Merge branch 'master' of ssh://bitbucket.org/cosmicvoids/void_identification

c_tools/mock/generateMock.cpp

@@ -260,7 +260,7 @@ void selectBox(SimuData *simu, std::vector<long>& targets, generateMock_info& ar
 	acceptance = 
 	  acceptance &&
 	  (simu->Pos[j][i] > ranges[j][0]) && 
-	  (simu->Pos[j][i] < ranges[j][1]);	
+	  (simu->Pos[j][i] <= ranges[j][1]);	
         p.Pos[j] = simu->Pos[j][i];
         p.Vel[j] = (simu->Vel[j] != 0) ? simu->Vel[j][i] : 0;
       }
@@ -274,7 +274,7 @@ void selectBox(SimuData *simu, std::vector<long>& targets, generateMock_info& ar
         numAccepted++; 
       }
     }
-  cout << "Num accepted here = " << numAccepted <<  " / input = " << simu->NumPart << endl; 
+  cout << "SELECTBOX: Num accepted here = " << numAccepted <<  " / input = " << simu->NumPart << " (after resubsampling)" << endl; 
 }
 
 class PreselectParticles: public SimulationPreprocessor
@@ -385,7 +385,7 @@ void buildBox(SimuData *simu, long num_targets, long loaded,
     }
 }
 
-void saveBox(SimuData *&boxed, const std::string& outbox)
+void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& args_info)
 {
   double *ranges = boxed->as<double>("ranges");
   NcFile f(outbox.c_str(), NcFile::Replace, 0, 0, NcFile::Netcdf4);
@@ -395,6 +395,11 @@ void saveBox(SimuData *&boxed, const std::string& outbox)
   int num_snapshots = *boxed->as<int>("num_snapshots");
   long *uniqueID = boxed->as<long>("uniqueID");
 
+  if (!f.is_valid())
+    {
+      cerr << "Could not create parameter file '" << outbox << "'. Aborting." << endl;
+      exit(1);
+    }
   f.add_att("range_x_min", ranges[0]);
   f.add_att("range_x_max", ranges[1]);
   f.add_att("range_y_min", ranges[2]);
@@ -403,6 +408,7 @@ void saveBox(SimuData *&boxed, const std::string& outbox)
   f.add_att("range_z_max", ranges[5]);
   f.add_att("mask_index", -1);
   f.add_att("is_observation", 0);
+  f.add_att("data_subsampling", args_info.subsample_arg);
 
   NcDim *NumPart_dim = f.add_dim("numpart_dim", boxed->NumPart);
   NcDim *NumSnap_dim = f.add_dim("numsnap_dim", num_snapshots);
@@ -446,6 +452,13 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
   boxed->time = simu->time;
   boxed->BoxSize = simu->BoxSize;
 
+  NcAtt *d_sub = f.get_att("data_subsampling");
+  if (d_sub == 0 || d_sub->as_double(0)/args_info.subsample_arg-1. > 1.e-5)
+   {
+     cerr << "Parameter file was not generated with the same simulation subsampling argument. Particles will be different. Stop here." << d_sub->as_double(0) << " " << args_info.subsample_arg <<endl;
+     exit(1);
+   }
+
   NcVar *v_id = f.get_var("particle_ids");
   NcVar *v_snap = f.get_var("snapshot_split");
   long *edges1;
@@ -710,7 +723,7 @@ int main(int argc, char **argv)
       delete[] efac;
     }
 
-  saveBox(simuOut, args_info.outputParameter_arg);
+  saveBox(simuOut, args_info.outputParameter_arg, args_info);
   generateOutput(simuOut, args_info.axis_arg, 
                  args_info.output_arg);
   delete preselector;

c_tools/mock/loaders/multidark_loader.cpp

@@ -20,13 +20,16 @@
 
 
 #include <cassert>
+#include <boost/format.hpp>
 #include <string>
 #include <fstream>
 #include <iostream>
 #include <CosmoTool/loadRamses.hpp>
 #include <CosmoTool/fortran.hpp>
 #include "simulation_loader.hpp"
+#include <libsdf/cosmo.h>
 
+using boost::format;
 using namespace std;
 using namespace CosmoTool;
 
@@ -82,6 +85,12 @@ public:
 
     double tempData;
 
+    double shift = 0.5*simu->BoxSize;
+    double rescale_position = simu->Hubble*1.e-5*100./simu->time;
+    double rescale_velocity = one_kpc/one_Gyr;
+#define INFINITY std::numeric_limits<float>::max()
+    float min_pos[3] = {INFINITY,INFINITY, INFINITY}, max_pos[3] = {-INFINITY,-INFINITY,-INFINITY};
+
     cout << "loading multidark particles" << endl;
     long actualNumPart = 0;
 
@@ -96,6 +105,17 @@ public:
           p.Pos[2] == -99 && p.Vel[2] == -99)
         break;
 
+      //p.Pos[0] = p.Pos[0]*rescale_position + shift;
+      //p.Pos[1] = p.Pos[1]*rescale_position + shift;
+      //p.Pos[2] = p.Pos[2]*rescale_position + shift;
+      //p.Vel[2] = p.Vel[2]*rescale_velocity;
+
+      // enforce box size in case of roundoff error
+      for (int k = 0; k < 3; k++) {
+        if (p.Pos[k] < 0) p.Pos[k] += simu->BoxSize;
+        if (p.Pos[k] >= simu->BoxSize) p.Pos[k] -= simu->BoxSize;
+      }
+
       if (preproc != 0 && !preproc->accept(p))
         continue;
 
@@ -110,7 +130,14 @@ public:
           reallocArray(uniqueID, allocated, actualNumPart);
           reallocArray(index, allocated, actualNumPart);
         }
-      }
+
+       for (int k = 0; k < 3; k++) {
+         min_pos[k] = std::min(min_pos[k], p.Pos[k]);
+         max_pos[k] = std::max(max_pos[k], p.Pos[k]);
+       }
+    }
+    for (int k = 0; k < 3; k++) cout << boost::format("min[%d] = %g, max[%d] = %g") % k % min_pos[k] % k %max_pos[k] << endl;
+
     applyTransformations(simu);
     simu->NumPart = actualNumPart;
     simu->TotalNumPart = actualNumPart;

c_tools/mock/loaders/sdf_loader.cpp

@@ -190,7 +190,7 @@ public:
     if (load_flags & (NEED_POSITION | NEED_VELOCITY))
       rescaleParticles(d, d->Hubble*1e-5, one_kpc/one_Gyr);
 
-//    enforceBoxSize(d);
+    enforceBoxSize(d);
     applyTransformations(d);
     basicPreprocessing(d, preproc);