cosmotool/sample/simple3DFilter.cpp

/*+
This is CosmoTool (./sample/simple3DFilter.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)

guilhem.lavaux@gmail.com

This software is a computer program whose purpose is to provide a toolbox for cosmological
data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)

This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info". 

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability. 

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or 
data to be ensured and,  more generally, to use and operate it in the 
same conditions as regards security. 

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
+*/
#include <cassert>
#include "yorick.hpp"
#include "sphSmooth.hpp"
#include "mykdtree.hpp"
#include "miniargs.hpp"
#include <H5Cpp.h>
#include "hdf5_array.hpp"
#include <iostream>

using namespace std;
using namespace CosmoTool;

#define N_SPH 16

struct VCoord{
  float v[3];
};

template<int i>
ComputePrecision getVelocity(const VCoord& v)
{
  return v.v[i];
}

ComputePrecision getUnity(const VCoord& v)
{
  return 1.0;
}

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

int main(int argc, char **argv)
{
  typedef boost::multi_array<float, 2> array_type;
  typedef boost::multi_array<float, 3> array3_type;
  typedef boost::multi_array<float, 4> array4_type;

  char *fname1, *fname2;
  double rLimit, boxsize, rLimit2, cx, cy, cz;
  int Nres;

  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 },
    { 0, 0, MINIARG_NULL }
  };

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

  H5::H5File in_f(fname1, 0);
  H5::H5File out_f("fields.h5", H5F_ACC_TRUNC);
  array_type v1_data;
  uint32_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] == 6);

  N1_points = v1_data.shape()[0];
  
  cout << "Got " << N1_points << " in the first file." << endl;

  MyCell *allCells_1 = new MyCell[N1_points];
  
  for (long i = 0; i < Nres*Nres*Nres; i++)
    bins.data()[i] = 0;

  cout << "Shuffling data in cells..." << endl;
  for (int 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].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;
	  
      bins[rx][ry][rz]++;
    }
  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);

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

  array3_type out_den_1(boost::extents[Nres][Nres][Nres]);
  array4_type out_v3d_1(boost::extents[Nres][Nres][Nres][3]);
  array3_type out_rad_1(boost::extents[Nres][Nres][Nres]);
 
  cout << "Weighing..." << endl;

#pragma omp parallel
  {
    MySmooth smooth1(&tree1, N_SPH);
    
#pragma omp for schedule(dynamic) 
    for (int rz = 0; rz < Nres; rz++)
     {
        double pz = (rz)*boxsize/Nres-cz;

        cout << rz << " / " << Nres << endl;
        for (int ry = 0; ry < Nres; ry++)
          {
            double py = (ry)*boxsize/Nres-cy;
            for (int rx = 0; rx < Nres; rx++)
              {
                double px = (rx)*boxsize/Nres-cx;
                
                MyTree::coords c = { px, py, 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);
#pragma omp critical
                smooth1.addGridSite(c);
              }
          }
      }  
  }
  
  cout << "Interpolating..." << endl;
#pragma omp parallel
  {
    MySmooth smooth1(&tree1, N_SPH);
    
#pragma omp for schedule(dynamic) 
    for (int rz = 0; rz < Nres; rz++)
      {
        double pz = (rz)*boxsize/Nres-cz;

        cout << rz << " / " << Nres << endl;
        for (int ry = 0; ry < Nres; ry++)
          {
            double py = (ry)*boxsize/Nres-cy;
            for (int rx = 0; rx < Nres; rx++)
              {
                double px = (rx)*boxsize/Nres-cx;
                
                MyTree::coords c = { px, py, pz };

                double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
                if (r2 > rLimit2)
                  {
                    out_v3d_1[rx][ry][rz][0] = 0;
                    out_v3d_1[rx][ry][rz][1] = 0;
                    out_v3d_1[rx][ry][rz][2] = 0;
                    out_den_1[rx][ry][rz] = 0;
                    out_rad_1[rx][ry][rz] = -1;
                    continue;
                  }

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

                float val;

                out_rad_1[rx][ry][rz] = smooth1.getSmoothingLen();
                out_v3d_1[rx][ry][rz][0] = smooth1.computeSmoothedValue(c, getVelocity<0>);
                out_v3d_1[rx][ry][rz][1] = smooth1.computeSmoothedValue(c, getVelocity<1>);
                out_v3d_1[rx][ry][rz][2] = smooth1.computeSmoothedValue(c, getVelocity<2>);
                out_den_1[rx][ry][rz] = smooth1.computeSmoothedValue(c, getUnity);
              }
          }
      }
  }
      
  hdf5_write_array(out_f, "radii", out_rad_1);
  hdf5_write_array(out_f, "velocity", out_v3d_1);
  hdf5_write_array(out_f, "density", out_den_1);

  return 0;
};