mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-05 07:41:11 +00:00
Implemented (yet another) new boundary handling scheme, whereby we scan radially along survey edge while flagging nearest galaxies. The prepObservation routine was significantly cleaned up to accommodate this, but it was ultimately implemented in python (surveyTools.py) for ease of prototyping, with the intent to move it back into C later.
Some general housekeeping, making sure some new parameters are passed around correctly, and removing the storage of some unused files. This update is considered HIGHLY UNSTABLE. It will almost certainly break somewhere for simulations. Still under active development.
This commit is contained in:
Paul M. Sutter
parent
62dd66be79
commit
3dce2593d9
9 changed files with 348 additions and 454 deletions
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@ -18,9 +18,9 @@
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+*/
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#include <healpix_map.h>
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#include <healpix_map_fitsio.h>
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#include <pointing.h>
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#include <boost/format.hpp>
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#include <iostream>
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#include <fstream>
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@ -30,7 +30,6 @@
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#include "contour_pixels.hpp"
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#include <netcdf>
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#include <CosmoTool/fortran.hpp>
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#include <gsl/gsl_interp.h>
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#include <gsl/gsl_integration.h>
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#define LIGHT_SPEED 299792.458
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@ -65,10 +64,10 @@ struct ParticleData
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vector<double> redshift;
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vector<double> catalogID;
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vector<long> uniqueID;
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int id_mask;
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// PMS
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int mask_index;
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// END PMS
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int edgeFlag = 0;
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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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@ -122,15 +121,13 @@ void loadData(const string& fname, NYU_VData & data)
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}
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void placeGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
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bool useComoving, double omegaM)
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{
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bool useComoving, double omegaM) {
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double d2r = M_PI/180;
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gsl_function expanF;
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expanF.function = &expanFun;
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struct my_expan_params expanParams;
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double maxZ = 2.0, z, result, error, *dL, *redshifts;
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int numZ = 1000, iZ;
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double result, error;
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size_t nEval;
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expanParams.Om = omegaM;
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@ -138,20 +135,6 @@ void placeGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
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expanParams.wa = 0.0;
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expanF.params = &expanParams;
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dL = (double *) malloc(numZ * sizeof(double));
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redshifts = (double *) malloc(numZ * sizeof(double));
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for (iZ = 0; iZ < numZ; iZ++) {
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z = iZ * maxZ/numZ;
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//gsl_integration_qng(&expanF, 0.0, z, 1.e-6, 1.e-6, &result, &error, &nEval);
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dL[iZ] = result;
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redshifts[iZ] = z;
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}
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gsl_interp *interp = gsl_interp_alloc(gsl_interp_linear, numZ);
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gsl_interp_init(interp, redshifts, dL, numZ);
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gsl_interp_accel *acc = gsl_interp_accel_alloc();
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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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output_data.ra.resize(data.size());
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@ -168,43 +151,36 @@ void placeGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
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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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double Dc = data[i].cz;
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Position& p = output_data.pos[i];
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if (useComoving) {
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//double pos = gsl_interp_eval(interp, redshifts, dL, data[i].cz, acc);
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// Maubert - Lower boundary in redshift set to 0 to be consistent with pruneVoids (was 1.e-6 before).
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gsl_integration_qng(&expanF, 0.0, data[i].cz/LIGHT_SPEED,
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1.e-6,
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1.e-6, &result, &error, &nEval);
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double Dc = result*LIGHT_SPEED;
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p.xyz[0] = Dc*cos(ra)*cos(dec);
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p.xyz[1] = Dc*sin(ra)*cos(dec);
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p.xyz[2] = Dc*sin(dec);
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} else {
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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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1.e-6, 1.e-6, &result, &error, &nEval);
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Dc = result*LIGHT_SPEED;
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}
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//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]));
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p.xyz[0] = Dc*cos(ra)*cos(dec);
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p.xyz[1] = Dc*sin(ra)*cos(dec);
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p.xyz[2] = Dc*sin(dec);
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output_data.id_gal[i] = data[i].index;
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output_data.ra[i] = ra;
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output_data.dec[i] = dec;
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output_data.redshift[i] = data[i].cz;
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output_data.uniqueID[i] = data[i].uniqueID;
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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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//printf("INSERT GAL %d %e %e %e\n", output_data.id_gal[i], p.xyz[0], p.xyz[1], p.xyz[2]);
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for (int j = 0; j < 3; j++) {
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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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// normalize box
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float left = 1.e99;
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float right = -1.e99;
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// normalize the box volume
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float left = INFINITY;
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float right = -INFINITY;
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for (int j = 0; j < 3; j++) {
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if (output_data.box[j][1] < left) left = output_data.box[j][1];
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if (output_data.box[j][0] > right) right = output_data.box[j][0];
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@ -214,24 +190,27 @@ void placeGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
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output_data.box[j][0] = right;
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}
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double Rmax = -1;
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for (int j = 0; j < 3; j++) {
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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("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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gsl_interp_free(interp);
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}
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void generateSurfaceMask(prepObservation_info& args ,
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void flagEdgeGalaxies(prepObservation_info& args ,
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Healpix_Map<float>& mask,
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vector<int>& pixel_list,
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vector<int>& full_mask_list,
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vector<int>& contourPixels,
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NYU_VData& data,
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ParticleData& output_data,
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bool useComoving,
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double omegaM)
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{
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double omegaM) {
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//Maubert - Needed for comobile distance in mock_sphere
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gsl_function expanF;
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@ -242,38 +221,14 @@ void generateSurfaceMask(prepObservation_info& args ,
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expanParams.wa = 0.0;
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expanF.params = &expanParams;
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double result, error ;
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double result, error;
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size_t nEval;
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//End Maubert - Needed for comobile distance in mock_sphere
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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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// PMS
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// TODO - REMOVE THIS
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output_data.mask_index = output_data.id_gal.size();
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// END PMS
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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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// PMS - write a small text file with galaxy position (for diagnostic purposes)
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// write a small text file with galaxy position (for diagnostic purposes)
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FILE *fp;
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fp = fopen("galaxies.txt", "w");
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for (int i = 0; i < data.size(); i++) {
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@ -284,208 +239,82 @@ void generateSurfaceMask(prepObservation_info& args ,
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(p.xyz[2]));
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}
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fclose(fp);
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// END PMS
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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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// TEST NOT USING MOCK PARTICLES
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numToInsert = 0;
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// END TEST
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cout << format("3d volume to fill: %g (Mpc/h)^3") % volume << endl;
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/* NOTE: temporarily moved to python for quick debugging. Will move back to
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here once it's all sorted
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cout << format("Will insert %d particles") % numToInsert << endl;
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fp = fopen("mock_galaxies.txt", "w");
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double pct = 0;
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for (int i = 0; i < numToInsert; i++) {
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double new_pct = i*100./numToInsert;
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if (new_pct-pct > 5.) {
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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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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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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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// PMS : write mock galaxies to a small file for diagnostic purposes
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fprintf(fp, "%e %e %e\n",
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(p.xyz[0]),
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(p.xyz[1]),
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(p.xyz[2]));
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// END PMS
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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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output_data.ra.push_back(-1);
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output_data.dec.push_back(-1);
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output_data.redshift.push_back(-1);
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output_data.uniqueID.push_back(-1);
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//printf("INSERT MOCK %d %e %e %e\n", idx, p.xyz[0], p.xyz[1], p.xyz[2]);
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insertion++;
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}
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fclose(fp);
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// PMS
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// TEST - insert mock galaxies along box edge - this is for tesselation safety
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fp = fopen("mock_boundary.txt", "w");
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double dx[3];
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dx[0] = output_data.box[0][1] - output_data.box[0][0];
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dx[1] = output_data.box[1][1] - output_data.box[1][0];
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dx[2] = output_data.box[2][1] - output_data.box[2][0];
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int nPart = 100;
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// TEST
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for (int iDir = 0; iDir < 0; iDir++) {
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for (int iFace = 0; iFace < 0; iFace++) {
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//for (int iDir = 0; iDir < 3; iDir++) {
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//for (int iFace = 0; iFace < 2; iFace++) {
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int iy = (iDir + 1) % 3;
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int iz = (iDir + 2) % 3;
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for (int i = 0; i < nPart; i++) {
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for (int j = 0; j < nPart; j++) {
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Position p;
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p.xyz[iDir] = output_data.box[iDir][iFace];
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p.xyz[iy] = i * dx[iy]/nPart + output_data.box[iy][0];
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p.xyz[iz] = j * dx[iz]/nPart + output_data.box[iz][0];
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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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output_data.ra.push_back(-1);
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output_data.dec.push_back(-1);
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output_data.redshift.push_back(-1);
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output_data.uniqueID.push_back(-1);
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insertion++;
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fprintf(fp, "%e %e %e\n",
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(p.xyz[0]),
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(p.xyz[1]),
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(p.xyz[2]));
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}
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}
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}
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}
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fclose(fp);
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// END PMS
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// PMS
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// TEST - insert mock galaxies along spheres of survey redshift boundaries
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fp = fopen("mock_sphere.txt", "w");
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//Maubert - insert mock galaxies according to useComoving specification
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// Added & compute rmin & rmax out of loop
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double rmin ;
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double rmax ;
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// convert redshift boundaries to covmoving if necessary
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double rmin;
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double rmax;
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if (useComoving) {
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gsl_integration_qng(&expanF, 0.0, args.zMin_arg,
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1.e-6,
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1.e-6, &result, &error, &nEval);
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rmin = result* LIGHT_SPEED;
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gsl_integration_qng(&expanF, 0.0, args.zMin_arg, 1.e-6, 1.e-6, &result,
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&error, &nEval);
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rmin = result*LIGHT_SPEED;
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gsl_integration_qng(&expanF, 0.0, args.zMax_arg,
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1.e-6,
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1.e-6, &result, &error, &nEval);
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rmax = result* LIGHT_SPEED;
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gsl_integration_qng(&expanF, 0.0, args.zMax_arg, 1.e-6, 1.e-6, &result,
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&error, &nEval);
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rmax = result*LIGHT_SPEED;
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} else {
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rmin = args.zMin_arg * LIGHT_SPEED;
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rmax = args.zMax_arg * LIGHT_SPEED;
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rmin = args.zMin_arg * LIGHT_SPEED;
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rmax = args.zMax_arg * LIGHT_SPEED;
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}
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// TEST NOT USING BOUNDARY PARTICLES
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for (int q = 0; q < 0; q++) {
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//for (int q = 0; q < full_mask_list.size(); q++) {
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vec3 v = mask.pix2vec(full_mask_list[q]);
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Position p;
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if (rmin > 0.) {
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p.xyz[0] = v.x * rmin;
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p.xyz[1] = v.y * rmin;
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p.xyz[2] = v.z * rmin;
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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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output_data.ra.push_back(-1);
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output_data.dec.push_back(-1);
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output_data.redshift.push_back(-1);
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output_data.uniqueID.push_back(-1);
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insertion++;
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fprintf(fp, "%e %e %e\n",
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(p.xyz[0]),
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(p.xyz[1]),
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(p.xyz[2]));
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}
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p.xyz[0] = v.x * rmax;
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p.xyz[1] = v.y * rmax;
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p.xyz[2] = v.z * rmax;
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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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output_data.ra.push_back(-1);
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output_data.dec.push_back(-1);
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output_data.redshift.push_back(-1);
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output_data.uniqueID.push_back(-1);
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insertion++;
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fprintf(fp, "%e %e %e\n",
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(p.xyz[0]),
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(p.xyz[1]),
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(p.xyz[2]));
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}
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fclose(fp);
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// END PMS
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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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NcDim d = f.addDim("space", 3);
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NcDim p = f.addDim("Np", pdata.pos.size());
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NcVar v = f.addVar("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.putVar({size_t(j), 0}, {1, pdata.pos.size()}, x);
|
||||
}
|
||||
|
||||
v = f.addVar("id_gal", ncInt, std::vector<NcDim>({p}));
|
||||
v.putVar(&pdata.id_gal[0]);
|
||||
|
||||
delete[] x;
|
||||
|
||||
}
|
||||
double dx = args.meanPartSep_arg;
|
||||
int nSteps = floor( (rmax - rmin) / dx);
|
||||
cout << "Assumed resolution element: " << dx << " " << nSteps << endl;
|
||||
|
||||
void saveForZobov(ParticleData& pdata, const string& fname, const string& paramname)
|
||||
// flag galaxies near mask edges
|
||||
// using the "ray marching" algorithm: follow rays along lines of sight
|
||||
// of all mask edges, flagging nearest neighbor galaxies as we go
|
||||
// TODO - replace this with faster kd-tree search
|
||||
cout << "Flagging galaxies on edges of survey..." << endl;
|
||||
|
||||
// explore rays along mask contours
|
||||
for (int pixel : contourPixels) {
|
||||
cout << "Working with pixel " << pixel << endl;
|
||||
vec3 v = mask.pix2vec(pixel);
|
||||
//cout << v*rmin << " " << v*rmax << endl;
|
||||
|
||||
// march along single ray and find nearest neighbors
|
||||
for (int n = 0; n <= nSteps; n++) {
|
||||
double r = n*dx + rmin;
|
||||
vec3 rayPos = v*r;
|
||||
|
||||
double x = rayPos.x;
|
||||
double y = rayPos.y;
|
||||
double z = rayPos.z;
|
||||
|
||||
//cout << "Step " << n << " " << rayPos << endl;
|
||||
|
||||
// scan all galaxies
|
||||
double minDist = INFINITY;
|
||||
double dist = 0;
|
||||
int closestGal = -1;
|
||||
for (int i = 0; i < data.size(); i++) {
|
||||
Position& galPos = output_data.pos[i];
|
||||
|
||||
dist = pow(galPos.xyz[0] - x, 2) +
|
||||
pow(galPos.xyz[1] - y, 2) +
|
||||
pow(galPos.xyz[2] - z, 2);
|
||||
|
||||
if (dist < minDist) closestGal = i;
|
||||
} // galaxy search
|
||||
|
||||
|
||||
} // marching along one ray
|
||||
|
||||
} // all contours
|
||||
|
||||
|
||||
// flag galaxies near redshift boundaries
|
||||
cout << "Flagging galaxies at redshift boundaries..." << endl;
|
||||
|
||||
*/
|
||||
|
||||
} // end flagEdgeGalaxies
|
||||
|
||||
void saveForZobov(ParticleData& pdata, const string& fname,
|
||||
const string& paramname)
|
||||
{
|
||||
UnformattedWrite f(fname);
|
||||
static const char axis[] = { 'X', 'Y', 'Z' };
|
||||
|
|
@ -562,21 +391,6 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn
|
|||
v.putVar({0}, {size_t(nOutputPart)}, &pdata.id_gal[0]);
|
||||
//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)
|
||||
|
|
@ -608,40 +422,40 @@ int main(int argc, char **argv)
|
|||
|
||||
prepObservation_conf_print_version();
|
||||
|
||||
cout << "Loading data " << args_info.catalog_arg << "..." << endl;
|
||||
cout << "Loading galaxy data " << args_info.catalog_arg << "..." << endl;
|
||||
vector<NYU_Data> data;
|
||||
Healpix_Map<float> o_mask;
|
||||
vector<int> pixel_list;
|
||||
vector<int> full_mask_list;
|
||||
vector<int> contourPixels;
|
||||
ParticleData output_data;
|
||||
|
||||
loadData(args_info.catalog_arg, data);
|
||||
|
||||
|
||||
cout << "Loading mask..." << endl;
|
||||
Healpix_Map<float> mask;
|
||||
Healpix_Map<float> o_mask;
|
||||
|
||||
int newNside = args_info.nsideForContour_arg;
|
||||
read_Healpix_map_from_fits(args_info.mask_arg, o_mask);
|
||||
|
||||
Healpix_Map<float> mask;
|
||||
if (newNside == -1) newNside = o_mask.Nside();
|
||||
|
||||
mask.SetNside(128, RING);
|
||||
mask.SetNside(newNside, 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
|
||||
computeContourPixels(mask, contourPixels);
|
||||
|
||||
cout << "Placing galaxies..." << endl;
|
||||
placeGalaxiesInCube(data, output_data, args_info.useComoving_flag,
|
||||
args_info.omegaM_arg);
|
||||
generateSurfaceMask(args_info, mask, pixel_list, full_mask_list,
|
||||
data, output_data,args_info.useComoving_flag,
|
||||
args_info.omegaM_arg);
|
||||
|
||||
args_info.omegaM_arg);
|
||||
|
||||
|
||||
//cout << "Flagging edge galaxies..." << endl;
|
||||
flagEdgeGalaxies(args_info, mask, contourPixels,
|
||||
data, output_data,args_info.useComoving_flag,
|
||||
args_info.omegaM_arg);
|
||||
|
||||
saveForZobov(output_data, args_info.output_arg, args_info.params_arg);
|
||||
// saveData(output_data);
|
||||
|
||||
// PMS
|
||||
// PMS - TODO REMOVE THIS
|
||||
FILE *fp = fopen("mask_index.txt", "w");
|
||||
fprintf(fp, "%d", output_data.mask_index);
|
||||
fclose(fp);
|
||||
|
|
@ -650,6 +464,7 @@ int main(int argc, char **argv)
|
|||
fprintf(fp, "%d", output_data.pos.size());
|
||||
fclose(fp);
|
||||
printf("Done!\n");
|
||||
// END PMS
|
||||
// END PMS - TODO REMOVE THIS
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -17,3 +17,7 @@ option "params" - "Output parameters of the datacube" string required
|
|||
option "useComoving" - "Convert to real space using LCDM cosmology" flag off
|
||||
|
||||
option "omegaM" - "Omega Matter for fiducial cosmology" double optional default="0.27"
|
||||
|
||||
option "nsideForContour" - "HEALPix NSIDE resolution for figuring out mask contours" int optional default="-1"
|
||||
|
||||
option "meanPartSep" - "Estimated mean tracer seperation in h^3 / Mpc^3" double optional default="1"
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue