color_by_ == PlotColorBy::cells ? 0 : 2;
    xt::xtensor<int32_t, 2> data_slice =
      xt::view(ids.data_, xt::all(), xt::all(), idx);
    xt::xtensor<int32_t, 2> data_flipped = xt::flip(data_slice, 0);

    // Write to HDF5 dataset
    voxel_write_slice(z, dspace, dset, memspace, data_flipped.data());

    // update progress bar
    pb.set_value(
      100. * static_cast<double>(z + 1) / static_cast<double>((pixels_[2])));
  }

  voxel_finalize(dspace, dset, memspace);
  file_close(file_id);
}

void voxel_init(hid_t file_id, const hsize_t* dims, hid_t* dspace, hid_t* dset,
  hid_t* memspace)
{
  // Create dataspace/dataset for voxel data
  *dspace = H5Screate_simple(3, dims, nullptr);
  *dset = H5Dcreate(file_id, "data", H5T_NATIVE_INT, *dspace, H5P_DEFAULT,
    H5P_DEFAULT, H5P_DEFAULT);

  // Create dataspace for a slice of the voxel
  hsize_t dims_slice[2] {dims[1], dims[2]};
  *memspace = H5Screate_simple(2, dims_slice, nullptr);

  // Select hyperslab in dataspace
  hsize_t start[3] {0, 0, 0};
  hsize_t count[3] {1, dims[1], dims[2]};
  H5Sselect_hyperslab(*dspace, H5S_SELECT_SET, start, nullptr, count, nullptr);
}

void voxel_write_slice(
  int x, hid_t dspace, hid_t dset, hid_t memspace, void* buf)
{
  hssize_t offset[3] {x, 0, 0};
  H5Soffset_simple(dspace, offset);
  H5Dwrite(dset, H5T_NATIVE_INT, memspace, dspace, H5P_DEFAULT, buf);
}

void voxel_finalize(hid_t dspace, hid_t dset, hid_t memspace)
{
  H5Dclose(dset);
  H5Sclose(dspace);
  H5Sclose(memspace);
}

RGBColor random_color(void)
{
  return {int(prn(&model::plotter_seed) * 255),
    int(prn(&model::plotter_seed) * 255), int(prn(&model::plotter_seed) * 255)};
}

RayTracePlot::RayTracePlot(pugi::xml_node node) : PlottableInterface(node)
{
  set_look_at(node);
  set_camera_position(node);
  set_field_of_view(node);
  set_pixels(node);
  set_orthographic_width(node);
  set_output_path(node);

  if (check_for_node(node, "orthographic_width") &&
      check_for_node(node, "field_of_view"))
    fatal_error("orthographic_width and field_of_view are mutually exclusive "
                "parameters.");

  // Get centerline vector for camera-to-model. We create vectors around this
  // that form a pixel array, and then trace rays along that.
  auto up = up_ / up_.norm();
  Direction looking_direction = look_at_ - camera_position_;
  looking_direction /= looking_direction.norm();
  if (std::abs(std::abs(looking_direction.dot(up)) - 1.0) < 1e-9)
    fatal_error("Up vector cannot align with vector between camera position "
                "and look_at!");
  Direction cam_yaxis = looking_direction.cross(up);
  cam_yaxis /= cam_yaxis.norm();
  Direction cam_zaxis = cam_yaxis.cross(looking_direction);
  cam_zaxis /= cam_zaxis.norm();

  // Cache the camera-to-model matrix
  camera_to_model_ = {looking_direction.x, cam_yaxis.x, cam_zaxis.x,
    looking_direction.y, cam_yaxis.y, cam_zaxis.y, looking_direction.z,
    cam_yaxis.z, cam_zaxis.z};
}

WireframeRayTracePlot::WireframeRayTracePlot(pugi::xml_node node)
  : RayTracePlot(node)
{
  set_opacities(node);
  set_wireframe_thickness(node);
  set_wireframe_ids(node);
  set_wireframe_color(node);
}

void WireframeRayTracePlot::set_wireframe_color(pugi::xml_node plot_node)
{
  // Copy plot wireframe color
  if (check_for_node(plot_node, "wireframe_color")) {
    vector<int> w_rgb = get_node_array<int>(plot_node, "wireframe_color");
    if (w_rgb.size() == 3) {
      wireframe_color_ = w_rgb;
    } else {
      fatal_error(fmt::format("Bad wireframe RGB in plot {}", id()));
    }
  }
}

void RayTracePlot::set_output_path(pugi::xml_node node)
{
  // Set output file path
  std::string filename;

  if (check_for_node(node, "filename")) {
    filename = get_node_value(node, "filename");
  } else {
    filename = fmt::format("plot_{}", id());
  }

#ifdef USE_LIBPNG
  if (!file_extension_present(filename, "png"))
    filename.append(".png");
#else
  if (!file_extension_present(filename, "ppm"))
    filename.append(".ppm");
#endif
  path_plot_ = filename;
}

bool WireframeRayTracePlot::trackstack_equivalent(
  const std::vector<TrackSegment>& track1,
  const std::vector<TrackSegment>& track2) const
{
  if (wireframe_ids_.empty()) {
    // Draw wireframe for all surfaces/cells/materials
    if (track1.size() != track2.size())
      return false;
    for (int i = 0; i < track1.size(); ++i) {
      if (track1[i].id != track2[i].id ||
          track1[i].surface_index != track2[i].surface_index) {
        return false;
      }
    }
    return true;
  } else {
    // This runs in O(nm) where n is the intersection stack size
    // and m is the number of IDs we are wireframing. A simpler
    // algorithm can likely be found.
    for (const int id : wireframe_ids_) {
      int t1_i = 0;
      int t2_i = 0;

      // Advance to first instance of the ID
      while (t1_i < track1.size() && t2_i < track2.size()) {
        while (t1_i < track1.size() && track1[t1_i].id != id)
          t1_i++;
        while (t2_i < track2.size() && track2[t2_i].id != id)
          t2_i++;

        // This one is really important!
        if ((t1_i == track1.size() && t2_i != track2.size()) ||
            (t1_i != track1.size() && t2_i == track2.size()))
          return false;
        if (t1_i == track1.size() && t2_i == track2.size())
          break;
        // Check if surface different
        if (track1[t1_i].surface_index != track2[t2_i].surface_index)
          return false;

        // Pretty sure this should not be used:
        // if (t2_i != track2.size() - 1 &&
        //     t1_i != track1.size() - 1 &&
        //     track1[t1_i+1].id != track2[t2_i+1].id) return false;
        if (t2_i != 0 && t1_i != 0 &&
            track1[t1_i - 1].surface_index != track2[t2_i - 1].surface_index)
          return false;

        // Check if neighboring cells are different
        // if (track1[t1_i ? t1_i - 1 : 0].id != track2[t2_i ? t2_i - 1 : 0].id)
        // return false; if (track1[t1_i < track1.size() - 1 ? t1_i + 1 : t1_i
        // ].id !=
        //    track2[t2_i < track2.size() - 1 ? t2_i + 1 : t2_i].id) return
        //    false;
        t1_i++, t2_i++;
      }
    }
    return true;
  }
}

std::pair<Position, Direction> RayTracePlot::get_pixel_ray(
  int horiz, int vert) const
{
  // Compute field of view in radians
  constexpr double DEGREE_TO_RADIAN = M_PI / 180.0;
  double horiz_fov_radians = horizontal_field_of_view_ * DEGREE_TO_RADIAN;
  double p0 = static_cast<double>(pixels_[0]);
  double p1 = static_cast<double>(pixels_[1]);
  double vert_fov_radians = horiz_fov_radians * p1 / p0;

  // focal_plane_dist can be changed to alter the perspective distortion
  // effect. This is in units of cm. This seems to look good most of the
  // time. TODO let this variable be set through XML.
  constexpr double focal_plane_dist = 10.0;
  const double dx = 2.0 * focal_plane_dist * std::tan(0.5 * horiz_fov_radians);
  const double dy = p1 / p0 * dx;

  std::pair<Position, Direction> result;

  // Generate the starting position/direction of the ray
  if (orthographic_width_ == C_NONE) { // perspective projection
    Direction camera_local_vec;
    camera_local_vec.x = focal_plane_dist;
    camera_local_vec.y = -0.5 * dx + horiz * dx / p0;
    camera_local_vec.z = 0.5 * dy - vert * dy / p1;
    camera_local_vec /= camera_local_vec.norm();

    result.first = camera_position_;
    result.second = camera_local_vec.rotate(camera_to_model_);
  } else { // orthographic projection

    double x_pix_coord = (static_cast<double>(horiz) - p0 / 2.0) / p0;
    double y_pix_coord = (static_cast<double>(vert) - p1 / 2.0) / p1;

    result.first = camera_position_ +
                   camera_y_axis() * x_pix_coord * orthographic_width_ +
                   camera_z_axis() * y_pix_coord * orthographic_width_;
    result.second = camera_x_axis();
  }

  return result;
}

void WireframeRayTracePlot::create_output() const
{
  size_t width = pixels_[0];
  size_t height = pixels_[1];
  ImageData data({width, height}, not_found_);

  // This array marks where the initial wireframe was drawn. We convolve it with
  // a filter that gets adjusted with the wireframe thickness in order to
  // thicken the lines.
  xt::xtensor<int, 2> wireframe_initial({width, height}, 0);

  /* Holds all of the track segments for the current rendered line of pixels.
   * old_segments holds a copy of this_line_segments from the previous line.
   * By holding both we can check if the cell/material intersection stack
   * differs from the left or upper neighbor. This allows a robustly drawn
   * wireframe. If only checking the left pixel (which requires substantially
   * less memory), the wireframe tends to be spotty and be disconnected for
   * surface edges oriented horizontally in the rendering.
   *
   * Note that a vector of vectors is required rather than a 2-tensor,
   * since the stack size varies within each column.
   */
  const int n_threads = num_threads();
  std::vector<std::vector<std::vector<TrackSegment>>> this_line_segments(
    n_threads);
  for (int t = 0; t < n_threads; ++t) {
    this_line_segments[t].resize(pixels_[0]);
  }

  // The last thread writes to this, and the first thread reads from it.
  std::vector<std::vector<TrackSegment>> old_segments(pixels_[0]);

#pragma omp parallel
  {
    const int n_threads = num_threads();
    const int tid = thread_num();

    int vert = tid;
    for (int iter = 0; iter <= pixels_[1] / n_threads; iter++) {

      // Save bottom line of current work chunk to compare against later. This
      // used to be inside the below if block, but it causes a spurious line to
      // be drawn at the bottom of the image. Not sure why, but moving it here
      // fixes things.
      if (tid == n_threads - 1)
        old_segments = this_line_segments[n_threads - 1];

      if (vert < pixels_[1]) {

        for (int horiz = 0; horiz < pixels_[0]; ++horiz) {

          // RayTracePlot implements camera ray generation
          std::pair<Position, Direction> ru = get_pixel_ray(horiz, vert);

          this_line_segments[tid][horiz].clear();
          ProjectionRay ray(
            ru.first, ru.second, *this, this_line_segments[tid][horiz]);

          ray.trace();

          // Now color the pixel based on what we have intersected...
          // Loops backwards over intersections.
          Position current_color(
            not_found_.red, not_found_.green, not_found_.blue);
          const auto& segments = this_line_segments[tid][horiz];

          // There must be at least two cell intersections to color, front and
          // back of the cell. Maybe an infinitely thick cell could be present
          // with no back, but why would you want to color that? It's easier to
          // just skip that edge case and not even color it.
          if (segments.size() <= 1)
            continue;

          for (int i = segments.size() - 2; i >= 0; --i) {
            int colormap_idx = segments[i].id;
            RGBColor seg_color = colors_[colormap_idx];
            Position seg_color_vec(
              seg_color.red, seg_color.green, seg_color.blue);
            double mixing =
              std::exp(-xs_[colormap_idx] *
                       (segments[i + 1].length - segments[i].length));
            current_color =
              current_color * mixing + (1.0 - mixing) * seg_color_vec;
          }

          // save result converting from double-precision color coordinates to
          // byte-sized
          RGBColor result;
          result.red = static_cast<uint8_t>(current_color.x);
          result.green = static_cast<uint8_t>(current_color.y);
          result.blue = static_cast<uint8_t>(current_color.z);
          data(horiz, vert) = result;

          // Check to draw wireframe in horizontal direction. No inter-thread
          // comm.
          if (horiz > 0) {
            if (!trackstack_equivalent(this_line_segments[tid][horiz],
                  this_line_segments[tid][horiz - 1])) {
              wireframe_initial(horiz, vert) = 1;
            }
          }
        }
      } // end "if" vert in correct range

      // We require a barrier before comparing vertical neighbors' intersection
      // stacks. i.e. all threads must be done with their line.
#pragma omp barrier

      // Now that the horizontal line has finished rendering, we can fill in
      // wireframe entries that require comparison among all the threads. Hence
      // the omp barrier being used. It has to be OUTSIDE any if blocks!
      if (vert < pixels_[1]) {
        // Loop over horizontal pixels, checking intersection stack of upper
        // neighbor

        const std::vector<std::vector<TrackSegment>>* top_cmp = nullptr;
        if (tid == 0)
          top_cmp = &old_segments;
        else
          top_cmp = &this_line_segments[tid - 1];

        for (int horiz = 0; horiz < pixels_[0]; ++horiz) {
          if (!trackstack_equivalent(
                this_line_segments[tid][horiz], (*top_cmp)[horiz])) {
            wireframe_initial(horiz, vert) = 1;
          }
        }
      }

      // We need another barrier to ensure threads don't proceed to modify their
      // intersection stacks on that horizontal line while others are
      // potentially still working on the above.
#pragma omp barrier
      vert += n_threads;
    }
  } // end omp parallel

  // Now thicken the wireframe lines and apply them to our image
  for (int vert = 0; vert < pixels_[1]; ++vert) {
    for (int horiz = 0; horiz < pixels_[0]; ++horiz) {
      if (wireframe_initial(horiz, vert)) {
        if (wireframe_thickness_ == 1)
          data(horiz, vert) = wireframe_color_;
        for (int i = -wireframe_thickness_ / 2; i < wireframe_thickness_ / 2;
             ++i)
          for (int j = -wireframe_thickness_ / 2; j < wireframe_thickness_ / 2;
               ++j)
            if (i * i + j * j < wireframe_thickness_ * wireframe_thickness_) {

              // Check if wireframe pixel is out of bounds
              int w_i = std::max(std::min(horiz + i, pixels_[0] - 1), 0);
              int w_j = std::max(std::min(vert + j, pixels_[1] - 1), 0);
              data(w_i, w_j) = wireframe_color_;
            }
      }
    }
  }

#ifdef USE_LIBPNG
  output_png(path_plot(), data);
#else
  output_ppm(path_plot(), data);
#endif
}

void RayTracePlot::print_info() const
{
  fmt::print("Camera position: {} {} {}\n", camera_position_.x,
    camera_position_.y, camera_position_.z);
  fmt::print("Look at: {} {} {}\n", look_at_.x, look_at_.y, look_at_.z);
  fmt::print(
    "Horizontal field of view: {} degrees\n", horizontal_field_of_view_);
  fmt::print("Pixels: {} {}\n", pixels_[0], pixels_[1]);
}

void WireframeRayTracePlot::print_info() const
{
  fmt::print("Plot Type: Wireframe ray-traced\n");
  RayTracePlot::print_info();
}

void WireframeRayTracePlot::set_opacities(pugi::xml_node node)
{
  xs_.resize(colors_.size(), 1e6); // set to large value for opaque by default

  for (auto cn : node.children("color")) {
    // Make sure 3 values are specified for RGB
    double user_xs = std::stod(get_node_value(cn, "xs"));
    int col_id = std::stoi(get_node_value(cn, "id"));

    // Add RGB
    if (PlotColorBy::cells == color_by_) {
      if (model::cell_map.find(col_id) != model::cell_map.end()) {
        col_id = model::cell_map[col_id];
        xs_[col_id] = user_xs;
      } else {
        warning(fmt::format(
          "Could not find cell {} specified in plot {}", col_id, id()));
      }
    } else if (PlotColorBy::mats == color_by_) {
      if (model::material_map.find(col_id) != model::material_map.end()) {
        col_id = model::material_map[col_id];
        xs_[col_id] = user_xs;
      } else {
        warning(fmt::format(
          "Could not find material {} specified in plot {}", col_id, id()));
      }
    }
  }
}

void RayTracePlot::set_orthographic_width(pugi::xml_node node)
{
  if (check_for_node(node, "orthographic_width")) {
    double orthographic_width =
      std::stod(get_node_value(node, "orthographic_width", true));
    if (orthographic_width < 0.0)
      fatal_error("Requires positive orthographic_width");
    orthographic_width_ = orthographic_width;
  }
}

void WireframeRayTracePlot::set_wireframe_thickness(pugi::xml_node node)
{
  if (check_for_node(node, "wireframe_thickness")) {
    int wireframe_thickness =
      std::stoi(get_node_value(node, "wireframe_thickness", true));
    if (wireframe_thickness < 0)
      fatal_error("Requires non-negative wireframe thickness");
    wireframe_thickness_ = wireframe_thickness;
  }
}

void WireframeRayTracePlot::set_wireframe_ids(pugi::xml_node node)
{
  if (check_for_node(node, "wireframe_ids")) {
    wireframe_ids_ = get_node_array<int>(node, "wireframe_ids");
    // It is read in as actual ID values, but we have to convert to indices in
    // mat/cell array
    for (auto& x : wireframe_ids_)
      x = color_by_ == PlotColorBy::mats ? model::material_map[x]
                                         : model::cell_map[x];
  }
  // We make sure the list is sorted in order to later use
  // std::binary_search.
  std::sort(wireframe_ids_.begin(), wireframe_ids_.end());
}

void RayTracePlot::set_pixels(pugi::xml_node node)
{
  vector<int> pxls = get_node_array<int>(node, "pixels");
  if (pxls.size() != 2)
    fatal_error(
      fmt::format("<pixels> must be length 2 in projection plot {}", id()));
  pixels_[0] = pxls[0];
  pixels_[1] = pxls[1];
}

void RayTracePlot::set_camera_position(pugi::xml_node node)
{
  vector<double> camera_pos = get_node_array<double>(node, "camera_position");
  if (camera_pos.size() != 3) {
    fatal_error(fmt::format(
      "camera_position element must have three floating point values"));
  }
  camera_position_.x = camera_pos[0];
  camera_position_.y = camera_pos[1];
  camera_position_.z = camera_pos[2];
}

void RayTracePlot::set_look_at(pugi::xml_node node)
{
  vector<double> look_at = get_node_array<double>(node, "look_at");
  if (look_at.size() != 3) {
    fatal_error("look_at element must have three floating point values");
  }
  look_at_.x = look_at[0];
  look_at_.y = look_at[1];
  look_at_.z = look_at[2];
}

void RayTracePlot::set_field_of_view(pugi::xml_node node)
{
  // Defaults to 70 degree horizontal field of view (see .h file)
  if (check_for_node(node, "horizontal_field_of_view")) {
    double fov =
      std::stod(get_node_value(node, "horizontal_field_of_view", true));
    if (fov < 180.0 && fov > 0.0) {
      horizontal_field_of_view_ = fov;
    } else {
      fatal_error(fmt::format("Horizontal field of view for plot {} "
                              "out-of-range. Must be in (0, 180) degrees.",
        id()));
    }
  }
}

SolidRayTracePlot::SolidRayTracePlot(pugi::xml_node node) : RayTracePlot(node)
{
  set_opaque_ids(node);
  set_diffuse_fraction(node);
  set_light_position(node);
}

void SolidRayTracePlot::print_info() const
{
  fmt::print("Plot Type: Solid ray-traced\n");
  RayTracePlot::print_info();
}

void SolidRayTracePlot::create_output() const
{
  size_t width = pixels_[0];
  size_t height = pixels_[1];
  ImageData data({width, height}, not_found_);

#pragma omp parallel for schedule(dynamic) collapse(2)
  for (int horiz = 0; horiz < pixels_[0]; ++horiz) {
    for (int vert = 0; vert < pixels_[1]; ++vert) {
      // RayTracePlot implements camera ray generation
      std::pair<Position, Direction> ru = get_pixel_ray(horiz, vert);
      PhongRay ray(ru.first, ru.second, *this);
      ray.trace();
      data(horiz, vert) = ray.result_color();
    }
  }

#ifdef USE_LIBPNG
  output_png(path_plot(), data);
#else
  output_ppm(path_plot(), data);
#endif
}

void SolidRayTracePlot::set_opaque_ids(pugi::xml_node node)
{
  if (check_for_node(node, "opaque_ids")) {
    auto opaque_ids_tmp = get_node_array<int>(node, "opaque_ids");

    // It is read in as actual ID values, but we have to convert to indices in
    // mat/cell array
    for (auto& x : opaque_ids_tmp)
      x = color_by_ == PlotColorBy::mats ? model::material_map[x]
                                         : model::cell_map[x];

    opaque_ids_.insert(opaque_ids_tmp.begin(), opaque_ids_tmp.end());
  }
}

void SolidRayTracePlot::set_light_position(pugi::xml_node node)
{
  if (check_for_node(node, "light_position")) {
    auto light_pos_tmp = get_node_array<double>(node, "light_position");

    if (light_pos_tmp.size() != 3)
      fatal_error("Light position must be given as 3D coordinates");

    light_location_.x = light_pos_tmp[0];
    light_location_.y = light_pos_tmp[1];
    light_location_.z = light_pos_tmp[2];
  } else {
    light_location_ = camera_position();
  }
}

void SolidRayTracePlot::set_diffuse_fraction(pugi::xml_node node)
{
  if (check_for_node(node, "diffuse_fraction")) {
    diffuse_fraction_ = std::stod(get_node_value(node, "diffuse_fraction"));
    if (diffuse_fraction_ < 0.0 || diffuse_fraction_ > 1.0) {
      fatal_error("Must have 0 <= diffuse fraction <= 1");
    }
  }
}

void Ray::compute_distance()
{
  boundary() = distance_to_boundary(*this);
}

void Ray::trace()
{
  // To trace the ray from its origin all the way through the model, we have
  // to proceed in two phases. In the first, the ray may or may not be found
  // inside the model. If the ray is already in the model, phase one can be
  // skipped. Otherwise, the ray has to be advanced to the boundary of the
  // model where all the cells are defined. Importantly, this is assuming that
  // the model is convex, which is a very reasonable assumption for any
  // radiation transport model.
  //
  // After phase one is done, we can starting tracing from cell to cell within
  // the model. This step can use neighbor lists to accelerate the ray tracing.

  // Attempt to initialize the particle. We may have to enter a loop to move
  // it up to the edge of the model.
  bool inside_cell = exhaustive_find_cell(*this, settings::verbosity >= 10);

  // Advance to the boundary of the model
  while (!inside_cell) {
    advance_to_boundary_from_void();
    inside_cell = exhaustive_find_cell(*this, settings::verbosity >= 10);

    // If true this means no surface was intersected. See cell.cpp and search
    // for numeric_limits to see where we return it.
    if (surface() == std::numeric_limits<int>::max()) {
      warning(fmt::format("Lost a ray, r = {}, u = {}", r(), u()));
      return;
    }

    // Exit this loop and enter into cell-to-cell ray tracing (which uses
    // neighbor lists)
    if (inside_cell)
      break;

    // if there is no intersection with the model, we're done
    if (boundary().surface() == SURFACE_NONE)
      return;

    event_counter_++;
    if (event_counter_ > MAX_INTERSECTIONS) {
      warning("Likely infinite loop in ray traced plot");
      return;
    }
  }

  // Call the specialized logic for this type of ray. This is for the
  // intersection for the first intersection if we had one.
  if (boundary().surface() != SURFACE_NONE) {
    // set the geometry state's surface attribute to be used for
    // surface normal computation
    surface() = boundary().surface();
    on_intersection();
    if (stop_)
      return;
  }

  // reset surface attribute to zero after the first intersection so that it
  // doesn't perturb surface crossing logic from here on out
  surface() = 0;

  // This is the ray tracing loop within the model. It exits after exiting
  // the model, which is equivalent to assuming that the model is convex.
  // It would be nice to factor out the on_intersection at the end of this
  // loop and then do "while (inside_cell)", but we can't guarantee it's
  // on a surface in that case. There might be some other way to set it
  // up that is perhaps a little more elegant, but this is what works just
  // fine.
  while (true) {

    compute_distance();

    // There are no more intersections to process
    // if we hit the edge of the model, so stop
    // the particle in that case. Also, just exit
    // if a negative distance was somehow computed.
    if (boundary().distance() == INFTY || boundary().distance() == INFINITY ||
        boundary().distance() < 0) {
      return;
    }

    // See below comment where call_on_intersection is checked in an
    // if statement for an explanation of this.
    bool call_on_intersection {true};
    if (boundary().distance() < 10 * TINY_BIT) {
      call_on_intersection = false;
    }

    // DAGMC surfaces expect us to go a little bit further than the advance
    // distance to properly check cell inclusion.
    boundary().distance() += TINY_BIT;

    // Advance particle, prepare for next intersection
    for (int lev = 0; lev < n_coord(); ++lev) {
      coord(lev).r() += boundary().distance() * coord(lev).u();
    }
    surface() = boundary().surface();
    n_coord_last() = n_coord();
    n_coord() = boundary().coord_level();
    if (boundary().lattice_translation()[0] != 0 ||
        boundary().lattice_translation()[1] != 0 ||
        boundary().lattice_translation()[2] != 0) {
      cross_lattice(*this, boundary(), settings::verbosity >= 10);
    }

    // Record how far the ray has traveled
    traversal_distance_ += boundary().distance();
    inside_cell = neighbor_list_find_cell(*this, settings::verbosity >= 10);

    // Call the specialized logic for this type of ray. Note that we do not
    // call this if the advance distance is very small. Unfortunately, it seems
    // darn near impossible to get the particle advanced to the model boundary
    // and through it without sometimes accidentally calling on_intersection
    // twice. This incorrectly shades the region as occluded when it might not
    // actually be. By screening out intersection distances smaller than a
    // threshold 10x larger than the scoot distance used to advance up to the
    // model boundary, we can avoid that situation.
    if (call_on_intersection) {
      on_intersection();
      if (stop_)
        return;
    }

    if (!inside_cell)
      return;

    event_counter_++;
    if (event_counter_ > MAX_INTERSECTIONS) {
      warning("Likely infinite loop in ray traced plot");
      return;
    }
  }
}

void ProjectionRay::on_intersection()
{
  // This records a tuple with the following info
  //
  // 1) ID (material or cell depending on color_by_)
  // 2) Distance traveled by the ray through that ID
  // 3) Index of the intersected surface (starting from 1)

  line_segments_.emplace_back(
    plot_.color_by_ == PlottableInterface::PlotColorBy::mats
      ? material()
      : lowest_coord().cell(),
    traversal_distance_, boundary().surface_index());
}

void PhongRay::on_intersection()
{
  // Check if we hit an opaque material or cell
  int hit_id = plot_.color_by_ == PlottableInterface::PlotColorBy::mats
                 ? material()
                 : lowest_coord().cell();

  // If we are reflected and have advanced beyond the camera,
  // the ray is done. This is checked here because we should
  // kill the ray even if the material is not opaque.
  if (reflected_ && (r() - plot_.camera_position()).dot(u()) >= 0.0) {
    stop();
    return;
  }

  // Anything that's not opaque has zero impact on the plot.
  if (plot_.opaque_ids_.find(hit_id) == plot_.opaque_ids_.end())
    return;

  if (!reflected_) {
    // reflect the particle and set the color to be colored by
    // the normal or the diffuse lighting contribution
    reflected_ = true;
    result_color_ = plot_.colors_[hit_id];
    Direction to_light = plot_.light_location_ - r();
    to_light /= to_light.norm();

    // TODO
    // Not sure what can cause a surface token to be invalid here, although it
    // sometimes happens for a few pixels. It's very very rare, so proceed by
    // coloring the pixel with the overlap color. It seems to happen only for a
    // few pixels on the outer boundary of a hex lattice.
    //
    // We cannot detect it in the outer loop, and it only matters here, so
    // that's why the error handling is a little different than for a lost
    // ray.
    if (surface() == 0) {
      result_color_ = plot_.overlap_color_;
      stop();
      return;
    }

    // Get surface pointer
    const auto& surf = model::surfaces.at(surface_index());

    Direction normal = surf->normal(r_local());
    normal /= normal.norm();

    // Need to apply translations to find the normal vector in
    // the base level universe's coordinate system.
    for (int lev = n_coord() - 2; lev >= 0; --lev) {
      if (coord(lev + 1).rotated()) {
        const Cell& c {*model::cells[coord(lev).cell()]};
        normal = normal.inverse_rotate(c.rotation_);
      }
    }

    // use the normal opposed to the ray direction
    if (normal.dot(u()) > 0.0) {
      normal *= -1.0;
    }

    // Facing away from the light means no lighting
    double dotprod = normal.dot(to_light);
    dotprod = std::max(0.0, dotprod);

    double modulation =
      plot_.diffuse_fraction_ + (1.0 - plot_.diffuse_fraction_) * dotprod;
    result_color_ *= modulation;

    // Now point the particle to the camera. We now begin
    // checking to see if it's occluded by another surface
    u() = to_light;

    orig_hit_id_ = hit_id;

    // OpenMC native CSG and DAGMC surfaces have some slight differences
    // in how they interpret particles that are sitting on a surface.
    // I don't know exactly why, but this makes everything work beautifully.
    if (surf->geom_type() == GeometryType::DAG) {
      surface() = 0;
    } else {
      surface() = -surface(); // go to other side
    }

    // Must fully restart coordinate search. Why? Not sure.
    clear();

    // Note this could likely be faster if we cached the previous
    // cell we were in before the reflection. This is the easiest
    // way to fully initialize all the sub-universe coordinates and
    // directions though.
    bool found = exhaustive_find_cell(*this);
    if (!found) {
      fatal_error("Lost particle after reflection.");
    }

    // Must recalculate distance to boundary due to the
    // direction change
    compute_distance();

  } else {
    // If it's not facing the light, we color with the diffuse contribution, so
    // next we check if we're going to occlude the last reflected surface. if
    // so, color by the diffuse contribution instead

    if (orig_hit_id_ == -1)
      fatal_error("somehow a ray got reflected but not original ID set?");

    result_color_ = plot_.colors_[orig_hit_id_];
    result_color_ *= plot_.diffuse_fraction_;
    stop();
  }
}

extern "C" int openmc_id_map(const void* plot, int32_t* data_out)
{

  auto plt = reinterpret_cast<const SlicePlotBase*>(plot);
  if (!plt) {
    set_errmsg("Invalid slice pointer passed to openmc_id_map");
    return OPENMC_E_INVALID_ARGUMENT;
  }

  if (plt->slice_color_overlaps_ && model::overlap_check_count.size() == 0) {
    model::overlap_check_count.resize(model::cells.size());
  }

  auto ids = plt->get_map<IdData>();

  // write id data to array
  std::copy(ids.data_.begin(), ids.data_.end(), data_out);

  return 0;
}

extern "C" int openmc_property_map(const void* plot, double* data_out)
{

  auto plt = reinterpret_cast<const SlicePlotBase*>(plot);
  if (!plt) {
    set_errmsg("Invalid slice pointer passed to openmc_id_map");
    return OPENMC_E_INVALID_ARGUMENT;
  }

  if (plt->slice_color_overlaps_ && model::overlap_check_count.size() == 0) {
    model::overlap_check_count.resize(model::cells.size());
  }

  auto props = plt->get_map<PropertyData>();

  // write id data to array
  std::copy(props.data_.begin(), props.data_.end(), data_out);

  return 0;
}

} // namespace openmc

openmc-dev / openmc / 20161997379

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