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vide_public/c_tools/mock/generateFromCatalog.cpp
Guilhem Lavaux aa38661b65 Added copyright/license notice
2013-03-02 18:30:40 -05:00

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/*+
VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateFromCatalog.cpp
Copyright (C) 2010-2013 Guilhem Lavaux
Copyright (C) 2011-2013 Paul M. Sutter
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+*/
#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;
long uniqueID;
};
struct Position
{
double xyz[3];
};
struct ParticleData
{
vector<int> id_gal;
vector<double> ra;
vector<double> dec;
vector<double> redshift;
vector<double> catalogID;
vector<long> uniqueID;
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;
d.uniqueID = d.index;
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());
output_data.uniqueID.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;
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;
output_data.uniqueID[i] = data[i].uniqueID;
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);
output_data.uniqueID.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);
output_data.uniqueID.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 q = 0; q < 0; q++) {
//for (int p = 0; p < full_mask_list.size(); p++) {
vec3 v = mask.pix2vec(full_mask_list[q]);
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);
output_data.uniqueID.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);
output_data.uniqueID.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;
double r2d = 180./M_PI;
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();
}
cout << format("Writing RA...") << endl;
f.beginCheckpoint();
for (uint32_t i = 0; i < pdata.pos.size(); i++) {
f.writeReal32(pdata.ra[i]*r2d);
}
f.endCheckpoint();
cout << format("Writing Dec...") << endl;
f.beginCheckpoint();
for (uint32_t i = 0; i < pdata.pos.size(); i++) {
f.writeReal32(pdata.dec[i]*r2d);
}
f.endCheckpoint();
cout << format("Writing Redshift...") << endl;
f.beginCheckpoint();
for (uint32_t i = 0; i < pdata.pos.size(); i++) {
f.writeReal32(pdata.redshift[i]);
}
f.endCheckpoint();
cout << format("Writing Unique ID...") << endl;
f.beginCheckpoint();
for (uint32_t i = 0; i < pdata.pos.size(); i++) {
f.writeInt64(pdata.uniqueID[i]);
}
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
fp.add_att("is_observation", 1); // 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 *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);
//v2->put(expansion_fac, pdata.pos.size());
//delete[] expansion_fac;
/*
FILE *infoFile = fopen("sample_info.txt", "w");
fprintf(infoFile, "x_min = %f\n", -Lmax/100.);
fprintf(infoFile, "x_max = %f\n", Lmax/100.);
fprintf(infoFile, "y_min = %f\n", -Lmax/100.);
fprintf(infoFile, "y_max = %f\n", Lmax/100.);
fprintf(infoFile, "z_min = %f\n", -Lmax/100.);
fprintf(infoFile, "z_max = %f\n", Lmax/100.);
fprintf(infoFile, "mask_index = %d\n", pdata.mask_index);
fprintf(infoFile, "total_particles = %d\n", pdata.pos.size());
fclose(infoFile);
*/
}
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 data " << args_info.catalog_arg << "..." << 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);
computeMaskPixels(mask,full_mask_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("total_particles.txt", "w");
fprintf(fp, "%d", output_data.pos.size());
fclose(fp);
printf("Done!\n");
// END PMS
return 0;
}
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