Add Distance filter

sample/CMakeLists.txt

@@ -89,7 +89,10 @@ if (Boost_FOUND)
     add_executable(simple3DFilter simple3DFilter.cpp)
     target_link_libraries(simple3DFilter ${tolink})
 
-    install(TARGETS simple3DFilter
+    add_executable(simpleDistanceFilter simpleDistanceFilter.cpp)
+    target_link_libraries(simpleDistanceFilter ${tolink})
+
+    install(TARGETS simple3DFilter simpleDistanceFilter
         RUNTIME DESTINATION bin
         LIBRARY DESTINATION lib
         ARCHIVE DESTINATION lib)

sample/simpleDistanceFilter.cpp

@@ -0,0 +1,86 @@
+#include "openmp.hpp"
+#include "omptl/algorithm"
+#include <cassert>
+#include "yorick.hpp"
+#include "sphSmooth.hpp"
+#include "mykdtree.hpp"
+#include "miniargs.hpp"
+#include <H5Cpp.h>
+#include "hdf5_array.hpp"
+#include <iostream>
+#include <boost/format.hpp>
+#include <boost/bind.hpp>
+
+using namespace std;
+using namespace CosmoTool;
+
+struct VCoord{
+};
+
+using boost::format;
+using boost::str;
+typedef boost::multi_array<float, 2> array_type_2d;
+typedef boost::multi_array<float, 1> array_type_1d;
+
+typedef KDTree<3,float> MyTree;
+typedef MyTree::Cell MyCell;
+
+int main(int argc, char **argv)
+{
+
+  char *fname1, *fname2;
+
+  MiniArgDesc args[] = {
+    { "INPUT DATA1", &fname1, MINIARG_STRING },
+    { 0, 0, MINIARG_NULL }
+  };
+
+  if (!parseMiniArgs(argc, argv, args))
+    return 1;
+
+  H5::H5File in_f(fname1, 0);
+  H5::H5File out_f("distances.h5", H5F_ACC_TRUNC);
+  array_type_2d v1_data;
+  array_type_1d dist_data;
+  uint32_t N1_points;
+  
+  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];
+  
+  cout << "Shuffling data in cells..." << endl;
+#pragma omp parallel for schedule(static)
+  for (int i = 0 ; i < N1_points; i++)
+    {
+      for (int j = 0; j < 3; j++)
+        allCells_1[i].coord[j] = v1_data[i][j];
+      allCells_1[i].active = true;
+    }
+  dist_data.resize(boost::extents[N1_points]);
+  
+  cout << "Building trees..." << endl;
+  MyTree tree1(allCells_1, N1_points);
+#pragma omp parallel
+  {
+    MyCell **foundCells = new MyCell *[2];
+
+    #pragma omp for
+    for (size_t i = 0; i < N1_points; i++) {
+      double dists[2];
+
+      tree1.getNearestNeighbours(allCells_1[i].coord, 2, foundCells, dists);
+      dist_data[i] = dists[1];
+    }
+
+    delete[] foundCells;
+  }
+  
+  hdf5_write_array(out_f, "distances", dist_data);
+  
+  return 0;
+};

src/loadRamses.cpp

@@ -34,7 +34,7 @@ knowledge of the CeCILL license and that you accept its terms.
 +*/
 
 #include <sys/types.h>
-#include <regex.h>
+#include "/usr/include/regex.h"
 #include <cmath>
 #include <cstring>
 #include <cstdlib>