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Added Healpix detection facilities
This commit is contained in:
Guilhem Lavaux
parent
160ed45c12
commit
4df341f9ba
5 changed files with 252 additions and 8 deletions
42
mytools/FindHealpix.cmake
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42
mytools/FindHealpix.cmake
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@ -0,0 +1,42 @@
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OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
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#
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# OpenMP handling
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#
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INCLUDE(FindOpenMP)
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IF(ENABLE_OPENMP)
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IF (NOT OPENMP_FOUND)
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MESSAGE(ERROR "No known compiler option for enabling OpenMP")
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ENDIF(NOT OPENMP_FOUND)
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SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
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SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKED_FLAGS} ${OpenMP_C_FLAGS}")
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ENDIF(ENABLE_OPENMP)
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SET(HEALPIX_BASE_PATH $ENV{HEALPIX})
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SET(HEALPIX_TARGET $ENV{HEALPIX_TARGET})
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SET(HEALPIX_PATH ${HEALPIX_BASE_PATH}/src/cxx/${HEALPIX_TARGET})
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SET(HEALPIX_HINT_INCLUDE ${HEALPIX_PATH}/include)
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SET(HEALPIX_HINT_LIB ${HEALPIX_PATH}/lib)
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find_path(HEALPIX_INCLUDE_PATH NAMES healpix_map.h PATHS ${HEALPIX_HINT_INCLUDE})
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find_library(HEALPIX_LIBRARY healpix_cxx PATHS ${HEALPIX_HINT_LIB})
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find_library(FFTPACK_LIBRARY fftpack PATHS ${HEALPIX_HINT_LIB})
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find_library(CFITSIO_LIBRARY cfitsio PATHS ${HEALPIX_HINT_LIB})
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find_library(CXXSUPPORT_LIBRARY cxxsupport PATHS ${HEALPIX_HINT_LIB})
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find_library(PSHT_LIBRARY psht PATHS ${HEALPIX_HINT_LIB})
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find_library(CUTILS_LIBRARY c_utils PATHS ${HEALPIX_HINT_LIB})
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SET(HEALPIX_LIBRARIES
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${HEALPIX_LIBRARY} ${EXTRA_HEALPIX_LIBRARIES}
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${FFTPACK_LIBRARY} ${CXXSUPPORT_LIBRARY} ${CFITSIO_LIBRARY}
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)
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@ -7,7 +7,7 @@ using namespace std;
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static const bool DEBUG = true;
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void computeContourPixels(Healpix_Map<float>& m, vector<int> contour)
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void computeContourPixels(Healpix_Map<float>& m, vector<int>& contour)
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{
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for (int p = 0; p < m.Npix(); p++)
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{
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@ -19,7 +19,7 @@ void computeContourPixels(Healpix_Map<float>& m, vector<int> contour)
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if (result[q] < 0)
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continue;
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delta = (m[p]-0.5)*(m[result[q]]-0.5);
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float delta = (m[p]-0.5)*(m[result[q]]-0.5);
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if (delta < 0)
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{
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contour.push_back(p);
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@ -33,7 +33,7 @@ void computeContourPixels(Healpix_Map<float>& m, vector<int> contour)
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{
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Healpix_Map<int> contour_map;
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contour_map.SetNside(RING, m.Nside());
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contour_map.SetNside(m.Nside(), RING);
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contour_map.fill(0);
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for (int p = 0; p < contour.size(); p++)
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{
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@ -4,6 +4,6 @@
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#include <vector>
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#include <healpix_map.h>
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void computeContourPixels(Healpix_Map<float>& map, std::vector<int> contour);
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void computeContourPixels(Healpix_Map<float>& map, std::vector<int>& contour);
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#endif
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@ -7,9 +7,12 @@
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#include <string>
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#include "generateFromCatalog_conf.h"
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#include "contour_pixels.hpp"
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#include <netcdfcpp.h>
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#include <CosmoTool/fortran.hpp>
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using namespace std;
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using boost::format;
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using namespace CosmoTool;
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struct NYU_Data
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{
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@ -22,7 +25,23 @@ struct NYU_Data
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double phi_z;
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};
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void loadData(const string& fname, vector<NYU_Data> & data)
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struct Position
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{
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double xyz[3];
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};
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struct ParticleData
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{
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vector<int> id_gal;
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int id_mask;
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vector<Position> pos;
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double box[3][2];
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double Lmax;
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};
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typedef vector<NYU_Data> NYU_VData;
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void loadData(const string& fname, NYU_VData & data)
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{
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ifstream f(fname.c_str());
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@ -34,6 +53,173 @@ void loadData(const string& fname, vector<NYU_Data> & data)
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}
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}
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void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data)
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{
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double d2r = M_PI/180;
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output_data.pos.resize(data.size());
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output_data.id_gal.resize(data.size());
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for (int j = 0; j < 3; j++)
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{
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output_data.box[j][0] = -INFINITY;
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output_data.box[j][1] = INFINITY;
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}
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for (int i = 0; i < data.size(); i++)
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{
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double ra = data[i].ra*d2r, dec = data[i].dec*d2r;
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Position& p = output_data.pos[i];
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p.xyz[0] = data[i].cz*cos(ra)*cos(dec);
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p.xyz[1] = data[i].cz*sin(ra)*cos(dec);
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p.xyz[2] = data[i].cz*sin(dec);
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output_data.id_gal[i] = data[i].index;
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for (int j = 0; j < 3; j++)
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{
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if (p.xyz[j] > output_data.box[j][0])
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output_data.box[j][0] = p.xyz[j];
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if (p.xyz[j] < output_data.box[j][1])
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output_data.box[j][1] = p.xyz[j];
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}
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}
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cout << format("Galaxy position generated: %d galaxies") % output_data.pos.size() << endl;
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cout << format("box is %g < x < %g; %g < y < %g; %g < z < %g")
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% (1e-2*output_data.box[0][1]) % (1e-2*output_data.box[0][0])
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% (1e-2*output_data.box[1][1]) % (1e-2*output_data.box[1][0])
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% (1e-2*output_data.box[2][1]) % (1e-2*output_data.box[2][0]) << endl;
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}
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void generateSurfaceMask(generateFromCatalog_info& args ,
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Healpix_Map<float>& mask,
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vector<int>& pixel_list,
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NYU_VData& data,
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ParticleData& output_data)
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{
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// Find the first free index
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int idx = -1;
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int insertion = 0;
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double volume = pixel_list.size()*1.0/mask.Npix()*4*M_PI;
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int numToInsert;
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for (int i = 0; i < output_data.id_gal.size(); i++)
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{
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if (idx < output_data.id_gal[i])
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idx = output_data.id_gal[i]+1;
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}
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output_data.id_mask = idx;
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cout << "Generate surface mask..." << endl;
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double Rmax = -1;
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for (int j = 0; j < 3; j++)
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{
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Rmax = max(Rmax, max(output_data.box[j][0], -output_data.box[j][1]));
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}
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output_data.Lmax = Rmax;
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cout << format("Rmax is %g, surface volume is %g") % (Rmax/100) % (volume/(4*M_PI)) << endl;
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volume *= Rmax*Rmax*Rmax/3/1e6;
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numToInsert = (int)floor(volume*args.density_fake_arg);
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cout << format("3d volume to fill: %g (Mpc/h)^3") % volume << endl;
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cout << format("Will insert %d particles") % numToInsert << endl;
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double pct = 0;
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for (int i = 0; i < numToInsert; i++)
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{
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double new_pct = i*100./numToInsert;
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if (new_pct-pct > 5.)
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{
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pct = new_pct;
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cout << format(" .. %3.0f %%") % pct << endl;
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}
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Position p;
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bool stop_here;
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do
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{
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int p0 = (int)floor(drand48()*pixel_list.size());
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vec3 v = mask.pix2vec(pixel_list[p0]);
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double r = Rmax*pow(drand48(),1./3);
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p.xyz[0] = v.x * r;
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p.xyz[1] = v.y * r;
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p.xyz[2] = v.z * r;
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stop_here = true;
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for (int j = 0; j < 3; j++)
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{
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if (p.xyz[j] > output_data.box[j][0] ||
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p.xyz[j] < output_data.box[j][1])
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stop_here = false;
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}
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}
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while (!stop_here);
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output_data.pos.push_back(p);
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output_data.id_gal.push_back(idx);
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insertion++;
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}
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cout << format("Done. Inserted %d particles.") % insertion << endl;
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}
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void saveData(ParticleData& pdata)
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{
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NcFile f("particles.nc", NcFile::Replace);
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assert(f.is_valid());
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NcDim *d = f.add_dim("space", 3);
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NcDim *p = f.add_dim("Np", pdata.pos.size());
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NcVar *v = f.add_var("particles", ncDouble, d, p);
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double *x = new double[pdata.pos.size()];
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for (int j = 0; j < 3; j++)
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{
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for (int i = 0; i < pdata.pos.size(); i++)
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x[i] = pdata.pos[i].xyz[j];
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v->put_rec(d, x, j);
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}
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v = f.add_var("id_gal", ncInt, p);
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v->put(&pdata.id_gal[0], pdata.id_gal.size());
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delete[] x;
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}
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void saveForZobov(ParticleData& pdata, const string& fname)
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{
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UnformattedWrite f(fname);
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static const char axis[] = { 'X', 'Y', 'Z' };
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double Lmax = pdata.Lmax;
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f.beginCheckpoint();
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f.writeInt32(pdata.pos.size());
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f.endCheckpoint();
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for (int j = 0; j < 3; j++)
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{
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cout << format("Writing %c components...") % axis[j] << endl;
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f.beginCheckpoint();
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for (uint32_t i = 0; i < pdata.pos.size(); i++)
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{
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f.writeReal32((pdata.pos[i].xyz[j]+Lmax)/(2*Lmax));
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}
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f.endCheckpoint();
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}
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}
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int main(int argc, char **argv)
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{
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@ -66,14 +252,30 @@ int main(int argc, char **argv)
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cout << "Loading NYU data..." << endl;
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vector<NYU_Data> data;
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Healpix_Map<float> mask;
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Healpix_Map<float> o_mask;
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vector<int> pixel_list;
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ParticleData output_data;
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loadData(args_info.catalog_arg, data);
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cout << "Loading mask..." << endl;
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read_Healpix_map_from_fits(args_info.mask_arg, mask);
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read_Healpix_map_from_fits(args_info.mask_arg, o_mask);
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Healpix_Map<float> mask;
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mask.SetNside(128, RING);
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mask.Import(o_mask);
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computeContourPixels(mask,pixel_list);
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// We compute a cube holding all the galaxies + the survey surface mask
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generateGalaxiesInCube(data, output_data);
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generateSurfaceMask(args_info, mask, pixel_list, data, output_data);
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saveForZobov(output_data, args_info.output_arg);
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// saveData(output_data);
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return 0;
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}
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@ -44,7 +44,7 @@ int delaunadj (coordT *points, int nvp, int nvpbuf, int nvpall, PARTADJ **adjs)
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}
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/* Delaunay triangulation*/
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sprintf (flags, "qhull s d");
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sprintf (flags, "qhull s d QJ");
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exitcode= qh_new_qhull (dim, nvpall, points, ismalloc,
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flags, outfile, errfile);
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