mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
Slight re-organization of C/C++ tools. Significant modifications to support observational data. Python and pipeline scripts added
This commit is contained in:
P.M. Sutter
parent
15496df4ff
commit
14abbc2018
42 changed files with 16252 additions and 557 deletions
531
c_tools/mock/generateFromCatalog.cpp
Normal file
531
c_tools/mock/generateFromCatalog.cpp
Normal file
|
|
@ -0,0 +1,531 @@
|
|||
#include <healpix_map.h>
|
||||
#include <healpix_map_fitsio.h>
|
||||
#include <boost/format.hpp>
|
||||
#include <iostream>
|
||||
#include <fstream>
|
||||
#include <vector>
|
||||
#include <string>
|
||||
#include "generateFromCatalog_conf.h"
|
||||
#include "contour_pixels.hpp"
|
||||
#include <netcdfcpp.h>
|
||||
#include <CosmoTool/fortran.hpp>
|
||||
#include <gsl/gsl_interp.h>
|
||||
#include <gsl/gsl_integration.h>
|
||||
|
||||
#define LIGHT_SPEED 299792.458
|
||||
|
||||
using namespace std;
|
||||
using boost::format;
|
||||
using namespace CosmoTool;
|
||||
|
||||
struct NYU_Data
|
||||
{
|
||||
int index;
|
||||
int sector;
|
||||
int region;
|
||||
double ra, dec;
|
||||
double cz;
|
||||
double fgotten;
|
||||
double phi_z;
|
||||
};
|
||||
|
||||
struct Position
|
||||
{
|
||||
double xyz[3];
|
||||
};
|
||||
|
||||
struct ParticleData
|
||||
{
|
||||
vector<int> id_gal;
|
||||
vector<double> ra;
|
||||
vector<double> dec;
|
||||
vector<double> redshift;
|
||||
int id_mask;
|
||||
// PMS
|
||||
int mask_index;
|
||||
// END PMS
|
||||
vector<Position> pos;
|
||||
double box[3][2];
|
||||
double Lmax;
|
||||
};
|
||||
|
||||
typedef vector<NYU_Data> NYU_VData;
|
||||
|
||||
// this defines the expansion function that we will integrate
|
||||
// Laveaux & Wandelt (2012) Eq. 24
|
||||
struct my_expan_params { double Om; double w0; double wa; };
|
||||
double expanFun (double z, void * p) {
|
||||
struct my_expan_params * params = (struct my_expan_params *)p;
|
||||
double Om = (params->Om);
|
||||
double w0 = (params->w0);
|
||||
double wa = (params->wa);
|
||||
|
||||
//const double h0 = 1.0;
|
||||
const double h0 = 0.71;
|
||||
double ez;
|
||||
|
||||
double wz = w0 + wa*z/(1+z);
|
||||
|
||||
ez = Om*pow(1+z,3) + (1.-Om);
|
||||
//ez = Om*pow(1+z,3) + pow(h0,2) * (1.-Om)*pow(1+z,3+3*wz);
|
||||
|
||||
ez = sqrt(ez);
|
||||
//ez = sqrt(ez)/h0;
|
||||
|
||||
ez = 1./ez;
|
||||
|
||||
return ez;
|
||||
}
|
||||
|
||||
void loadData(const string& fname, NYU_VData & data)
|
||||
{
|
||||
ifstream f(fname.c_str());
|
||||
|
||||
while (!f.eof())
|
||||
{
|
||||
NYU_Data d;
|
||||
f >> d.index >> d.sector >> d.region >> d.ra >> d.dec >> d.cz >> d.fgotten >> d.phi_z;
|
||||
data.push_back(d);
|
||||
}
|
||||
}
|
||||
|
||||
void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
|
||||
bool useLCDM)
|
||||
{
|
||||
double d2r = M_PI/180;
|
||||
|
||||
gsl_function expanF;
|
||||
expanF.function = &expanFun;
|
||||
struct my_expan_params expanParams;
|
||||
double maxZ = 2.0, z, result, error, *dL, *redshifts;
|
||||
int numZ = 1000, iZ;
|
||||
size_t nEval;
|
||||
|
||||
expanParams.Om = 0.27;
|
||||
expanParams.w0 = -1.0;
|
||||
expanParams.wa = 0.0;
|
||||
expanF.params = &expanParams;
|
||||
|
||||
dL = (double *) malloc(numZ * sizeof(double));
|
||||
redshifts = (double *) malloc(numZ * sizeof(double));
|
||||
|
||||
for (iZ = 0; iZ < numZ; iZ++) {
|
||||
z = iZ * maxZ/numZ;
|
||||
//gsl_integration_qng(&expanF, 0.0, z, 1.e-6, 1.e-6, &result, &error, &nEval);
|
||||
dL[iZ] = result;
|
||||
redshifts[iZ] = z;
|
||||
}
|
||||
|
||||
gsl_interp *interp = gsl_interp_alloc(gsl_interp_linear, numZ);
|
||||
gsl_interp_init(interp, redshifts, dL, numZ);
|
||||
gsl_interp_accel *acc = gsl_interp_accel_alloc();
|
||||
|
||||
output_data.pos.resize(data.size());
|
||||
output_data.id_gal.resize(data.size());
|
||||
output_data.ra.resize(data.size());
|
||||
output_data.dec.resize(data.size());
|
||||
output_data.redshift.resize(data.size());
|
||||
|
||||
for (int j = 0; j < 3; j++)
|
||||
{
|
||||
output_data.box[j][0] = -INFINITY;
|
||||
output_data.box[j][1] = INFINITY;
|
||||
}
|
||||
|
||||
for (int i = 0; i < data.size(); i++)
|
||||
{
|
||||
double ra = data[i].ra*d2r, dec = data[i].dec*d2r;
|
||||
Position& p = output_data.pos[i];
|
||||
|
||||
if (useLCDM) {
|
||||
//double pos = gsl_interp_eval(interp, redshifts, dL, data[i].cz, acc);
|
||||
gsl_integration_qng(&expanF, 1.e-6, data[i].cz/LIGHT_SPEED,
|
||||
1.e-6,
|
||||
1.e-6, &result, &error, &nEval);
|
||||
double Dc = result*LIGHT_SPEED;
|
||||
cout << "HELLO " << data[i].cz << " " << Dc << endl;
|
||||
p.xyz[0] = Dc*cos(ra)*cos(dec);
|
||||
p.xyz[1] = Dc*sin(ra)*cos(dec);
|
||||
p.xyz[2] = Dc*sin(dec);
|
||||
} else {
|
||||
p.xyz[0] = data[i].cz*cos(ra)*cos(dec);
|
||||
p.xyz[1] = data[i].cz*sin(ra)*cos(dec);
|
||||
p.xyz[2] = data[i].cz*sin(dec);
|
||||
}
|
||||
//printf("CREATE %e %e\n", data[i].cz, sqrt(p.xyz[0]*p.xyz[0] + p.xyz[1]*p.xyz[1] + p.xyz[2]*p.xyz[2]));
|
||||
output_data.id_gal[i] = data[i].index;
|
||||
output_data.ra[i] = ra;
|
||||
output_data.dec[i] = dec;
|
||||
output_data.redshift[i] = data[i].cz;
|
||||
|
||||
for (int j = 0; j < 3; j++)
|
||||
{
|
||||
if (p.xyz[j] > output_data.box[j][0])
|
||||
output_data.box[j][0] = p.xyz[j];
|
||||
if (p.xyz[j] < output_data.box[j][1])
|
||||
output_data.box[j][1] = p.xyz[j];
|
||||
}
|
||||
//printf("INSERT GAL %d %e %e %e\n", output_data.id_gal[i], p.xyz[0], p.xyz[1], p.xyz[2]);
|
||||
}
|
||||
cout << format("Galaxy position generated: %d galaxies") % output_data.pos.size() << endl;
|
||||
cout << format("box is %g < x < %g; %g < y < %g; %g < z < %g")
|
||||
% (1e-2*output_data.box[0][1]) % (1e-2*output_data.box[0][0])
|
||||
% (1e-2*output_data.box[1][1]) % (1e-2*output_data.box[1][0])
|
||||
% (1e-2*output_data.box[2][1]) % (1e-2*output_data.box[2][0]) << endl;
|
||||
|
||||
gsl_interp_free(interp);
|
||||
}
|
||||
|
||||
void generateSurfaceMask(generateFromCatalog_info& args ,
|
||||
Healpix_Map<float>& mask,
|
||||
vector<int>& pixel_list,
|
||||
vector<int>& full_mask_list,
|
||||
NYU_VData& data,
|
||||
ParticleData& output_data)
|
||||
{
|
||||
// Find the first free index
|
||||
int idx = -1;
|
||||
int insertion = 0;
|
||||
double volume = pixel_list.size()*1.0/mask.Npix()*4*M_PI;
|
||||
int numToInsert;
|
||||
|
||||
for (int i = 0; i < output_data.id_gal.size(); i++)
|
||||
{
|
||||
if (idx < output_data.id_gal[i])
|
||||
idx = output_data.id_gal[i]+1;
|
||||
}
|
||||
|
||||
output_data.id_mask = idx;
|
||||
|
||||
// PMS
|
||||
output_data.mask_index = output_data.id_gal.size();
|
||||
// END PMS
|
||||
cout << "Generate surface mask..." << endl;
|
||||
|
||||
double Rmax = -1;
|
||||
for (int j = 0; j < 3; j++)
|
||||
{
|
||||
Rmax = max(Rmax, max(output_data.box[j][0], -output_data.box[j][1]));
|
||||
}
|
||||
|
||||
output_data.Lmax = Rmax;
|
||||
|
||||
// PMS - write a small text file with galaxy position
|
||||
FILE *fp;
|
||||
fp = fopen("galaxies.txt", "w");
|
||||
for (int i = 0; i < data.size(); i++) {
|
||||
Position& p = output_data.pos[i];
|
||||
fprintf(fp, "%e %e %e\n",
|
||||
(p.xyz[0]),
|
||||
(p.xyz[1]),
|
||||
(p.xyz[2]));
|
||||
}
|
||||
fclose(fp);
|
||||
// END PMS
|
||||
|
||||
cout << format("Rmax is %g, surface volume is %g") % (Rmax/100) % (volume/(4*M_PI)) << endl;
|
||||
volume *= Rmax*Rmax*Rmax/3/1e6;
|
||||
numToInsert = (int)floor(volume*args.density_fake_arg);
|
||||
cout << format("3d volume to fill: %g (Mpc/h)^3") % volume << endl;
|
||||
|
||||
cout << format("Will insert %d particles") % numToInsert << endl;
|
||||
|
||||
fp = fopen("mock_galaxies.txt", "w");
|
||||
|
||||
double pct = 0;
|
||||
for (int i = 0; i < numToInsert; i++) {
|
||||
double new_pct = i*100./numToInsert;
|
||||
|
||||
if (new_pct-pct > 5.) {
|
||||
pct = new_pct;
|
||||
cout << format(" .. %3.0f %%") % pct << endl;
|
||||
}
|
||||
|
||||
Position p;
|
||||
bool stop_here;
|
||||
|
||||
do {
|
||||
int p0 = (int)floor(drand48()*pixel_list.size());
|
||||
vec3 v = mask.pix2vec(pixel_list[p0]);
|
||||
double r = Rmax*pow(drand48(),1./3);
|
||||
|
||||
p.xyz[0] = v.x * r;
|
||||
p.xyz[1] = v.y * r;
|
||||
p.xyz[2] = v.z * r;
|
||||
|
||||
stop_here = true;
|
||||
for (int j = 0; j < 3; j++) {
|
||||
if (p.xyz[j] > output_data.box[j][0] ||
|
||||
p.xyz[j] < output_data.box[j][1])
|
||||
stop_here = false;
|
||||
}
|
||||
}
|
||||
while (!stop_here);
|
||||
|
||||
// PMS : write mock galaxies to a small file for plotting
|
||||
fprintf(fp, "%e %e %e\n",
|
||||
(p.xyz[0]),
|
||||
(p.xyz[1]),
|
||||
(p.xyz[2]));
|
||||
// END PMS
|
||||
output_data.pos.push_back(p);
|
||||
output_data.id_gal.push_back(idx);
|
||||
output_data.ra.push_back(-1);
|
||||
output_data.dec.push_back(-1);
|
||||
output_data.redshift.push_back(-1);
|
||||
//printf("INSERT MOCK %d %e %e %e\n", idx, p.xyz[0], p.xyz[1], p.xyz[2]);
|
||||
insertion++;
|
||||
}
|
||||
|
||||
fclose(fp);
|
||||
|
||||
// PMS
|
||||
// TEST - insert mock galaxies along box edge
|
||||
fp = fopen("mock_boundary.txt", "w");
|
||||
double dx[3];
|
||||
dx[0] = output_data.box[0][1] - output_data.box[0][0];
|
||||
dx[1] = output_data.box[1][1] - output_data.box[1][0];
|
||||
dx[2] = output_data.box[2][1] - output_data.box[2][0];
|
||||
|
||||
int nPart = 100;
|
||||
// TEST
|
||||
for (int iDir = 0; iDir < 0; iDir++) {
|
||||
for (int iFace = 0; iFace < 0; iFace++) {
|
||||
//for (int iDir = 0; iDir < 3; iDir++) {
|
||||
//for (int iFace = 0; iFace < 2; iFace++) {
|
||||
|
||||
int iy = (iDir + 1) % 3;
|
||||
int iz = (iDir + 2) % 3;
|
||||
|
||||
for (int i = 0; i < nPart; i++) {
|
||||
for (int j = 0; j < nPart; j++) {
|
||||
Position p;
|
||||
|
||||
p.xyz[iDir] = output_data.box[iDir][iFace];
|
||||
p.xyz[iy] = i * dx[iy]/nPart + output_data.box[iy][0];
|
||||
p.xyz[iz] = j * dx[iz]/nPart + output_data.box[iz][0];
|
||||
|
||||
output_data.pos.push_back(p);
|
||||
output_data.id_gal.push_back(idx);
|
||||
output_data.ra.push_back(-1);
|
||||
output_data.dec.push_back(-1);
|
||||
output_data.redshift.push_back(-1);
|
||||
insertion++;
|
||||
|
||||
fprintf(fp, "%e %e %e\n",
|
||||
(p.xyz[0]),
|
||||
(p.xyz[1]),
|
||||
(p.xyz[2]));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
fclose(fp);
|
||||
// END PMS
|
||||
|
||||
// PMS
|
||||
// TEST - insert mock galaxies along spheres of survey redshift boundaries
|
||||
fp = fopen("mock_sphere.txt", "w");
|
||||
|
||||
for (int p = 0; p < full_mask_list.size(); p++) {
|
||||
vec3 v = mask.pix2vec(full_mask_list[p]);
|
||||
|
||||
Position p;
|
||||
double r = args.zMin_arg * LIGHT_SPEED;
|
||||
if (r > 0.) {
|
||||
p.xyz[0] = v.x * r;
|
||||
p.xyz[1] = v.y * r;
|
||||
p.xyz[2] = v.z * r;
|
||||
output_data.pos.push_back(p);
|
||||
output_data.id_gal.push_back(idx);
|
||||
output_data.ra.push_back(-1);
|
||||
output_data.dec.push_back(-1);
|
||||
output_data.redshift.push_back(-1);
|
||||
insertion++;
|
||||
fprintf(fp, "%e %e %e\n",
|
||||
(p.xyz[0]),
|
||||
(p.xyz[1]),
|
||||
(p.xyz[2]));
|
||||
}
|
||||
|
||||
r = args.zMax_arg * LIGHT_SPEED;
|
||||
p.xyz[0] = v.x * r;
|
||||
p.xyz[1] = v.y * r;
|
||||
p.xyz[2] = v.z * r;
|
||||
output_data.pos.push_back(p);
|
||||
output_data.id_gal.push_back(idx);
|
||||
output_data.ra.push_back(-1);
|
||||
output_data.dec.push_back(-1);
|
||||
output_data.redshift.push_back(-1);
|
||||
insertion++;
|
||||
fprintf(fp, "%e %e %e\n",
|
||||
(p.xyz[0]),
|
||||
(p.xyz[1]),
|
||||
(p.xyz[2]));
|
||||
}
|
||||
fclose(fp);
|
||||
// END PMS
|
||||
|
||||
cout << format("Done. Inserted %d particles.") % insertion << endl;
|
||||
}
|
||||
|
||||
void saveData(ParticleData& pdata)
|
||||
{
|
||||
NcFile f("particles.nc", NcFile::Replace);
|
||||
|
||||
assert(f.is_valid());
|
||||
|
||||
NcDim *d = f.add_dim("space", 3);
|
||||
NcDim *p = f.add_dim("Np", pdata.pos.size());
|
||||
NcVar *v = f.add_var("particles", ncDouble, d, p);
|
||||
double *x = new double[pdata.pos.size()];
|
||||
|
||||
for (int j = 0; j < 3; j++)
|
||||
{
|
||||
|
||||
for (int i = 0; i < pdata.pos.size(); i++)
|
||||
x[i] = pdata.pos[i].xyz[j];
|
||||
|
||||
v->put_rec(d, x, j);
|
||||
}
|
||||
|
||||
v = f.add_var("id_gal", ncInt, p);
|
||||
v->put(&pdata.id_gal[0], pdata.id_gal.size());
|
||||
|
||||
delete[] x;
|
||||
|
||||
}
|
||||
|
||||
void saveForZobov(ParticleData& pdata, const string& fname, const string& paramname)
|
||||
{
|
||||
UnformattedWrite f(fname);
|
||||
static const char axis[] = { 'X', 'Y', 'Z' };
|
||||
double Lmax = pdata.Lmax;
|
||||
|
||||
f.beginCheckpoint();
|
||||
f.writeInt32(pdata.pos.size());
|
||||
f.endCheckpoint();
|
||||
|
||||
|
||||
for (int j = 0; j < 3; j++)
|
||||
{
|
||||
cout << format("Writing %c components...") % axis[j] << endl;
|
||||
f.beginCheckpoint();
|
||||
for (uint32_t i = 0; i < pdata.pos.size(); i++)
|
||||
{
|
||||
f.writeReal32((pdata.pos[i].xyz[j]+Lmax)/(2*Lmax));
|
||||
}
|
||||
f.endCheckpoint();
|
||||
}
|
||||
|
||||
NcFile fp(paramname.c_str(), NcFile::Replace);
|
||||
|
||||
fp.add_att("range_x_min", -Lmax/100.);
|
||||
fp.add_att("range_x_max", Lmax/100.);
|
||||
fp.add_att("range_y_min", -Lmax/100.);
|
||||
fp.add_att("range_y_max", Lmax/100.);
|
||||
fp.add_att("range_z_min", -Lmax/100.);
|
||||
fp.add_att("range_z_max", Lmax/100.);
|
||||
fp.add_att("mask_index", pdata.mask_index); // PMS
|
||||
|
||||
int nOutputPart = pdata.mask_index;
|
||||
//int nOutputPart = pdata.pos.size();
|
||||
|
||||
NcDim *NumPart_dim = fp.add_dim("numpart_dim", nOutputPart);
|
||||
NcVar *v = fp.add_var("particle_ids", ncInt, NumPart_dim);
|
||||
NcVar *vra = fp.add_var("RA", ncInt, NumPart_dim);
|
||||
NcVar *vdec = fp.add_var("DEC", ncInt, NumPart_dim);
|
||||
NcVar *vredshift = fp.add_var("z", ncInt, NumPart_dim);
|
||||
//NcVar *v2 = fp.add_var("expansion", ncDouble, NumPart_dim);
|
||||
|
||||
//double *expansion_fac = new double[pdata.pos.size()];
|
||||
|
||||
//for (int i = 0; i < pdata.pos.size(); i++)
|
||||
// expansion_fac[i] = 1.0;
|
||||
|
||||
v->put(&pdata.id_gal[0], nOutputPart);
|
||||
vra->put(&pdata.ra[0], nOutputPart);
|
||||
vdec->put(&pdata.dec[0], nOutputPart);
|
||||
vredshift->put(&pdata.redshift[0], nOutputPart);
|
||||
//v2->put(expansion_fac, pdata.pos.size());
|
||||
|
||||
//delete[] expansion_fac;
|
||||
}
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
generateFromCatalog_info args_info;
|
||||
generateFromCatalog_conf_params args_params;
|
||||
|
||||
generateFromCatalog_conf_init(&args_info);
|
||||
generateFromCatalog_conf_params_init(&args_params);
|
||||
|
||||
args_params.check_required = 0;
|
||||
if (generateFromCatalog_conf_ext (argc, argv, &args_info, &args_params))
|
||||
return 1;
|
||||
|
||||
if (!args_info.configFile_given)
|
||||
{
|
||||
if (generateFromCatalog_conf_required (&args_info, GENERATEFROMCATALOG_CONF_PACKAGE))
|
||||
return 1;
|
||||
}
|
||||
else
|
||||
{
|
||||
args_params.check_required = 1;
|
||||
args_params.initialize = 0;
|
||||
if (generateFromCatalog_conf_config_file (args_info.configFile_arg,
|
||||
&args_info,
|
||||
&args_params))
|
||||
return 1;
|
||||
}
|
||||
|
||||
generateFromCatalog_conf_print_version();
|
||||
|
||||
cout << "Loading NYU data..." << endl;
|
||||
vector<NYU_Data> data;
|
||||
Healpix_Map<float> o_mask;
|
||||
vector<int> pixel_list;
|
||||
vector<int> full_mask_list;
|
||||
ParticleData output_data;
|
||||
|
||||
loadData(args_info.catalog_arg, data);
|
||||
|
||||
|
||||
cout << "Loading mask..." << endl;
|
||||
read_Healpix_map_from_fits(args_info.mask_arg, o_mask);
|
||||
|
||||
Healpix_Map<float> mask;
|
||||
|
||||
mask.SetNside(128, RING);
|
||||
mask.Import(o_mask);
|
||||
|
||||
computeContourPixels(mask,pixel_list);
|
||||
|
||||
// We compute a cube holding all the galaxies + the survey surface mask
|
||||
|
||||
cout << "Placing galaxies..." << endl;
|
||||
generateGalaxiesInCube(data, output_data, args_info.useLCDM_flag);
|
||||
generateSurfaceMask(args_info, mask, pixel_list, full_mask_list,
|
||||
data, output_data);
|
||||
|
||||
saveForZobov(output_data, args_info.output_arg, args_info.params_arg);
|
||||
// saveData(output_data);
|
||||
|
||||
// PMS
|
||||
FILE *fp = fopen("mask_index.txt", "w");
|
||||
fprintf(fp, "%d", output_data.mask_index);
|
||||
fclose(fp);
|
||||
|
||||
fp = fopen("sample_info.txt", "w");
|
||||
fprintf(fp, "Lmax = %f\n", output_data.Lmax);
|
||||
fprintf(fp, "mask_index = %d\n", output_data.mask_index);
|
||||
fprintf(fp, "total_particles = %d\n", output_data.pos.size());
|
||||
fclose(fp);
|
||||
|
||||
fp = fopen("total_particles.txt", "w");
|
||||
fprintf(fp, "%d", output_data.pos.size());
|
||||
fclose(fp);
|
||||
printf("Done!\n");
|
||||
// END PMS
|
||||
return 0;
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue