cosmotool/sample/simple3DFilter.cpp

#include "hdf5_array.hpp"
#include "miniargs.hpp"
#include "mykdtree.hpp"
#include "omptl/algorithm"
#include "openmp.hpp"
#include "sphSmooth.hpp"
#include "yorick.hpp"
#include <H5Cpp.h>
#include <boost/bind.hpp>
#include <boost/format.hpp>
#include <cassert>
#include <iostream>

using namespace std;
using namespace CosmoTool;

#define N_SPH 32

struct VCoord {
  float v[3];
  float mass;
};

using boost::format;
using boost::str;
typedef boost::multi_array<float, 2> array_type;
typedef boost::multi_array<float, 3> array3_type;
typedef boost::multi_array<float, 4> array4_type;

ComputePrecision getVelocity(const VCoord &v, int i) { return v.mass * v.v[i]; }

ComputePrecision getMass(const VCoord &v) { return v.mass; }

typedef SPHSmooth<VCoord> MySmooth;
typedef MySmooth::SPHTree MyTree;
typedef MyTree::Cell MyCell;

template <typename FuncT>
void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres,
                              double cx, double cy, double cz,
                              array3_type &bins, array3_type &arr, FuncT func,
                              double rLimit2) {
  int rz_max = 0;
#pragma omp parallel shared(rz_max)
  {
    MySmooth smooth1(tree1, N_SPH);

#pragma omp for collapse(3) schedule(dynamic)
    for (int rz = 0; rz < Nres; rz++) {

      for (int ry = 0; ry < Nres; ry++) {
        for (int rx = 0; rx < Nres; rx++) {
          if (rz > rz_max) {
            rz_max = rz;
            cout << format("[%d] %d / %d") % smp_get_thread_id() % rz % Nres
                 << endl;
          }
          double px = (rx)*boxsize / Nres - cx;
          double py = (ry)*boxsize / Nres - cy;
          double pz = (rz)*boxsize / Nres - cz;

          MyTree::coords c = {float(px), float(py), float(pz)};

          double r2 = c[0] * c[0] + c[1] * c[1] + c[2] * c[2];
          if (r2 > rLimit2) {
            arr[rx][ry][rz] = 0;
            continue;
          }

          uint32_t numInCell = bins[rx][ry][rz];
          if (numInCell > N_SPH)
            smooth1.fetchNeighbours(c, numInCell);
          else
            smooth1.fetchNeighbours(c);

          arr[rx][ry][rz] = smooth1.computeSmoothedValue(c, func);
        }
      }
    }
  }
}

int main(int argc, char **argv) {
  char *fname1, *outFile;
  double rLimit, boxsize, rLimit2, cx, cy, cz;
  int Nres;
  int periodic;

  MiniArgDesc args[] = {{"INPUT DATA1", &fname1, MINIARG_STRING},
                        {"RADIUS LIMIT", &rLimit, MINIARG_DOUBLE},
                        {"BOXSIZE", &boxsize, MINIARG_DOUBLE},
                        {"RESOLUTION", &Nres, MINIARG_INT},
                        {"CX", &cx, MINIARG_DOUBLE},
                        {"CY", &cy, MINIARG_DOUBLE},
                        {"CZ", &cz, MINIARG_DOUBLE},
                        {"OUTPUT FILE", &outFile, MINIARG_STRING},
                        {"PERIODIC", &periodic, MINIARG_INT},
                        {0, 0, MINIARG_NULL}};

  if (!parseMiniArgs(argc, argv, args))
    return 1;

  H5::H5File in_f(fname1, 0);
  H5::H5File out_f(outFile, H5F_ACC_TRUNC);
  array_type v1_data;
  uint64_t N1_points, N2_points;

  array3_type bins(boost::extents[Nres][Nres][Nres]);

  rLimit2 = rLimit * rLimit;

  hdf5_read_array(in_f, "particles", v1_data);
  assert(v1_data.shape()[1] == 7);

  N1_points = v1_data.shape()[0];

  cout << "Got " << N1_points << " in the first file." << endl;

  MyCell *allCells_1 = new MyCell[N1_points];

#pragma omp parallel for schedule(static)
  for (uint32_t i = 0; i < Nres * Nres * Nres; i++)
    bins.data()[i] = 0;

  cout << "Shuffling data in cells..." << endl;
#pragma omp parallel for schedule(static)
  for (uint64_t i = 0; i < N1_points; i++) {
    for (int j = 0; j < 3; j++)
      allCells_1[i].coord[j] = v1_data[i][j];
    for (int k = 0; k < 3; k++)
      allCells_1[i].val.pValue.v[k] = v1_data[i][3 + k];
    allCells_1[i].val.pValue.mass = v1_data[i][6];
    allCells_1[i].active = true;
    allCells_1[i].val.weight = 0.0;

    long rx = floor((allCells_1[i].coord[0] + cx) * Nres / boxsize + 0.5);
    long ry = floor((allCells_1[i].coord[1] + cy) * Nres / boxsize + 0.5);
    long rz = floor((allCells_1[i].coord[2] + cz) * Nres / boxsize + 0.5);

    if (rx < 0 || rx >= Nres || ry < 0 || ry >= Nres || rz < 0 || rz >= Nres)
      continue;

    auto &b = bins[rx][ry][rz];
#pragma omp atomic
    b++;
  }
  v1_data.resize(boost::extents[1][1]);

  hdf5_write_array(out_f, "num_in_cell", bins);

  cout << "Building trees..." << endl;
  MyTree tree1(allCells_1, N1_points);
  tree1.setPeriodic(periodic != 0);

  cout << "Creating smoothing filter..." << endl;

  //  array3_type out_rad_1(boost::extents[Nres][Nres][Nres]);

  cout << "Weighing..." << endl;

  int rz_max = 0;
#pragma omp parallel shared(rz_max)
  {
    MySmooth smooth1(&tree1, N_SPH);

#pragma omp for collapse(3) schedule(dynamic, 8)
    for (int rz = 0; rz < Nres; rz++) {
      for (int ry = 0; ry < Nres; ry++) {
        for (int rx = 0; rx < Nres; rx++) {
          if (rz > rz_max) {
            rz_max = rz;
            (cout << rz << " / " << Nres << endl).flush();
          }
          double pz = (rz)*boxsize / Nres - cz;
          double py = (ry)*boxsize / Nres - cy;
          double px = (rx)*boxsize / Nres - cx;

          MyTree::coords c = {float(px), float(py), float(pz)};

          double r2 = c[0] * c[0] + c[1] * c[1] + c[2] * c[2];
          if (r2 > rLimit2) {
            continue;
          }

          uint32_t numInCell = bins[rx][ry][rz];
          if (numInCell > N_SPH)
            smooth1.fetchNeighbours(c, numInCell);
          else
            smooth1.fetchNeighbours(c);
          smooth1.addGridSite(c);
        }
      }
    }
  }

  cout << "Interpolating..." << endl;

  array3_type interpolated(boost::extents[Nres][Nres][Nres]);

  computeInterpolatedField(&tree1, boxsize, Nres, cx, cy, cz, bins,
                           interpolated, getMass, rLimit2);
  hdf5_write_array(out_f, "density", interpolated);
  // out_f.flush();
  for (int i = 0; i < 3; i++) {
    computeInterpolatedField(&tree1, boxsize, Nres, cx, cy, cz, bins,
                             interpolated, boost::bind(getVelocity, _1, i),
                             rLimit2);
    hdf5_write_array(out_f, str(format("p%d") % i), interpolated);
  }

  return 0;
};