#include "Headers/Catalogue.h"

Inherited by cbl::catalogue::CatalogueChainMesh.

Public Member Functions
Constructors/destructors
	Catalogue ()=default
	default constructor

	Catalogue (const Catalogue &obj)
	Copy constructor for the Catalogue class. More...

	Catalogue (Catalogue &&obj)
	move constructor for the Catalogue class More...

Catalogue &	operator= (const Catalogue &obj)
	copy assignment for the Catalogue class More...

Catalogue &	operator= (Catalogue &&obj) noexcept
	move assignment for the Catalogue class More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< double > coord1, const std::vector< double > coord2, const std::vector< double > coord3, const std::vector< double > weight={}, const cosmology::Cosmology &cosm={}, const CoordinateUnits inputUnits=CoordinateUnits::_radians_)
	constructor More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< double > coord1, const std::vector< double > coord2, const std::vector< double > coord3, const cosmology::Cosmology &cosm, const CoordinateUnits inputUnits=CoordinateUnits::_radians_)
	constructor More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< std::string > file, const int col1=1, const int col2=2, const int col3=3, const int colWeight=-1, const int colRegion=-1, const double nSub=1.1, const double fact=1., const cosmology::Cosmology &cosm={}, const CoordinateUnits inputUnits=CoordinateUnits::_radians_, const CharEncode charEncode=CharEncode::_ascii_, const std::string comment="#", const int seed=3213)
	constructor, reading a file with coordinates More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< std::string > file, const cosmology::Cosmology &cosm, const CoordinateUnits inputUnits=CoordinateUnits::_radians_)
	constructor, reading a file with coordinates More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< Var > attribute, const std::vector< int > column, const std::vector< std::string > file, const int comments=0, const double nSub=1.1, const double fact=1, const cosmology::Cosmology &cosm={}, const CoordinateUnits inputUnits=CoordinateUnits::_radians_, const char delimiter='\t', const int seed=3213)
	constructor, reading a file with attributes of the catalogue More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< std::string > file, const std::vector< std::string > column_names, const bool read_weights, const bool read_regions, const double nSub, const double fact, const cosmology::Cosmology &cosm={}, const CoordinateUnits inputUnits=CoordinateUnits::_radians_, const int seed=3213)
	constructor, reading a file in FITS format More...

	Catalogue (const ObjectType objectType, const CoordinateType coordinateType, const std::vector< std::string > file, const std::vector< std::string > column_names, const std::vector< Var > attribute, const double nSub, const double fact, const cosmology::Cosmology &cosm={}, const CoordinateUnits inputUnits=CoordinateUnits::_radians_, const int seed=3213)
	constructor, reading a file in FITS format More...

template<typename T >
	Catalogue (std::vector< T > object)
	constructor, using vectors of generic objects More...

	Catalogue (std::vector< std::shared_ptr< Object > > sample)
	constructor, using vectors of pointers to generic objects More...

	Catalogue (const ObjectType objectType, const std::vector< Var > attribute, const std::vector< int > column, const std::vector< std::string > file, const int comments=0, const double nSub=1.1, const int seed=3213)
	constructor, reading a file with attributes of the catalogue More...

	Catalogue (const Catalogue input_catalogue, const Catalogue target_catalogue, const Var var_name, const int nbin, const int seed=3213)
	constructor, creating a catalogue by matching the distribution of one quantity from a target catalogue More...

	Catalogue (const Catalogue input_catalogue, const Catalogue target_catalogue, const cbl::catalogue::Var var_name1, const int nbin1, const cbl::catalogue::Var var_name2, const int nbin2, const int seed=3213)
	constructor, creating a catalogue by matching the distributions of two quantities from a target catalogue More...

	Catalogue (const Catalogue halo_catalogue, const cosmology::Cosmology &cosm, const HODType HOD_Type, const double threshold, const bool substructures=true, std::vector< double > parameter={})
	constructor that creates a catalogue of galaxies using an HOD model to popolate the haloes More...

	~Catalogue ()=default
	default destructor

Constructors of random catalogues
	Catalogue (const RandomType type, const cosmology::Cosmology &real_cosm, const cosmology::Cosmology &test_cosm, const std::string dir_in, const double Zguess_min, const double Zguess_max)
	constructor that creates a random catalogue in a cubic box, warped by geometric distortions More...

	Catalogue (const RandomType type, const Catalogue catalogue, const double N_R, const int nbin=10, const cosmology::Cosmology &cosm={}, const bool conv=false, const double sigma=0., const std::vector< double > redshift={}, const std::vector< double > RA={}, const std::vector< double > Dec={}, int z_ndigits=10, const int seed=3213)
	constructor that creates a random catalogue with either the square geometry or with 'the shuffle' method More...

	Catalogue (const RandomType type, const int N_R, const double z_step, const Catalogue catalogue, const cosmology::Cosmology &cosm={}, const std::vector< double > RA={}, const std::vector< double > Dec={}, const double sigma_kernel=0.01, const int nbins=100, int z_ndigits=10, const int times_default=5, double times_change=0.5, const double tolerance=0.05, const std::string out_path_nz=par::defaultString, const std::string out_file_nz=par::defaultString, const int seed=3213)
	constructor that creates a random catalogue with the 'shuffle' method. More...

	Catalogue (const RandomType type, const Catalogue catalogue, const double N_R, const int nbin, const double Angle, const std::vector< double > redshift, const cosmology::Cosmology &cosm={}, const bool conv=false, const double sigma=0., const int seed=3213)
	constructor that creates a random catalogue in a cone More...

	Catalogue (const RandomType type, const std::vector< std::string > mangle_mask, const Catalogue catalogue, const double N_R, const int nbin, const cosmology::Cosmology cosm, const bool conv=false, const double sigma=0., const int seed=3213)
	constructor that creates a random catalogue using the a mask in the MANGLE format for the angular distribution and taking the redshift distribution from an input catalogue More...

	Catalogue (const RandomType type, const Catalogue catalogue, const double N_R, const bool dndz_per_stripe, const int nbin, const cosmology::Cosmology cosm, const bool conv=false, const double sigma=0, const int seed=3213)
	constructor that creates a random catalogue using the SDSS stripes. More...

	Catalogue (const RandomType type, Catalogue catalogue, const double N_R, const cosmology::Cosmology cosm, const std::vector< double > RA_range, const std::vector< double > DEC_range, const unsigned int nbin, const int seed)
	constructor that creates a random catalogue for light cones homogeneous in RA and Dec and with redshift dependent density. More...

Constructor of Void catalogues
	Catalogue (const VoidAlgorithm algorithm, Catalogue tracer_catalogue, Catalogue random_catalogue, const std::string dir_output, const std::string output, const double cellsize, const int n_rec=1, const double step_size=2.5/3., const double threshold=0., const std::vector< bool > print={true, true})
	constructor that creates a void catalogue extracting cosmic voids from a catalogue of tracers, for COMOVING coordinates. This void finder is based on dynamical criteria: the density field is reconstructed from the displacement field generated by the back-in-time evolution of the tracers. Voids are therefore classified as regions of negative velocity divergence. More...

	Catalogue (const VoidAlgorithm algorithm, Catalogue tracer_catalogue, Catalogue random_catalogue, const std::string dir_output, const std::string output, const double cellsize, const cbl::cosmology::Cosmology cosm, const std::vector< double > RA_range, const std::vector< double > DEC_range, const int n_rec=1, const double step_size=2.5/3., const double threshold=0.)
	constructor that creates a void catalogue extracting cosmic voids from a catalogue of tracers for OBSERVED COORDINATES. This void finder is based on dynamical criteria: the density field is reconstructed from the displacement field generated by the back-in-time evolution of the tracers. Voids are therefore classified as regions of negative velocity divergence. More...

Constructors used to read catalogues from standard GADGET files
	Catalogue (const ObjectType objectType, const std::string file_cn=par::defaultString, const bool snapformat=false, const bool swap=false, const double fact=0.001, const bool read_catalogue=true, const double nSub=1.1, const std::string component_to_read="ALL", const std::vector< std::vector< double >> edges={{par::defaultDouble, par::defaultDouble},{par::defaultDouble, par::defaultDouble},{par::defaultDouble, par::defaultDouble}})
	constructor that reads object of selected type from Gadget snapshots More...

	Catalogue (const int snap, const std::string basedir, const bool swap=false, const bool long_ids=false, const double scaleFact=1.0, const double massFact=1.0, const EstimateCriterion estimate_crit=EstimateCriterion::_m200_, const bool veldisp=false, const bool masstab=false, const bool add_satellites=false, const bool verbose=false)
	constructor that reads objects of class HostHalo with satellite dependencies from group and subgroup files generated by the gadget implementation of the FoF and SUBFIND algorithms (respectively) More...

Member functions used to get the private members and their properties
std::vector< std::shared_ptr< Object > >	sample () const
	get the private member Catalogue::m_object More...

double	xx (const int i) const
	get the private member Catalogue::m_object[i]->m_xx More...

double	yy (const int i) const
	get the private member Catalogue::m_object[i]->m_yy More...

double	zz (const int i) const
	get the private member Catalogue::m_object[i]->m_zz More...

double	vx (const int i) const
	get the private member Catalogue::m_object[i]->m_vx More...

double	vy (const int i) const
	get the private member Catalogue::m_object[i]->m_vy More...

double	vz (const int i) const
	get the private member Catalogue::m_object[i]->m_vz More...

double	dc (const int i) const
	get the private member Catalogue::m_object[i]->m_dc More...

double	ra (const int i) const
	get the private member Catalogue::m_object[i]->m_ra More...

double	dec (const int i) const
	get the private member Catalogue::m_object[i]->m_dec More...

double	ra_tile (const int i) const
	get the private member Catalogue::m_object[i]->m_ra_tile More...

double	dec_tile (const int i) const
	get the private member Catalogue::m_object[i]->m_dec_tile More...

double	sn (const int i) const
	get the private member Catalogue::m_object[i]->m_sn More...

double	redshift (const int i) const
	get the private member Catalogue::m_object[i]->m_redshift More...

double	redshiftMin (const int i) const
	get the private member Catalogue::m_object[i]->m_redshiftMin More...

double	redshiftMax (const int i) const
	get the private member Catalogue::m_object[i]->m_redshiftMax More...

double	shear1 (const int i) const
	get the private member Catalogue::m_object[i]->m_shear1 More...

double	shear2 (const int i) const
	get the private member Catalogue::m_object[i]->m_shear2 More...

double	odds (const int i) const
	get the private member Catalogue::m_object[i]->m_odds More...

double	lensingWeight (const int i) const
	get the private member Catalogue::m_object[i]->m_lensingWeight More...

double	lensingCalib (const int i) const
	get the private member Catalogue::m_object[i]->m_lensingCalib More...

double	weight (const int i) const
	get the private member Catalogue::m_object[i]->m_weight More...

long	region (const int i) const
	get the private member Catalogue::m_object[i]->m_region More...

std::string	field (const int i) const
	get the private member Catalogue::m_object[i]->m_field More...

double	x_displacement (const int i) const
	get the private member Catalogue::m_object[i]->m_x_displacement More...

double	y_displacement (const int i) const
	get the private member Catalogue::m_object[i]->m_y_displacement More...

double	z_displacement (const int i) const
	get the private member Catalogue::m_object[i]->m_z_displacement More...

size_t	nRegions ()
	get the private member m_nRegions More...

std::vector< long >	region_list () const
	get the list of regions in which the catalogue is divided More...

std::vector< std::string >	field_list () const
	get the list of fields where the objects have been observed More...

size_t	nFields () const
	get the total number of fields where the objects have been observed More...

double	mass (const int i) const
	get the private member Catalogue::m_object[i]->m_mass More...

double	magnitude (const int i) const
	get the private member Catalogue::m_object[i]->m_magnitude More...

double	magnitudeU (const int i) const
	get the private member Catalogue::m_object[i]->m_magnitudeU More...

double	magnitudeG (const int i) const
	get the private member Catalogue::m_object[i]->m_magnitudeG More...

double	magnitudeR (const int i) const
	get the private member Catalogue::m_object[i]->m_magnitudeR More...

double	magnitudeI (const int i) const
	get the private member Catalogue::m_object[i]->m_magnitudeI More...

double	radius (const int i) const
	get the private member Catalogue::m_object[i]->m_radius More...

double	densityContrast (const int i) const
	get the private member Catalogue::m_object[i]->m_densityContrast More...

double	centralDensity (const int i) const
	get the private member Catalogue::m_object[i]->m_centralDensity More...

int	ID (const int i) const
	get the private member Catalogue::m_object[i]->m_ID More...

double	mass_proxy (const int i) const
	get the private member Catalogue::m_object[i]->m_mass_proxy More...

double	mass_proxy_error (const int i) const
	get the private member Catalogue::m_object[i]->m_mass_proxy_error More...

int	IDHost (const int i) const
	get the private member Catalogue::m_object[i]->m_IDHost More...

double	galaxyTag (const int i) const
	get the private member Catalogue::m_object[i]->m_galaxyTag More...

double	mstar (const int i) const
	get the private member Catalogue::m_object[i]->m_mstar More...

double	massinfall (const int i) const
	get the private member Catalogue::m_object[i]->m_minfall More...

double	generic (const int i) const
	get the private member Catalogue::m_object[i]->m_generic More...

double	tot_mass (const int i) const
	get the private member Catalogue::m_object[ii]->m_tot_mass More...

std::vector< long >	region () const
	get the values of the object regions More...

std::vector< std::string >	field () const
	get the values of the object fields More...

std::vector< std::shared_ptr< Object > >	satellites (const int index) const
	get the private member Catalogue::m_object[ii]->m_satellites More...

std::vector< unsigned int >	part (const int index) const
	get the private member Catalogue::m_object[index]->m_part of ChainMeshCell More...

std::vector< std::vector< unsigned int > >	nearCells (const int index) const
	get the private member Catalogue::m_object[index]->m_nearCells of ChainMeshCell More...

double	var (const int index, const Var var_name) const
	get the value of the i-th object variable More...

int	var_int (const int index, const Var var_name) const
	get the value of the i-th object integer variable More...

std::vector< double >	var (const Var var_name) const
	get the values of the object variables More...

std::vector< int >	var_int (const Var var_name) const
	get the values of the object integer variables More...

bool	isSetVar (const int index, const Var var_name) const
	check if the given variable of the i-th object is set More...

bool	isSetVar (const Var var_name) const
	check if the given object variables are set More...

std::shared_ptr< Object >	catalogue_object (const int i) const
	get the i-th object of the catalogue More...

std::shared_ptr< Object >	operator[] (const size_t i) const
	access the i-th Catalogue object More...

std::vector< std::shared_ptr< Object > >	catalogue_object () const
	get the object vector More...

std::vector< double >	coordinate (const int i) const
	get the X, Y, Z coordinates of the i-th object of the catalogue More...

size_t	nObjects () const
	get the number of objects of the catalogue More...

std::vector< size_t >	nObjects_lightCone (const int nbin) const
	get the number of objects of the catalogue for Light Cones More...

double	Min (const Var var_name) const
	get the minimum value of a variable of the catalogue objects More...

double	Max (const Var var_name) const
	get the maximum value of a variable of the catalogue objects More...

std::vector< double >	stats_var (const Var var_name) const
	get the mean, the median, the standard deviation, and the difference between the third and first quartiles of a variable More...

std::vector< std::vector< double > >	stats_var (const std::vector< Var > var_name) const
	get the mean, the median, the standard deviation, and the difference between the third and first quartiles of a vector of variables More...

void	var_distr (const Var var_name, std::vector< double > &_var, std::vector< double > &dist, std::vector< double > &err, const int nbin, const bool linear=true, const std::string file_out=par::defaultString, const double Volume=1., const bool norm=false, const double V1=par::defaultDouble, const double V2=par::defaultDouble, const std::string bin_type="Linear", const bool convolution=false, const double sigma=0.) const
	get the distribution of a variable More...

double	weightedN () const
	get the total weight of the objects of the catalogue More...

double	volume (const double boxside=par::defaultDouble) const
	compute the catalogue's comoving volume More...

double	numdensity (const double boxside=par::defaultDouble) const
	compute the catalogue's number density More...

double	numdensity_error (const double boxside=par::defaultDouble) const
	compute the catalogue's number density error More...

double	mps (const double boxside=par::defaultDouble) const
	compute the catalogue's mean particle separation More...

double	mps_error (const double boxside=par::defaultDouble) const
	compute the catalogue's mean particle separation error More...

std::vector< double >	z_bins (const int nbin) const
	get the catalogue's redshift bins More...

Member functions used to set the private members
void	set_region (const std::vector< long > region, const int nRegions=-1)
	set a private variable More...

void	set_region_number (const size_t nRegions)
	set the private variable m_nRegion More...

void	set_ra_dec_tile (const std::vector< double > RA_tile, const std::vector< double > Dec_tile, const CoordinateUnits inputUnits=CoordinateUnits::_degrees_)
	set the central R.A. and Dec of the tiles More...

void	set_field (const std::vector< std::string > field)
	set a private variable More...

void	set_var (const int index, const Var var_name, const double value, const cosmology::Cosmology cosmology={}, const bool update_coordinates=true)
	set a private variable More...

void	set_var (const int index, const Var var_name, const int value, const cosmology::Cosmology cosmology={})
	set a private variable More...

void	set_var (const Var var_name, const std::vector< double > var, const cosmology::Cosmology cosmology={}, const bool update_coordinates=true)
	set a private variable More...

void	set_var (const Var var_name, const std::vector< int > var, const cosmology::Cosmology cosmology={})
	set a private variable More...

void	set_satellite (const int index, const std::shared_ptr< Object > satellite={})
	set the private member HostHalo::m_satellites More...

void	set_satellites (const int index, const std::vector< std::shared_ptr< Object >> satellites={})
	set the private member HostHalo::m_satellites More...

void	set_part (const int index, const std::vector< unsigned int > part={})
	set the private member ChainMeshCell::m_part More...

void	set_nearCells (const int index, const std::vector< std::vector< unsigned int >> nearCells={})
	set the private member ChainMeshCell::m_nearCells More...

void	compute_centralDensity (const std::shared_ptr< Catalogue > tracers_catalogue, chainmesh::ChainMesh3D ChM, const double threshold)
	compute the central density of each object in a void catalogue. We define as central density the density contrast computed inside a spherical region grown around the void center, with a radius of $2$ times the mean particle separation of the tracer catalogue More...

void	compute_centralDensity (const std::shared_ptr< Catalogue > tracers_catalogue, chainmesh::ChainMesh3D ChM, const std::vector< double > par_numdensity, const double threshold)
	compute the central density of each object in a void catalogue. We define as central density the density contrast computed inside a spherical region grown around the void center, with a radius of $2$ times the mean particle separation of the tracer catalogue More...

void	compute_centralDensity (const std::shared_ptr< Catalogue > tracers_catalogue, chainmesh::ChainMesh3D ChM, const std::vector< std::vector< double >> data_numdensity, const std::string method_interpolation, const double threshold)
	compute the central density of each object in a void catalogue. We define as central density the density contrast computed inside a spherical region grown around the void center, with a radius of $2$ times the mean particle separation of the tracer catalogue More...

void	compute_densityContrast (const std::shared_ptr< Catalogue > tracers_catalogue, chainmesh::ChainMesh3D ChM, const double ratio=0.1)
	compute density contrast of cosmic voids in catalogue as the ratio between an inner and an outer sphere grown around the void centre More...

Member functions used to add or remove ojects to the catalogue
void	add_object (std::shared_ptr< Object > object)
	add one single object to the catalogue More...

template<typename T >
void	add_object (T object)
	add one single object to the catalogue More...

void	add_objects (std::vector< std::shared_ptr< Object > > sample)
	add some objects to the catalogue More...

template<typename T >
void	add_objects (std::vector< T > sample)
	add some objects to the catalogue More...

template<typename T >
void	replace_objects (std::vector< T > sample)
	replace existing objects with new ones More...

void	replace_objects (std::vector< std::shared_ptr< Object > > sample)
	replace existing objects with new ones More...

void	remove_objects ()
	remove all objects remove all objects of the catalogue

void	remove_object (const int index)
	remove an existing object More...

void	remove_objects (const std::vector< bool > index)
	remove a set of existing objects More...

void	swap_objects (const int ind1, const int ind2)
	swap two existing objects More...

void	sort (const Var var_name, const bool increasing=false)
	bubble sort of a catalogue wrt a variable More...

void	shuffle (const int seed)
	shuffle objects in the catalogue More...

Member functions used to operate on the ojects to the catalogue
void	computeComovingCoordinates (const cosmology::Cosmology &cosm, const CoordinateUnits inputUnits=CoordinateUnits::_radians_)
	compute the comoving coordinates (x, y, z) from the observed coordinates (R.A., Dec, redshift) More...

void	computePolarCoordinates (const CoordinateUnits outputUnits=CoordinateUnits::_radians_)
	compute the polar coordinates (R.A., Dec, d_c) from the comoving coordinates (x, y, z) More...

void	computePolarCoordinates (const cosmology::Cosmology &cosmology, const double z1=0., const double z2=10., const CoordinateUnits outputUnits=CoordinateUnits::_radians_)
	compute the polar coordinates (R.A., Dec, d_c, redshift) from the comoving (x, y, z), and assuming a cosmological model More...

void	normalizeComovingCoordinates ()
	normalize comoving coordinates More...

void	restoreComovingCoordinates ()
	restore comoving coordinates More...

void	Order (const std::vector< int > vv)
	order the catalogue according to the input vector More...

void	Order ()
	restore the original vector (i.e. the opposite of Order(std::vector<int>))

void	write_comoving_coordinates (const std::string outputFile) const
	write the comoving coordinates of the catalogue to an output file More...

void	write_obs_coordinates (const std::string outputFile) const
	write the polar coordinates of the catalogue to an output file More...

void	write_data (const std::string outputFile, const std::vector< Var > var_name={}, const std::string sep=" ", const std::string header="") const
	write both the comoving and polar coordinates, and the regions (if present) of the catalogue to an output file More...

double	distance (const int i, std::shared_ptr< Object > obj) const
	get the distrance between the i-th object of the catalogue and another object More...

double	angsep_xyz (const int i, std::shared_ptr< Object > obj) const
	get the angular distrance between the i-th object of the catalogue and another object More...

Catalogue	operator+= (std::shared_ptr< Catalogue > cc)
	overloading of the += operator, to sum two catalogues More...

Catalogue	operator+= (const Catalogue cc)
	overloading of the += operator, to sum two catalogues More...

Catalogue	sub_catalogue (const Var var_name, const double down, const double up, const bool excl=false) const
	create a sub-catalogue More...

Catalogue	sub_catalogue (const mask_function mask, const bool excl=false) const
	create a sub-catalogue More...

Catalogue	sub_catalogue (const MaskObject &mask, const bool excl=false) const
	create a sub-catalogue More...

Catalogue	sub_catalogue (catalogue::Catalogue &data, const double tile_width_RA, const double tile_width_Dec, const bool write_tiles=false, const std::string dir_tiles="./", const std::string file_tiles="tiles_coordinates.txt")
	find the Catalogue objects falling in the tiles of an input data catalogue, given the R.A.-Dec centres of the tiles. More...

Catalogue	mangle_cut (const std::string mangle_mask, const bool excl=false) const
	create a sub-catalogue More...

Catalogue	diluted_catalogue (const double nSub, const int seed=3213) const
	create a diluted catalogue More...

std::shared_ptr< Catalogue >	smooth (const double gridsize, const cosmology::Cosmology cosmology, const std::vector< Var > vars={}, const int SUB=1)
	create a smoothed version of the catalogue averaging quantities on a X, Y, Z grid More...

int	nObjects_condition (const Var var_name, const double down, const double up, const bool excl=false)
	return the number of objectes following a condition on the variable VAR More...

double	weightedN_condition (const Var var_name, const double down, const double up, const bool excl=false)
	return the weighted number of objectes following a condition on the variable VAR More...

std::vector< double >	compute_catalogueProperties_box (const double boxside)
	compute catalogue volume, number density and mean particle separation More...

std::vector< std::vector< double > >	compute_catalogueProperties_lightCone (cbl::cosmology::Cosmology cosmology, const std::vector< double > RA_range, const std::vector< double > DEC_range, const unsigned int nbin)
	compute catalogue volume, number density and mean particle separation in light cones More...

data::ScalarField3D	counts_in_cell (const double cell_size, const int interpolation_type=0, const bool useMass=false, const double minX=par::defaultDouble, const double maxX=par::defaultDouble, const double minY=par::defaultDouble, const double maxY=par::defaultDouble, const double minZ=par::defaultDouble, const double maxZ=par::defaultDouble) const
	return the density field from object positions More...

data::ScalarField3D	density_field (const double cell_size, const Catalogue mask_catalogue, const int interpolation_type=0, const double kernel_radius=0., const bool useMass=false) const
	return the density field from object position More...

void	equalize_random_lightCone (cbl::catalogue::Catalogue tracer_catalogue, cbl::cosmology::Cosmology cosm, const std::vector< double > RA_range, const std::vector< double > DEC_range, const int seed)
	equalize the number of objects in two Light Cones catalogues More...

void	equalize_random_box (cbl::catalogue::Catalogue tracer_catalogue, const int seed)
	equalize the number of objects in two Box catalogues More...

void	clean_void_catalogue (const bool initial_radius=false, const std::vector< double > delta_r={-1, 1000}, const double threshold=0.205, const bool rescale=true, const std::shared_ptr< Catalogue > tracers_catalogue={}, chainmesh::ChainMesh3D ChM={}, const double ratio=1.5, const bool checkoverlap=true, const Var ol_criterion=Var::_CentralDensity_)
	function that modifies a void catalogue according to a set of user selected criteria. If all the steps are selected the final result is a catalogue of spherical, not-overlapped voids. More...

void	clean_void_catalogue (const std::vector< double > par_numdensity, const bool initial_radius=false, const std::vector< double > delta_r={-1, 1000}, const double threshold=0.205, const bool rescale=true, const std::shared_ptr< Catalogue > tracers_catalogue={}, chainmesh::ChainMesh3D ChM={}, const double ratio=1.5, const bool checkoverlap=true, const Var ol_criterion=Var::_CentralDensity_)
	function that modifies a void catalogue according to a set of user selected criteria. If all the steps are selected the final result is a catalogue of spherical, not-overlapped voids. More...

void	clean_void_catalogue (const std::vector< std::vector< double >> data_numdensity, const std::string method_interpolation, const bool initial_radius=false, const std::vector< double > delta_r={-1, 1000}, const double threshold=0.205, const bool rescale=true, const std::shared_ptr< Catalogue > tracers_catalogue={}, chainmesh::ChainMesh3D ChM={}, const double ratio=1.5, const bool checkoverlap=true, const Var ol_criterion=Var::_CentralDensity_)
	function that modifies a void catalogue according to a set of user selected criteria. If all the steps are selected the final result is a catalogue of spherical, not-overlapped voids. More...

Private Attributes
std::vector< std::shared_ptr< Object > >	m_object
	vector containing the objects of the catalogue

std::vector< int >	m_index
	vector containing the object indexes

size_t	m_nRegions = 0
	number of regions

private variables and functions used to read catalogues from standard GADGET files
int	m_blockheader
	contains the block-header temporary value

SubFindTab_Header	m_read_header (std::ifstream &finh, const bool swap=false)
	read the GADGET subfind table header More...

Gadget_Header	m_swap_header (Gadget_Header header)
	swap endianism of the GADGET snapshot header More...

SubFindTab_Header	m_swap_header (SubFindTab_Header header)
	swap endianism of the GADGET subfind table header More...

void	m_check_it_in (std::ifstream &finr, const bool swap)
	Input function to check consistency in reading block-headers in binary GADGET snapshots. More...

void	m_check_it_out (std::ifstream &finr, const bool swap)
	Ouput function to check consistency in reading block-headers in binary GADGET snapshots. More...

Detailed Description

The class Catalogue.

This class is used to handle objects of type Catalogue

Definition at line 654 of file Catalogue.h.

Constructor & Destructor Documentation

◆ Catalogue() [1/26]

cbl::catalogue::Catalogue::Catalogue ( const Catalogue & obj )

inline

Copy constructor for the Catalogue class.

Parameters

obj	catalogue to be copied

Definition at line 746 of file Catalogue.h.

◆ Catalogue() [2/26]

cbl::catalogue::Catalogue::Catalogue ( Catalogue && obj )

inline

move constructor for the Catalogue class

Parameters

obj	catalogue to be moved

Definition at line 765 of file Catalogue.h.

◆ Catalogue() [3/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< double >	coord1,
		const std::vector< double >	coord2,
		const std::vector< double >	coord3,
		const std::vector< double >	weight = `{}`,
		const cosmology::Cosmology &	cosm = `{}`,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`
	)

constructor

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
coord1	vector containing the first coordinates, that can be either the x comoving coordinates, or the Right Ascensions (depending on coordtype)
coord2	vector containing the second coordinates, that can be either the y comoving coordinates, or the Declinations (depending on coordtype)
coord3	vector containing the third coordinates, that can be either the z comoving coordinates, or the redshits (depending on coordtype)
weight	vector containing the weights
cosm	object of class Cosmology
inputUnits	the units of the input coordinates

Definition at line 91 of file Catalogue.cpp.

◆ Catalogue() [4/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< double >	coord1,
		const std::vector< double >	coord2,
		const std::vector< double >	coord3,
		const cosmology::Cosmology &	cosm,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`
	)

inline

constructor

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
coord1	vector containing the first coordinates, that can be either the x comoving coordinates, or the Right Ascensions (depending on coordtype)
coord2	vector containing the second coordinates, that can be either the y comoving coordinates, or the Declinations (depending on coordtype)
coord3	vector containing the third coordinates, that can be either the z comoving coordinates, or the redshits (depending on coordtype)
cosm	object of class Cosmology
inputUnits	the units of the input coordinates

Definition at line 881 of file Catalogue.h.

◆ Catalogue() [5/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< std::string >	file,
		const int	col1 = `1`,
		const int	col2 = `2`,
		const int	col3 = `3`,
		const int	colWeight = `-1`,
		const int	colRegion = `-1`,
		const double	nSub = `1.1`,
		const double	fact = `1.`,
		const cosmology::Cosmology &	cosm = `{}`,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`,
		const CharEncode	charEncode = `CharEncode::_ascii_`,
		const std::string	comment = `"#"`,
		const int	seed = `3213`
	)

constructor, reading a file with coordinates

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
file	vector containing the files where the input catalogues are stored
col1	column of the input file containing the first coordinates, that can be either the x comoving coordinates, or the Right Ascensions (depending on coordtype)
col2	column of the input file containing the second coordinates, that can be either the y comoving coordinates, or the Declinations (depending on coordtype)
col3	column of the input file containing the third coordinates, that can be either the z comoving coordinates, or the redshits (depending on coordtype)
colWeight	column of the input file containing the weights
colRegion	column of the input file containing the regions (used for jackknife or bootstrap)
nSub	the fracton of objects that will be randomly selected (nSub=1 $ \rightarrow $ all objects are selected)
fact	a factor used to multiply the coordinates, i.e. coordinate_i=coordinate_i*fact
cosm	object of class Cosmology
inputUnits	the units of the input coordinates
charEncode	character encoding of input file, ascii or binary
comment	the string used to indicate a comment in the input file; all the data occurring on a line after a comment are discarded
seed	the seed for random number generation

Definition at line 124 of file Catalogue.cpp.

◆ Catalogue() [6/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< std::string >	file,
		const cosmology::Cosmology &	cosm,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`
	)

inline

constructor, reading a file with coordinates

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
file	vector containing the files where the input catalogues are stored
cosm	object of class Cosmology
inputUnits	the units of the input coordinates

Definition at line 955 of file Catalogue.h.

◆ Catalogue() [7/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< Var >	attribute,
		const std::vector< int >	column,
		const std::vector< std::string >	file,
		const int	comments = `0`,
		const double	nSub = `1.1`,
		const double	fact = `1`,
		const cosmology::Cosmology &	cosm = `{}`,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`,
		const char	delimiter = `'\t'`,
		const int	seed = `3213`
	)

constructor, reading a file with attributes of the catalogue

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
attribute	vector containing the list of attributes contained in the file, used to construct the catalogue
column	vector containing the column number which correspond to each element of the vector 'attributes', to be provided in ascending order; the column number corresponding to the first column is 1
file	vector containing the files where the input catalogues are stored
comments	number of rows to ignore at the beginning of the input file if its character encoding is ascii
nSub	the fracton of objects that will be randomly selected (nSub=1 $ \rightarrow $ all objects are selected)
fact	a factor used to multiply the coordinates, i.e. coordinate_i=coordinate_i*fact
cosm	object of class Cosmology
inputUnits	the units of the input coordinates
seed	the seed for random number generation
delimiter	the delimiter between the columns

Warning: The vector column must be sorted in ascending order. The column datas will be read as double types, unless a column corresponds to the variable type ID (in this case the values will be read as int)

Definition at line 245 of file Catalogue.cpp.

◆ Catalogue() [8/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< std::string >	file,
		const std::vector< std::string >	column_names,
		const bool	read_weights,
		const bool	read_regions,
		const double	nSub,
		const double	fact,
		const cosmology::Cosmology &	cosm = `{}`,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`,
		const int	seed = `3213`
	)

constructor, reading a file in FITS format

This constructor reads a FITS file that should contain at least the three object coordinates, and possibly also weights and regions

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
file	vector containing the files where the input catalogues are stored
column_names	vector containing the column names to read, i.e. at least the three coordinates, and possibly the weights and regions, in this order
read_weights	if true, read also the object weights from the FITS file
read_regions	if true, read also the object regions from the FITS file
nSub	the fracton of objects that will be randomly selected (nSub=1 $ \rightarrow $ all objects are selected)
fact	a factor used to multiply the coordinates, i.e. coordinate_i=coordinate_i*fact
cosm	object of class Cosmology
inputUnits	the units of the input coordinates
seed	the seed for random number generation

Definition at line 46 of file FITSCatalogue.cpp.

◆ Catalogue() [9/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const CoordinateType	coordinateType,
		const std::vector< std::string >	file,
		const std::vector< std::string >	column_names,
		const std::vector< Var >	attribute,
		const double	nSub,
		const double	fact,
		const cosmology::Cosmology &	cosm = `{}`,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`,
		const int	seed = `3213`
	)

constructor, reading a file in FITS format

This constructor reads a FITS file and associates each column name to a specific Catalogue variable

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
coordinateType	the coordinate type, specified in the cbl::CoordinateType enumeration
file	vector containing the files where the input catalogues are stored
column_names	vector containing the column names to read
attribute	vector containing the list of attributes contained in the file, which corresponds to each element of the vector 'column_names' (in the same order) and is specified in the cbl::catalogue::Var enumeration
nSub	the fracton of objects that will be randomly selected (nSub=1 $ \rightarrow $ all objects are selected)
fact	a factor used to multiply the coordinates, i.e. coordinate_i=coordinate_i*fact
cosm	object of class Cosmology
inputUnits	the units of the input coordinates
seed	the seed for random number generation

Definition at line 94 of file FITSCatalogue.cpp.

◆ Catalogue() [10/26]

template<typename T >

cbl::catalogue::Catalogue::Catalogue ( std::vector< T > object )

inline

constructor, using vectors of generic objects

Parameters

object objects of class T, specified in the cbl::catalogue::ObjectType enumeration

Definition at line 1091 of file Catalogue.h.

◆ Catalogue() [11/26]

cbl::catalogue::Catalogue::Catalogue ( std::vector< std::shared_ptr< Object > > sample )

inline

constructor, using vectors of pointers to generic objects

Parameters

sample vector of objects of type Object, specified in the cbl::catalogue::ObjectType enumeration

Definition at line 1103 of file Catalogue.h.

◆ Catalogue() [12/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const std::vector< Var >	attribute,
		const std::vector< int >	column,
		const std::vector< std::string >	file,
		const int	comments = `0`,
		const double	nSub = `1.1`,
		const int	seed = `3213`
	)

constructor, reading a file with attributes of the catalogue

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
attribute	vector containing the list of attributes contained in the file, used to construct the catalogue
column	vector containing the column number which correspond to each element of the vector 'attributes'
file	vector containing the files where the input catalogues are stored
comments	number of rows to ignore at the beginning of the input file if its character encoding is ascii
nSub	the fracton of objects that will be randomly selected (nSub=1 $ \rightarrow $ all objects are selected)
seed	the seed for random number generation

Definition at line 347 of file Catalogue.cpp.

◆ Catalogue() [13/26]

cbl::catalogue::Catalogue::Catalogue	(	const Catalogue	input_catalogue,
		const Catalogue	target_catalogue,
		const Var	var_name,
		const int	nbin,
		const int	seed = `3213`
	)

constructor, creating a catalogue by matching the distribution of one quantity from a target catalogue

Parameters

input_catalogue	the input catalogue
target_catalogue	the target catalogue
var_name	the type of variable, specified cbl::catalogue::Var enumeration
nbin	the binning for the variable
seed	the seed for random number generation

Definition at line 2405 of file Catalogue.cpp.

◆ Catalogue() [14/26]

cbl::catalogue::Catalogue::Catalogue	(	const Catalogue	input_catalogue,
		const Catalogue	target_catalogue,
		const cbl::catalogue::Var	var_name1,
		const int	nbin1,
		const cbl::catalogue::Var	var_name2,
		const int	nbin2,
		const int	seed = `3213`
	)

constructor, creating a catalogue by matching the distributions of two quantities from a target catalogue

Parameters

input_catalogue	the input catalogue
target_catalogue	the target catalogue
var_name1	the type of variable, specified cbl::catalogue::Var enumeration
nbin1	the binning for the variable
var_name2	the type of variable, specified cbl::catalogue::Var enumeration
nbin2	the binning for the variable
seed	the seed for random number generation

Definition at line 2444 of file Catalogue.cpp.

◆ Catalogue() [15/26]

cbl::catalogue::Catalogue::Catalogue	(	const Catalogue	halo_catalogue,
		const cosmology::Cosmology &	cosm,
		const HODType	HOD_Type,
		const double	threshold,
		const bool	substructures = `true`,
		std::vector< double >	parameter = `{}`
	)

constructor that creates a catalogue of galaxies using an HOD model to popolate the haloes

Parameters

halo_catalogue	the halo catalogue
cosm	the cosmology used to convert redshifts into coordinates
HOD_Type	the HOD model used to populate haloes with galaxies
threshold	the threshold above which the haloes are populated with galaxies. It is espressed in stellar mass if HODType is Moster10, or in magnitude if HODType is Zehavi05 or Zehavi11, the available magnitude threshold are ${-18,-18.5,-19,-19.5,-20,-20.5,-21,-21.5,-22}$ .
substructures	if true the halo catalogue is populated with galaxies and substructures; if false only with galaxies
parameter	vector of double which contains the parameters for the HOD. An empty vector takes the defaul values of the HOD model considered adopted. When HODType is Moster10 only the first 11 parameters are used, that are referrend to mean occupation numbers and to the conditional stellar mass function. The first five refer to the central galaxies, while the other refer to the satellite galaxies. They are respectively ${k_c,M_{1c}, \beta_c, \gamma_c, k_s, M_{1s}, \beta_s, \gamma_s, \phi_s, \alpha_s}$. The mean occupation numbers are:

\[\bigl \langle N_{c} (>M_{*,min},M)\bigl \rangle = \frac{1}{2}\left[1-erf\left(\frac{\log M_{*,min}/\bar M_{*,c}}{\sqrt{2}\sigma_c}\right)\right] \]

\[ \bigl \langle N_{s} (>M_{*,min},M)\bigl \rangle = \frac{\phi_s^*}{2}\Gamma\left[\frac{\alpha_s}{2} + \frac{1}{2},\left(\frac{M_{*,min}}{\bar M_{*,s}}\right)^2\right]\]

where the subscripts "c" and "s" refer to central and satellite galaxies, respectively, and $\bar M_{*} $ is the mean stellar mass for galaxies inside an halo of mass $M$

\[\bar M_{*} = 2Mk\left[\left(\frac{M}{M_{1}}\right)^{-\beta}+\left(\frac{M}{M_{1}}\right)^{\gamma}\right]^{-1}\]

When HODType is Zehavi05 or Zehavi11 the length of the parameters vector is 14 and 16 respectively. In Zehavi05 the first 3 are referred to the mean occupation numbers, while with Zehavi11 the first five are referred to the mean occupation number. While the other parameters are used to extract the stellar mass of each galaxy. The parameters vector with Zehavi05 is: ${M_{min},M_1,\alpha,k_c, M_{1c}, \beta_c, \gamma_c,k_s,M_{1s},\beta_s,\gamma_s,\phi_s,\alpha_s}$. The mean occupation number for central and satellite galaxies respectively are the follow:

\[\bigl \langle N_c(M) \bigl \rangle = \begin{cases} 0 \ \ \ \text{if $M<M_{min}$} \\ 1 \ \ \ \hfill \text{if $M>M_{min}$} \\ \end{cases}\]

\[\bigl \langle N_s (M)\bigl \rangle =\begin{cases} 0 \ \ \ \text{if $M<M_{min}$} \\ (\frac{M-M_{min}}{M_1})^{\alpha} \ \ \ \text{if $M>M_{min}$} \\ \end{cases}\]

The parameters vector with Zehavi11 is: ${logM_{min},\sigma_{logM},M_0,M_1,\alpha,k_c,M_{1c}, \beta_c,\gamma_c,k_s,M_{1s},\beta_s,\gamma_s,\phi_s,\alpha_s}$ The mean occupation number for central and satellite galaxies respectively are the follow:

\[\bigl \langle N_c (M)\bigl \rangle =\frac{1}{2}\left[1+erf \left(\frac{\log M-\log M_{min}}{\sigma_{logM}}\right)\right] \]

\[\bigl \langle N_s (M)\bigl \rangle= \frac{1}{2}\left[1+\left(\frac{M-M_0}{M'_1}\right)^\alpha\right]\]

The stellar masses for central and satellite galaxies are extracted from the following conditional stellar mass function:

\[\Phi_{c}(M_*|M)=\frac{1}{\sqrt{2\pi}\ln10 M_* \sigma_c}\exp\left[-\frac{\log^2\left(M_* /\bar M_{*,c}\right)}{2\sigma_c^2}\right] \]

\[ \Phi_{s}(M_*|M)=\frac{\phi^*_s}{\bar M_{*,s}}\left(\frac{m_*}{m_{*,s}}\right)^{\alpha_s} \exp\left[-\left(\frac{M_*}{\bar M_{*,s}}\right)^2\right] \]

Definition at line 84 of file HODCatalogue.cpp.

◆ Catalogue() [16/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		const cosmology::Cosmology &	real_cosm,
		const cosmology::Cosmology &	test_cosm,
		const std::string	dir_in,
		const double	Zguess_min,
		const double	Zguess_max
	)

constructor that creates a random catalogue in a cubic box, warped by geometric distortions

this function reads a cubic random catalogue from a file, generated in a given cosmology, and trasforms it into a new one in a different cosmology

Parameters

type	the type of random catalogue, that must be set to _createRandom_box_
real_cosm	object of class Cosmology representing the real (or assumed) cosmology
test_cosm	object of class Cosmology representing the test cosmology
dir_in	the input directory where the original random catalogue is stored
Zguess_min	minimum redshift used to search the redshift
Zguess_max	maximum redshift used to search the redshift

Warning: the input parameter type is used only to make the constructor type explicit

Definition at line 45 of file RandomCatalogue.cpp.

◆ Catalogue() [17/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		const Catalogue	catalogue,
		const double	N_R,
		const int	nbin = `10`,
		const cosmology::Cosmology &	cosm = `{}`,
		const bool	conv = `false`,
		const double	sigma = `0.`,
		const std::vector< double >	redshift = `{}`,
		const std::vector< double >	RA = `{}`,
		const std::vector< double >	Dec = `{}`,
		int	z_ndigits = `10`,
		const int	seed = `3213`
	)

constructor that creates a random catalogue with either the square geometry or with 'the shuffle' method

constructor that creates a random catalogue with either the square geometry in observed coordinates (R.A., Dec), or with the 'shuffle' method, i.e. using the R.A. and Dec coordinates of the input catalogue

Parameters

type	the type of random catalogue, that must be set to either _createRandom_box_, _createRandom_square_, _createRandom_shuffle_ or _createRandom_shuffleTOT_
catalogue	object of class Catalogue
N_R	fraction of random objects, i.e. N_R=N_random/N_objects
nbin	number of redshift bins used to compute the redshift distribution
cosm	object of class Cosmology
conv	true → compute the Gaussian convolvolution of the distribution; false → do not convolve
sigma	the standard deviation, σ, of the Gaussian kernel
redshift	vector containg the redshifts used to computed the redshift distribution for the random catalogue; if it is not provided, the redshifts of the input catalogue will be used
RA	vector containg the right ascensions of the random objects; if it is not provided, it will be created by the function
Dec	vector containg the declinations of the random objects; if it is not provided, it will be created by the function
z_ndigits	the number of digit figures used for the redshifts
seed	the seed for random number generation

Warning: the input parameter type is used only to make the constructor type explicit

Definition at line 88 of file RandomCatalogue.cpp.

◆ Catalogue() [18/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		const int	N_R,
		const double	z_step,
		const Catalogue	catalogue,
		const cosmology::Cosmology &	cosm = `{}`,
		const std::vector< double >	RA = `{}`,
		const std::vector< double >	Dec = `{}`,
		const double	sigma_kernel = `0.01`,
		const int	nbins = `100`,
		int	z_ndigits = `10`,
		const int	times_default = `5`,
		double	times_change = `0.5`,
		const double	tolerance = `0.05`,
		const std::string	out_path_nz = `par::defaultString`,
		const std::string	out_file_nz = `par::defaultString`,
		const int	seed = `3213`
	)

constructor that creates a random catalogue with the 'shuffle' method.

Only two random types are allowed:

cbl::catalogue::RandomType::_createRandom_shuffleTOT_: shuffle in R.A., Dec, redshift;
cbl::catalogue::RandomType::_createRandom_shuffle_: shuffle in R.A. and Dec, and random extraction of redshift positions only in the bins filled by the data. Such bins have dimension equal to $\Delta_z$, which is an input parameter of this constructor. More specifically, the redshift distribution of the data is smoothed with a Gaussian kernel, with rms equal to $\sigma_{\rm kernel}$. Random extractions are obtained from this smoothed distribution, and only those within the "good" redshift bins are kept.

If R.A., Dec or redshift are provided in input the code won't create them.

In the case of _createRandom_shuffle_, the code will extract (times_default $\times$ the requested number of random objects) redshift values from the smoothed $n(z)$. Then only those extractions falling in the good redshift bins are selected. The difference between the number of such good extractions and the requested number of random objects must be lower than the tolerance parameter, and higher than the requested number of random objects. If not, the code re-performs the extraction from $n(z)$ by multiplying times_default by $(1+times\_change)$ or by $(1-times\_change)$. Then, for example, the new variable $times = times\_default (1+times\_change)$ is used. The aim is obtaining a number of good extractions which is higher than the requested number of random objects, and then the extracitons in excess are uniformly excluded from the good redshift bins.

Author: Giorgio Lesci (giorg.nosp@m.io.l.nosp@m.esci2.nosp@m.@uni.nosp@m.bo.it)

Parameters

type	the type of random catalogue, that must be set to either _createRandom_shuffle_ or _createRandom_shuffleTOT_
N_R	fraction of random objects, i.e. N_R=N_random/N_objects
z_step	$\Delta_z$: step in redshift used to find the redshift intervals where the random objects have to be extracted, in the case of _createRandom_shuffle_
catalogue	object of class Catalogue
cosm	object of class Cosmology
RA	vector containg the right ascensions of the random objects; if it is not provided, it will be created by the function
Dec	vector containg the declinations of the random objects; if it is not provided, it will be created by the function
sigma_kernel	$\sigma_{\rm kernel}$, used only in the case of _createRandom_shuffle_
nbins	number of redshift bins used to compute the redshift distribution, used only in the case of _createRandom_shuffle_
z_ndigits	the number of digit figures used for the redshifts
times_default	number defining the random extractions from the smoothed $n(z)$, which is multiplied by the number of requested random objects. Used only if _createRandom_shuffle_ is selected
times_change	in case the number of extractions from $n(z)$ is too low or too high, this parameter regulates the change of times_default. Default is 50%
tolerance	tolerance for the difference between good random redshifts and requested number of random objects. Default is 5%
out_path_nz	used only if _createRandom_shuffle_ is selected. If provided the code writes a file containing, in the 0th column, the bin centres which depend on the input parameter nbins, while in the 1st colum there is the original smoothed redshift distribution (without holes), in the 2nd column the extracted distribution (still without holes), and in the 3rd column the final $n(z)$
out_file_nz	the file located at out_path_nz
seed	the seed for random number generation

Warning: the input parameter type is used only to make the constructor type explicit

Definition at line 225 of file RandomCatalogue.cpp.

◆ Catalogue() [19/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		const Catalogue	catalogue,
		const double	N_R,
		const int	nbin,
		const double	Angle,
		const std::vector< double >	redshift,
		const cosmology::Cosmology &	cosm = `{}`,
		const bool	conv = `false`,
		const double	sigma = `0.`,
		const int	seed = `3213`
	)

constructor that creates a random catalogue in a cone

Parameters

type	the type of random catalogue, that must be set to _createRandom_cone_
catalogue	object of class Catalogue
N_R	fraction of random objects, i.e. N_R=N_random/N_objects
nbin	number of redshift bins used to compute the redshift distribution
Angle	angle of the cone
redshift	vector containing the redshift of the objects in the catalogue
cosm	object of class Cosmology
conv	true → compute the Gaussian convolvolution of the distribution; false → do not convolve
sigma	the standard deviation, σ, of the Gaussian kernel
seed	the seed for random number generation

Warning: the input parameter type is used only to make the constructor type explicit

Definition at line 425 of file RandomCatalogue.cpp.

◆ Catalogue() [20/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		const std::vector< std::string >	mangle_mask,
		const Catalogue	catalogue,
		const double	N_R,
		const int	nbin,
		const cosmology::Cosmology	cosm,
		const bool	conv = `false`,
		const double	sigma = `0.`,
		const int	seed = `3213`
	)

constructor that creates a random catalogue using the a mask in the MANGLE format for the angular distribution and taking the redshift distribution from an input catalogue

Parameters

type	the type of random catalogue, that must be set to _createRandom_MANGLE_
mangle_mask	vector containing the input masks in MANGLE format
catalogue	object of class Catalogue
N_R	fraction of random objects, i.e. N_R=N_random/N_objects
nbin	number of redshift bins used to compute the redshift distribution
cosm	object of class Cosmology
conv	true → compute the Gaussian convolvolution of the distribution; false → do not convolve
sigma	the standard deviation, σ, of the Gaussian kernel
seed	the seed for random number generation

Warning: the input parameter type is used only to make the constructor type explicit

Definition at line 481 of file RandomCatalogue.cpp.

◆ Catalogue() [21/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		const Catalogue	catalogue,
		const double	N_R,
		const bool	dndz_per_stripe,
		const int	nbin,
		const cosmology::Cosmology	cosm,
		const bool	conv = `false`,
		const double	sigma = `0`,
		const int	seed = `3213`
	)

constructor that creates a random catalogue using the SDSS stripes.

Parameters

type	the type of random catalogue, that must be set to _createRandom_SDSS_stripes_
catalogue	object of class Catalogue
N_R	fraction of random objects, i.e. N_R=N_random/N_objects
dndz_per_stripe	true → set the redshift for the random sample shuffling redshift of data catalogue in each stripe; false → set the redshift for the random sample extracting from the total $ dn/dz$.
nbin	number of redshift bins used to compute the redshift distribution
cosm	object of class Cosmology
conv	true → compute the Gaussian convolvolution of the distribution; false → do not convolve
sigma	the standard deviation, σ, of the Gaussian kernel
seed	the seed for random number generation

Warning: the input parameter type is used only to make the constructor type explicit

Definition at line 546 of file RandomCatalogue.cpp.

◆ Catalogue() [22/26]

cbl::catalogue::Catalogue::Catalogue	(	const RandomType	type,
		Catalogue	catalogue,
		const double	N_R,
		const cosmology::Cosmology	cosm,
		const std::vector< double >	RA_range,
		const std::vector< double >	DEC_range,
		const unsigned int	nbin,
		const int	seed
	)

constructor that creates a random catalogue for light cones homogeneous in RA and Dec and with redshift dependent density.

Parameters

type	the type of random catalogue, that must be set to _createRandom_homogeneous_LC_
catalogue	object of class Catalogue
N_R	fraction of random objects, i.e. N_R=N_random/N_objects
cosm	object of class Cosmology
RA_range	range in RA [RA_min, RA_max]
DEC_range	range in DEC [DEC_min, DEC_max]
nbin	number of redshift bins used to compute the redshift distribution
seed	the seed for random number generation

Definition at line 623 of file RandomCatalogue.cpp.

◆ Catalogue() [23/26]

cbl::catalogue::Catalogue::Catalogue	(	const VoidAlgorithm	algorithm,
		Catalogue	tracer_catalogue,
		Catalogue	random_catalogue,
		const std::string	dir_output,
		const std::string	output,
		const double	cellsize,
		const int	n_rec = `1`,
		const double	step_size = `2.5/3.`,
		const double	threshold = `0.`,
		const std::vector< bool >	print = `{true, true}`
	)

constructor that creates a void catalogue extracting cosmic voids from a catalogue of tracers, for COMOVING coordinates. This void finder is based on dynamical criteria: the density field is reconstructed from the displacement field generated by the back-in-time evolution of the tracers. Voids are therefore classified as regions of negative velocity divergence.

Parameters

algorithm	the type of algorithm on which the reconstruction of the density field is based (LaZeVo or Exact)
tracer_catalogue	the input tracer catalogue
random_catalogue	Random catalogues. Simply declears as empty (={}) if the random catalogue is not available: a new random catalogue will be created with the same objects and geometry of the tracer catalogue
dir_output	path of the output directory where to store the different reconstructions, the divergence field, the subvoid and void catalogues
output	name of the output files
cellsize	minimum radius used for the chain mesh
n_rec	number of reconstructions of the density field: number of random catalogue used or generated
step_size	dimension of the grid cells used for the identification of subvoids, in units of the mean interparticle separation of the tracer catalogue. It is strongly recommended to keep this value greater than 0.75 (cell sizes too small compared to the resolution of the catalogue)
threshold	number of minimum couplings between a certain halo and a certain random particle necessary to couple them in a definitive way
print	boolean vector of two elements. If print[0] == true, the displacement field will be saved in a file. If print[1] == true, the divergence field will be saved in a file

Definition at line 56 of file VoidCatalogue.cpp.

◆ Catalogue() [24/26]

cbl::catalogue::Catalogue::Catalogue	(	const VoidAlgorithm	algorithm,
		Catalogue	tracer_catalogue,
		Catalogue	random_catalogue,
		const std::string	dir_output,
		const std::string	output,
		const double	cellsize,
		const cbl::cosmology::Cosmology	cosm,
		const std::vector< double >	RA_range,
		const std::vector< double >	DEC_range,
		const int	n_rec = `1`,
		const double	step_size = `2.5/3.`,
		const double	threshold = `0.`
	)

constructor that creates a void catalogue extracting cosmic voids from a catalogue of tracers for OBSERVED COORDINATES. This void finder is based on dynamical criteria: the density field is reconstructed from the displacement field generated by the back-in-time evolution of the tracers. Voids are therefore classified as regions of negative velocity divergence.

========================================================================================

Parameters

algorithm	the type of algorithm on which the reconstruction of the density field is based (LaZeVo or Exact)
tracer_catalogue	the input tracer catalogue
random_catalogue	Random catalogue. Simply declears as void (={}) if the random catalogue is not available: a new random catalogue will be created with the same objects and geometry of the tracer catalogue
dir_output	path of the output directory where to store the different reconstructions, the divergence field, the subvoid and void catalogues
output	name of the output files
cellsize	minimum radius used for the chain mesh
cosm	cosmology
RA_range	range of coordinate RA of the catalogue (from -pi/2 to pi/2)
DEC_range	range of coordinate Dec of the catalogue (from 0 to 2pi). if the catalog is located across the zero meridian, the minimum must be negative (e.g. [1.5pi, 0.5pi] -> [-0.5pi, 0.5pi]).
n_rec	number of reconstructions of the density field: number of random catalogue used or generated
step_size	dimension of the grid cells used for the identification of subvoids, in units of the mean interparticle separation of the tracer catalogue. It is strongly recommended to keep this value greater than 0.75 (cell sizes too small compared to the resolution of the catalogue)
threshold	number of minimum couplings between a certain halo and a certain random particle necessary to couple them in a definitive way

Definition at line 561 of file VoidCatalogue.cpp.

◆ Catalogue() [25/26]

cbl::catalogue::Catalogue::Catalogue	(	const ObjectType	objectType,
		const std::string	file_cn = `par::defaultString`,
		const bool	snapformat = `false`,
		const bool	swap = `false`,
		const double	fact = `0.001`,
		const bool	read_catalogue = `true`,
		const double	nSub = `1.1`,
		const std::string	component_to_read = `"ALL"`,
		const std::vector< std::vector< double >>	edges = `{{par::defaultDouble,par::defaultDouble},{par::defaultDouble,par::defaultDouble},{par::defaultDouble,par::defaultDouble}}`
	)

constructor that reads object of selected type from Gadget snapshots

Parameters

objectType	the object type, specified in the cbl::catalogue::ObjectType enumeration
file_cn	the the name common to all the files in which the gadget snapshot is divided (path/to/file/common_name)
snapformat	false -> gadget snapformat 1; true -> gadget snapformat 2; else -> wrong
swap	true = swap endianism, false = do not swap endianism
fact	a factor used to multiply the coordinates, i.e. coordinate_i=coordinate_i*fact
read_catalogue	true = the constructor actually reads the GADGET snapshot false = the constructor only reads the snapshot header and prints it on the screan
nSub	the fraction of objects that will be randomly selected (nSub=1 ⇒ all objects are selected)
component_to_read	which component to be read from the snapshot. "ALL" = read all the components positions, else select one of the following: "Gas", "Halo", "Disk", "Bulge", "Stars", "Boundary".
edges	edges of the subcatalogue, format: [ [x_min, x_max], [y_min, y_max], [z_min, z_max] ]

Definition at line 126 of file GadgetCatalogue.cpp.

◆ Catalogue() [26/26]

cbl::catalogue::Catalogue::Catalogue	(	const int	snap,
		const std::string	basedir,
		const bool	swap = `false`,
		const bool	long_ids = `false`,
		const double	scaleFact = `1.0`,
		const double	massFact = `1.0`,
		const EstimateCriterion	estimate_crit = `EstimateCriterion::_m200_`,
		const bool	veldisp = `false`,
		const bool	masstab = `false`,
		const bool	add_satellites = `false`,
		const bool	verbose = `false`
	)

constructor that reads objects of class HostHalo with satellite dependencies from group and subgroup files generated by the gadget implementation of the FoF and SUBFIND algorithms (respectively)

Parameters

snap	the snapshot number
basedir	the directory in which all the GADGET outputs are stored
swap	true = swap endianism, false = do not swap endianism
long_ids	true = IDs are stored in double precision, false = IDs are stored in single precision
scaleFact	a factor used to multiply the coordinates, i.e. coordinate_i=coordinate_i*scaleFact
massFact	a factor used to multiply the masses, i.e. mass_i=mass_i*scaleFact
estimate_crit	the criterion used to estimate mass, radius and velocity dispersion of the group
veldisp	whether the average velocity dispersion within the estimated radius has been computed or not in the GADGET run considered
masstab	whether the mass table is present or not
add_satellites	whether to add the satellites identified by the SUBFIND algorithm to the catalogue
verbose	true = build the catalogue verbosely, false = keep it quiet..

Definition at line 274 of file GadgetCatalogue.cpp.

Member Function Documentation

◆ add_object() [1/2]

void cbl::catalogue::Catalogue::add_object ( std::shared_ptr< Object > object )

inline

add one single object to the catalogue

Parameters

object pointer to an object of type Object

Definition at line 2641 of file Catalogue.h.

◆ add_object() [2/2]

template<typename T >

void cbl::catalogue::Catalogue::add_object ( T object )

inline

add one single object to the catalogue

Parameters

object object of type T

Definition at line 2648 of file Catalogue.h.

◆ add_objects() [1/2]

void cbl::catalogue::Catalogue::add_objects ( std::vector< std::shared_ptr< Object > > sample )

inline

add some objects to the catalogue

Parameters

sample vector of pointers to objects of type Object

Examples: catalogue.cpp.

Definition at line 2654 of file Catalogue.h.

◆ add_objects() [2/2]

template<typename T >

void cbl::catalogue::Catalogue::add_objects ( std::vector< T > sample )

inline

add some objects to the catalogue

Parameters

sample vector of objects of type T

Definition at line 2664 of file Catalogue.h.

◆ angsep_xyz()

double cbl::catalogue::Catalogue::angsep_xyz	(	const int	i,
		std::shared_ptr< Object >	obj
	)		const

get the angular distrance between the i-th object of the catalogue and another object

Parameters

i	the object index
obj	pointer to an object

Returns: distance between the i-th object of the catalogue and the object obj

Definition at line 2114 of file Catalogue.cpp.

◆ catalogue_object() [1/2]

std::vector<std::shared_ptr<Object> > cbl::catalogue::Catalogue::catalogue_object ( ) const

inline

get the object vector

Returns: vector of pointers to objects of the catalogue

Definition at line 2249 of file Catalogue.h.

◆ catalogue_object() [2/2]

std::shared_ptr<Object> cbl::catalogue::Catalogue::catalogue_object ( const int i ) const

inline

get the i-th object of the catalogue

Parameters

i	the object index

Returns: pointer to an object of the catalogue

Definition at line 2236 of file Catalogue.h.

◆ centralDensity()

double cbl::catalogue::Catalogue::centralDensity ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_centralDensity

Parameters

i	the object index

Returns: central density of the i-th object

Definition at line 2079 of file Catalogue.h.

◆ clean_void_catalogue() [1/3]

void cbl::catalogue::Catalogue::clean_void_catalogue	(	const bool	initial_radius = `false`,
		const std::vector< double >	delta_r = `{-1, 1000}`,
		const double	threshold = `0.205`,
		const bool	rescale = `true`,
		const std::shared_ptr< Catalogue >	tracers_catalogue = `{}`,
		chainmesh::ChainMesh3D	ChM = `{}`,
		const double	ratio = `1.5`,
		const bool	checkoverlap = `true`,
		const Var	ol_criterion = `Var::_CentralDensity_`
	)

function that modifies a void catalogue according to a set of user selected criteria. If all the steps are selected the final result is a catalogue of spherical, not-overlapped voids.

Parameters

initial_radius	erase voids outside a given interval delta_r of initial radius;
delta_r	the interval of accepted radii
threshold	the density threshold
rescale	true = for each void finds the larger radius enclosing density = threshold, false = skip the step
tracers_catalogue	object of class Catalogue with the tracers defining the void distribution (necessary if rescale = true)
ChM	object of ChainMesh3D class
ratio	distance from the void centre at which the density contrast is evaluated in units of the void radius. Ex: ratio = 0.1 $\rightarrow$ 10% of the void radius lenght
checkoverlap	true $\rightarrow$ erase all the voids wrt a given criterion, false $\rightarrow$ skip the step
ol_criterion	the criterion for the overlap step (valid criteria: Var::DensityContrast, Var::CentralDensity)

Examples: cleanVoidCatalogue.cpp.

Definition at line 1328 of file VoidCatalogue.cpp.

◆ clean_void_catalogue() [2/3]

void cbl::catalogue::Catalogue::clean_void_catalogue	(	const std::vector< double >	par_numdensity,
		const bool	initial_radius = `false`,
		const std::vector< double >	delta_r = `{-1, 1000}`,
		const double	threshold = `0.205`,
		const bool	rescale = `true`,
		const std::shared_ptr< Catalogue >	tracers_catalogue = `{}`,
		chainmesh::ChainMesh3D	ChM = `{}`,
		const double	ratio = `1.5`,
		const bool	checkoverlap = `true`,
		const Var	ol_criterion = `Var::_CentralDensity_`
	)

function that modifies a void catalogue according to a set of user selected criteria. If all the steps are selected the final result is a catalogue of spherical, not-overlapped voids.

Parameters

par_numdensity	coefficients of the polynomial describing the variation of the number density as a function of the redshift, from the highest to the lowest order. Ex.: par_density = {-0.001, 0.005, -0.01} $\rightarrow$ numdensity = $ -0.001 \cdot z^2 + 0.005 \cdot z -0.01 $
initial_radius	erase voids outside a given interval delta_r of initial radius;
delta_r	the interval of accepted radii
threshold	the density threshold
rescale	true = for each void finds the larger radius enclosing density = threshold, false = skip the step
tracers_catalogue	object of class Catalogue with the tracers defining the void distribution (necessary if rescale = true)
ChM	object of ChainMesh3D class
ratio	distance from the void centre at which the density contrast is evaluated in units of the void radius. Ex: ratio = 0.1 $\rightarrow$ 10% of the void radius lenght
checkoverlap	true $\rightarrow$ erase all the voids wrt a given criterion, false $\rightarrow$ skip the step
ol_criterion	the criterion for the overlap step (valid criteria: Var::DensityContrast, Var::CentralDensity)

Definition at line 1605 of file VoidCatalogue.cpp.

◆ clean_void_catalogue() [3/3]

void cbl::catalogue::Catalogue::clean_void_catalogue	(	const std::vector< std::vector< double >>	data_numdensity,
		const std::string	method_interpolation,
		const bool	initial_radius = `false`,
		const std::vector< double >	delta_r = `{-1, 1000}`,
		const double	threshold = `0.205`,
		const bool	rescale = `true`,
		const std::shared_ptr< Catalogue >	tracers_catalogue = `{}`,
		chainmesh::ChainMesh3D	ChM = `{}`,
		const double	ratio = `1.5`,
		const bool	checkoverlap = `true`,
		const Var	ol_criterion = `Var::_CentralDensity_`
	)

function that modifies a void catalogue according to a set of user selected criteria. If all the steps are selected the final result is a catalogue of spherical, not-overlapped voids.

Parameters

data_numdensity	2D matrix containing the sampled values of the mean number density as a function of redshift. These data will be interpolated to finf the value of the number desnity of the tracers at a specific redshift
method_interpolation	the type of method used for the interpolation: "Linear" → linear interpolation; "Poly" → polynomial interpolation; "Spline" → cubic spline interpolation; "Rat" → diagonal rational function interpolation; "BaryRat" → barycentric rational interpolation
initial_radius	erase voids outside a given interval delta_r of initial radius;
delta_r	the interval of accepted radii
threshold	the density threshold
rescale	true = for each void finds the larger radius enclosing density = threshold, false = skip the step
tracers_catalogue	object of class Catalogue with the tracers defining the void distribution (necessary if rescale = true)
ChM	object of ChainMesh3D class
ratio	distance from the void centre at which the density contrast is evaluated in units of the void radius. Ex: ratio = 0.1 $\rightarrow$ 10% of the void radius lenght
checkoverlap	true $\rightarrow$ erase all the voids wrt a given criterion, false $\rightarrow$ skip the step
ol_criterion	the criterion for the overlap step (valid criteria: Var::DensityContrast, Var::CentralDensity)

Definition at line 1878 of file VoidCatalogue.cpp.

◆ compute_catalogueProperties_box()

std::vector< double > cbl::catalogue::Catalogue::compute_catalogueProperties_box ( const double boxside )

compute catalogue volume, number density and mean particle separation

Parameters

boxside side lenght of the cubic catalogue box

Returns: vector with 5 elements: volume, numdensity, mps, numdensity_error, mps_error;

Definition at line 2571 of file Catalogue.cpp.

◆ compute_catalogueProperties_lightCone()

std::vector< std::vector< double > > cbl::catalogue::Catalogue::compute_catalogueProperties_lightCone	(	cbl::cosmology::Cosmology	cosmology,
		const std::vector< double >	RA_range,
		const std::vector< double >	DEC_range,
		const unsigned int	nbin
	)

compute catalogue volume, number density and mean particle separation in light cones

Parameters

cosmology	the cosmology used to compute the comoving distances
RA_range	range of coordinate RA of the catalogue (from -pi/2 to pi/2)
DEC_range	range of coordinate Dec of the catalogue (from 0 to 2pi). if the catalog is located across the zero meridian, the minimum must be negative (e.g. [1.5pi, 0.5pi] -> [-0.5pi, 0.5pi]).
nbin	number of bin in redshift

Returns: 7 vector of nbin elements. One for each of these properties: zbin, nObj, volume, numdensity, mps, numdensity_error, mps_error;

Definition at line 2595 of file Catalogue.cpp.

◆ compute_centralDensity() [1/3]

void cbl::catalogue::Catalogue::compute_centralDensity	(	const std::shared_ptr< Catalogue >	tracers_catalogue,
		chainmesh::ChainMesh3D	ChM,
		const double	threshold
	)

compute the central density of each object in a void catalogue. We define as central density the density contrast computed inside a spherical region grown around the void center, with a radius of $2$ times the mean particle separation of the tracer catalogue

Parameters

tracers_catalogue	the density field tracers catalogue
ChM	a 3D chain mesh object, used to speed-up the search of close pairs
threshold	the central density threshold

Definition at line 2150 of file VoidCatalogue.cpp.

◆ compute_centralDensity() [2/3]

void cbl::catalogue::Catalogue::compute_centralDensity	(	const std::shared_ptr< Catalogue >	tracers_catalogue,
		chainmesh::ChainMesh3D	ChM,
		const std::vector< double >	par_numdensity,
		const double	threshold
	)

compute the central density of each object in a void catalogue. We define as central density the density contrast computed inside a spherical region grown around the void center, with a radius of $2$ times the mean particle separation of the tracer catalogue

Parameters

tracers_catalogue	the density field tracers catalogue
ChM	a 3D chain mesh object, used to speed-up the search of close pairs
par_numdensity	coefficients of the polynomial describing the variation of the number density as a function of the redshift, from the highest to the lowest order. Ex.: par_density = {-0.001, 0.005, -0.01} $\rightarrow$ numdensity = $ -0.001 \cdot z^2 + 0.005 \cdot z -0.01 $
threshold	the central density threshold

Definition at line 2176 of file VoidCatalogue.cpp.

◆ compute_centralDensity() [3/3]

void cbl::catalogue::Catalogue::compute_centralDensity	(	const std::shared_ptr< Catalogue >	tracers_catalogue,
		chainmesh::ChainMesh3D	ChM,
		const std::vector< std::vector< double >>	data_numdensity,
		const std::string	method_interpolation,
		const double	threshold
	)

compute the central density of each object in a void catalogue. We define as central density the density contrast computed inside a spherical region grown around the void center, with a radius of $2$ times the mean particle separation of the tracer catalogue

Parameters

tracers_catalogue	the density field tracers catalogue
ChM	a 3D chain mesh object, used to speed-up the search of close pairs
data_numdensity	2D matrix containing the sampled values of the mean number density as a function of redshift. These data will be interpolated to finf the value of the number desnity of the tracers at a specific redshift
method_interpolation	the type of method used for the interpolation: "Linear" → linear interpolation; "Poly" → polynomial interpolation; "Spline" → cubic spline interpolation; "Rat" → diagonal rational function interpolation; "BaryRat" → barycentric rational interpolation
threshold	the central density threshold

Definition at line 2204 of file VoidCatalogue.cpp.

◆ compute_densityContrast()

void cbl::catalogue::Catalogue::compute_densityContrast	(	const std::shared_ptr< Catalogue >	tracers_catalogue,
		chainmesh::ChainMesh3D	ChM,
		const double	ratio = `0.1`
	)

compute density contrast of cosmic voids in catalogue as the ratio between an inner and an outer sphere grown around the void centre

Parameters

tracers_catalogue	the density field tracers catalogue
ChM	a 3D chain mesh object, used to speed-up the search of close pairs
ratio	the ratio $r$ used to compute the central density

Warning: to obtain the density contrast this function computes the central density of each void in the catalogue using the internal function compute_centralDensity; if the choice of $r$ is too low to select more than 3 tracers the program will select by dafault the 3 tracers closer to the void centre to map the central density.

Definition at line 2233 of file VoidCatalogue.cpp.

◆ computeComovingCoordinates()

void cbl::catalogue::Catalogue::computeComovingCoordinates	(	const cosmology::Cosmology &	cosm,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_radians_`
	)

compute the comoving coordinates (x, y, z) from the observed coordinates (R.A., Dec, redshift)

Parameters

cosm	object of class Cosmology
inputUnits	the units of the input coordinates

Definition at line 1553 of file Catalogue.cpp.

◆ computePolarCoordinates() [1/2]

void cbl::catalogue::Catalogue::computePolarCoordinates ( const CoordinateUnits outputUnits = CoordinateUnits::_radians_ )

compute the polar coordinates (R.A., Dec, d_c) from the comoving coordinates (x, y, z)

Parameters

outputUnits the units of the output coordinates

Definition at line 1587 of file Catalogue.cpp.

◆ computePolarCoordinates() [2/2]

void cbl::catalogue::Catalogue::computePolarCoordinates	(	const cosmology::Cosmology &	cosmology,
		const double	z1 = `0.`,
		const double	z2 = `10.`,
		const CoordinateUnits	outputUnits = `CoordinateUnits::_radians_`
	)

compute the polar coordinates (R.A., Dec, d_c, redshift) from the comoving (x, y, z), and assuming a cosmological model

Parameters

cosmology	object of class Cosmology
z1	the minimum redshift used in the computation
z2	the maximum redshift used in the computation
outputUnits	the units of the output coordinates

Definition at line 1638 of file Catalogue.cpp.

◆ coordinate()

std::vector<double> cbl::catalogue::Catalogue::coordinate ( const int i ) const

inline

get the X, Y, Z coordinates of the i-th object of the catalogue

Parameters

i	the object index

Returns: vector containing the three coordinates

Definition at line 2258 of file Catalogue.h.

◆ counts_in_cell()

data::ScalarField3D cbl::catalogue::Catalogue::counts_in_cell	(	const double	cell_size,
		const int	interpolation_type = `0`,
		const bool	useMass = `false`,
		const double	minX = `par::defaultDouble`,
		const double	maxX = `par::defaultDouble`,
		const double	minY = `par::defaultDouble`,
		const double	maxY = `par::defaultDouble`,
		const double	minZ = `par::defaultDouble`,
		const double	maxZ = `par::defaultDouble`
	)		const

return the density field from object positions

Parameters

cell_size	the minimum size of the density field
interpolation_type	the type of interpolation false → nearest-grid-point; true → cloud-in-cell
useMass	generate the density field using the mass information
minX	minimum value of the x coordinate
maxX	maximum value of the x coordinate
minY	minimum value of the y coordinate
maxY	maximum value of the y coordinate
minZ	minimum value of the z coordinate
maxZ	maximum value of the z coordinate

Returns: the density field

Definition at line 2266 of file Catalogue.cpp.

◆ dc()

double cbl::catalogue::Catalogue::dc ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_dc

Parameters

i	the object index

Returns: the comoving distance of the i-th object

Definition at line 1849 of file Catalogue.h.

◆ dec()

double cbl::catalogue::Catalogue::dec ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_dec

Parameters

i	the object index

Returns: the Declination of the i-th object

Definition at line 1863 of file Catalogue.h.

◆ dec_tile()

double cbl::catalogue::Catalogue::dec_tile ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_dec_tile

Parameters

i	the object index

Returns: the Declination of the i-th object

Definition at line 1877 of file Catalogue.h.

◆ density_field()

data::ScalarField3D cbl::catalogue::Catalogue::density_field	(	const double	cell_size,
		const Catalogue	mask_catalogue,
		const int	interpolation_type = `0`,
		const double	kernel_radius = `0.`,
		const bool	useMass = `false`
	)		const

return the density field from object position

Parameters

cell_size	the minimum size of the density field
mask_catalogue	catalogue containing points sampling the selecion function of the catalogue
interpolation_type	the type of interpolation false → nearest-grid-point; true → cloud-in-cell
kernel_radius	size of the kernel for the gaussian smoothing
useMass	generate the density field using the mass information

Returns: the density field

Definition at line 2341 of file Catalogue.cpp.

◆ densityContrast()

double cbl::catalogue::Catalogue::densityContrast ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_densityContrast

Parameters

i	the object index

Returns: density contrast of the i-th object

Definition at line 2072 of file Catalogue.h.

◆ diluted_catalogue()

Catalogue cbl::catalogue::Catalogue::diluted_catalogue	(	const double	nSub,
		const int	seed = `3213`
	)		const

create a diluted catalogue

Parameters

nSub	the fracton of objects that will be randomly selected (nSub=1 $ \rightarrow $ all objects are selected)
seed	the seed for random number generation

Returns: object of class Catalogue

Definition at line 2076 of file Catalogue.cpp.

◆ distance()

double cbl::catalogue::Catalogue::distance	(	const int	i,
		std::shared_ptr< Object >	obj
	)		const

get the distrance between the i-th object of the catalogue and another object

Parameters

i	the object index
obj	pointer to an object

Returns: distance between the i-th object of the catalogue and the object obj

Definition at line 2103 of file Catalogue.cpp.

◆ equalize_random_box()

void cbl::catalogue::Catalogue::equalize_random_box	(	cbl::catalogue::Catalogue	tracer_catalogue,
		const int	seed
	)

equalize the number of objects in two Box catalogues

Parameters

tracer_catalogue	input catalogue
seed	seed for generating random numbers

Definition at line 694 of file RandomCatalogue.cpp.

◆ equalize_random_lightCone()

void cbl::catalogue::Catalogue::equalize_random_lightCone	(	cbl::catalogue::Catalogue	tracer_catalogue,
		cbl::cosmology::Cosmology	cosm,
		const std::vector< double >	RA_range,
		const std::vector< double >	DEC_range,
		const int	seed
	)

equalize the number of objects in two Light Cones catalogues

Parameters

tracer_catalogue	input catalogue
cosm	the cosmology
RA_range	range of coordinate RA of the catalogue (from -pi/2 to pi/2)
DEC_range	range of coordinate Dec of the catalogue (from 0 to 2pi).
seed	seed for generating random numbers

Definition at line 650 of file RandomCatalogue.cpp.

◆ field() [1/2]

std::vector< std::string > cbl::catalogue::Catalogue::field ( ) const

get the values of the object fields

Returns: the object fields

Definition at line 436 of file Catalogue.cpp.

◆ field() [2/2]

std::string cbl::catalogue::Catalogue::field ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_field

Parameters

i	the object index

Returns: the field where the i-th object has been observed

Definition at line 1961 of file Catalogue.h.

◆ field_list()

std::vector<std::string> cbl::catalogue::Catalogue::field_list ( ) const

inline

get the list of fields where the objects have been observed

Returns: the list of fields

Definition at line 2008 of file Catalogue.h.

◆ galaxyTag()

double cbl::catalogue::Catalogue::galaxyTag ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_galaxyTag

Parameters

i	the object index

Returns: tag of a galaxy

Definition at line 2116 of file Catalogue.h.

◆ generic()

double cbl::catalogue::Catalogue::generic ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_generic

Parameters

i	the object index

Returns: generic properties of the i-th object

Definition at line 2137 of file Catalogue.h.

◆ ID()

int cbl::catalogue::Catalogue::ID ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_ID

Parameters

i	the object index

Returns: ID of the i-th object

Definition at line 2086 of file Catalogue.h.

◆ IDHost()

int cbl::catalogue::Catalogue::IDHost ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_IDHost

Parameters

i	the object index

Returns: ID of the Host halo i-th object

Definition at line 2109 of file Catalogue.h.

◆ isSetVar() [1/2]

bool cbl::catalogue::Catalogue::isSetVar	(	const int	index,
		const Var	var_name
	)		const

check if the given variable of the i-th object is set

Parameters

index	the index of the object
var_name	the variable name

Returns: if the variable is set $ \rightarrow $ true; else $ \rightarrow $ false

Definition at line 740 of file Catalogue.cpp.

◆ isSetVar() [2/2]

bool cbl::catalogue::Catalogue::isSetVar ( const Var var_name ) const

check if the given object variables are set

Parameters

var_name the variable name

Returns: if the given variables are set $ \rightarrow $ true; else $ \rightarrow $ false

Definition at line 918 of file Catalogue.cpp.

◆ lensingCalib()

double cbl::catalogue::Catalogue::lensingCalib ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_lensingCalib

Parameters

i	the object index

Returns: the lensing calibration factor of the i-th object

Definition at line 1940 of file Catalogue.h.

◆ lensingWeight()

double cbl::catalogue::Catalogue::lensingWeight ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_lensingWeight

Parameters

i	the object index

Returns: the lensing weight of the i-th object

Definition at line 1933 of file Catalogue.h.

◆ m_check_it_in()

void cbl::catalogue::Catalogue::m_check_it_in	(	std::ifstream &	finr,
		const bool	swap
	)

private

Input function to check consistency in reading block-headers in binary GADGET snapshots.

Parameters

finr	a pointer to an input stream class object
swap	true $\rightarrow$ swap endianism, false $\rightarrow$ do not swap endianism

Definition at line 110 of file GadgetCatalogue.cpp.

◆ m_check_it_out()

void cbl::catalogue::Catalogue::m_check_it_out	(	std::ifstream &	finr,
		const bool	swap
	)

private

Ouput function to check consistency in reading block-headers in binary GADGET snapshots.

Parameters

finr	a pointer to an input stream class object
swap	true $\rightarrow$ swap endianism, false $\rightarrow$ do not swap endianism

Definition at line 116 of file GadgetCatalogue.cpp.

◆ m_read_header()

cbl::catalogue::SubFindTab_Header cbl::catalogue::Catalogue::m_read_header	(	std::ifstream &	finh,
		const bool	swap = `false`
	)

private

read the GADGET subfind table header

Parameters

finh	an object of class std::ifstream
swap	whether to swap or not the header

Returns: an object of type SubFindTab_Header

Definition at line 40 of file GadgetCatalogue.cpp.

◆ m_swap_header() [1/2]

cbl::catalogue::Gadget_Header cbl::catalogue::Catalogue::m_swap_header ( Gadget_Header header )

private

swap endianism of the GADGET snapshot header

Parameters

header the un-swapped header

Returns: an object of type Gadget_Header

Definition at line 67 of file GadgetCatalogue.cpp.

◆ m_swap_header() [2/2]

cbl::catalogue::SubFindTab_Header cbl::catalogue::Catalogue::m_swap_header ( SubFindTab_Header header )

private

swap endianism of the GADGET subfind table header

Parameters

header the un-swapped header

Returns: an object of type SubFindTab_Header

Definition at line 94 of file GadgetCatalogue.cpp.

◆ magnitude()

double cbl::catalogue::Catalogue::magnitude ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_magnitude

Parameters

i	the object index

Returns: the magnitude of the i-th object

Definition at line 2030 of file Catalogue.h.

◆ magnitudeG()

double cbl::catalogue::Catalogue::magnitudeG ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_magnitudeG

Parameters

i	the object index

Returns: the g-band magnitude of the i-th object

Definition at line 2044 of file Catalogue.h.

◆ magnitudeI()

double cbl::catalogue::Catalogue::magnitudeI ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_magnitudeI

Parameters

i	the object index

Returns: the i-band magnitude of the i-th object

Definition at line 2058 of file Catalogue.h.

◆ magnitudeR()

double cbl::catalogue::Catalogue::magnitudeR ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_magnitudeR

Parameters

i	the object index

Returns: the r-band magnitude of the i-th object

Definition at line 2051 of file Catalogue.h.

◆ magnitudeU()

double cbl::catalogue::Catalogue::magnitudeU ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_magnitudeU

Parameters

i	the object index

Returns: the u-band magnitude of the i-th object

Definition at line 2037 of file Catalogue.h.

◆ mangle_cut()

Catalogue cbl::catalogue::Catalogue::mangle_cut	(	const std::string	mangle_mask,
		const bool	excl = `false`
	)		const

create a sub-catalogue

Parameters

mangle_mask	name of the mangle polygon file
excl	false → create a subcatalogue with objects inside the mask; true → create a subcatalogue outside the mask

Returns: object of class Catalogue

Definition at line 2027 of file Catalogue.cpp.

◆ mass()

double cbl::catalogue::Catalogue::mass ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_mass

Parameters

i	the object index

Returns: the mass of the i-th object

Definition at line 2023 of file Catalogue.h.

◆ mass_proxy()

double cbl::catalogue::Catalogue::mass_proxy ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_mass_proxy

Parameters

i	the object index

Returns: the mass proxy of the i-th object

Definition at line 2094 of file Catalogue.h.

◆ mass_proxy_error()

double cbl::catalogue::Catalogue::mass_proxy_error ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_mass_proxy_error

Parameters

i	the object index

Returns: the mass proxy error of the i-th object

Definition at line 2102 of file Catalogue.h.

◆ massinfall()

double cbl::catalogue::Catalogue::massinfall ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_minfall

Parameters

i	the object index

Returns: the infall mass of the i-th object

Definition at line 2130 of file Catalogue.h.

◆ Max()

double cbl::catalogue::Catalogue::Max ( const Var var_name ) const

inline

get the maximum value of a variable of the catalogue objects

Parameters

var_name the variable name

Returns: the maximum value of the variable

Examples: cleanVoidCatalogue.cpp.

Definition at line 2295 of file Catalogue.h.

◆ Min()

double cbl::catalogue::Catalogue::Min ( const Var var_name ) const

inline

get the minimum value of a variable of the catalogue objects

Parameters

var_name the variable name

Returns: the minimum value of the variable

Definition at line 2287 of file Catalogue.h.

◆ mps()

double cbl::catalogue::Catalogue::mps ( const double boxside = par::defaultDouble ) const

inline

compute the catalogue's mean particle separation

Parameters

boxside length of the side of the box

Returns: mps of the box

Examples: cleanVoidCatalogue.cpp.

Definition at line 2392 of file Catalogue.h.

◆ mps_error()

double cbl::catalogue::Catalogue::mps_error ( const double boxside = par::defaultDouble ) const

inline

compute the catalogue's mean particle separation error

Parameters

boxside length of the side of the box

Returns: error of the mps of the box

Definition at line 2402 of file Catalogue.h.

◆ mstar()

double cbl::catalogue::Catalogue::mstar ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_mstar

Parameters

i	the object index

Returns: the stellar mass of the i-th object

Definition at line 2123 of file Catalogue.h.

◆ nearCells()

std::vector<std::vector<unsigned int> > cbl::catalogue::Catalogue::nearCells ( const int index ) const

inline

get the private member Catalogue::m_object[index]->m_nearCells of ChainMeshCell

Parameters

index the object index

Returns: the matrix of the cells near the i-th object

Definition at line 2177 of file Catalogue.h.

◆ nFields()

size_t cbl::catalogue::Catalogue::nFields ( ) const

inline

get the total number of fields where the objects have been observed

Returns: the total number of fields

Definition at line 2016 of file Catalogue.h.

◆ nObjects()

size_t cbl::catalogue::Catalogue::nObjects ( ) const

inline

get the number of objects of the catalogue

Returns: the number of objects

Examples: catalogue.cpp.

Definition at line 2264 of file Catalogue.h.

◆ nObjects_condition()

int cbl::catalogue::Catalogue::nObjects_condition	(	const Var	var_name,
		const double	down,
		const double	up,
		const bool	excl = `false`
	)

return the number of objectes following a condition on the variable VAR

Parameters

var_name	the variable name
down	minimum variable used to cut the catalogue
up	maximum variable used to cut the catalogue
excl	false → count objects inside down-up; true → count objects outside down-up;

Returns: number of objects following the condition

Definition at line 2229 of file Catalogue.cpp.

◆ nObjects_lightCone()

std::vector<size_t> cbl::catalogue::Catalogue::nObjects_lightCone ( const int nbin ) const

inline

get the number of objects of the catalogue for Light Cones

Parameters

nbin	bins in redshift (number of centres: so, if 100 bins are requested, insert 100)

Returns: the number of objects in each shell

Definition at line 2271 of file Catalogue.h.

◆ normalizeComovingCoordinates()

void cbl::catalogue::Catalogue::normalizeComovingCoordinates ( )

normalize comoving coordinates

function to normalize comoving coordinates, that is it transforms (x, y, z) into (x/dc, y/dc, z/dc))

Definition at line 1684 of file Catalogue.cpp.

◆ nRegions()

size_t cbl::catalogue::Catalogue::nRegions ( )

get the private member m_nRegions

Returns: the total number of regions

Definition at line 396 of file Catalogue.cpp.

◆ numdensity()

double cbl::catalogue::Catalogue::numdensity ( const double boxside = par::defaultDouble ) const

inline

compute the catalogue's number density

Parameters

boxside length of the side of the box

Returns: numdensity of the box

Definition at line 2372 of file Catalogue.h.

◆ numdensity_error()

double cbl::catalogue::Catalogue::numdensity_error ( const double boxside = par::defaultDouble ) const

inline

compute the catalogue's number density error

Parameters

boxside length of the side of the box

Returns: error of the numdensity of the box

Definition at line 2382 of file Catalogue.h.

◆ odds()

double cbl::catalogue::Catalogue::odds ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_odds

Parameters

i	the object index

Returns: the odds of the i-th object

Definition at line 1926 of file Catalogue.h.

◆ operator+=() [1/2]

Catalogue cbl::catalogue::Catalogue::operator+= ( const Catalogue cc )

inline

overloading of the += operator, to sum two catalogues

Parameters

cc	object of class Catalogue

Returns: object of class Catalogue

Definition at line 2864 of file Catalogue.h.

◆ operator+=() [2/2]

Catalogue cbl::catalogue::Catalogue::operator+= ( std::shared_ptr< Catalogue > cc )

inline

overloading of the += operator, to sum two catalogues

Parameters

cc	object of class Catalogue

Returns: object of class Catalogue

Definition at line 2852 of file Catalogue.h.

◆ operator=() [1/2]

Catalogue& cbl::catalogue::Catalogue::operator= ( Catalogue && obj )

inlinenoexcept

move assignment for the Catalogue class

Parameters

obj	catalogue to be moved

Returns: object of type Catalogue

Definition at line 805 of file Catalogue.h.

◆ operator=() [2/2]

Catalogue& cbl::catalogue::Catalogue::operator= ( const Catalogue & obj )

inline

copy assignment for the Catalogue class

Parameters

obj	catalogue to be copied

Returns: object of type Catalogue

Definition at line 786 of file Catalogue.h.

◆ operator[]()

std::shared_ptr<Object> cbl::catalogue::Catalogue::operator[] ( const size_t i ) const

inline

access the i-th Catalogue object

Parameters

i	object index

Returns: reference to Catalogue object

Definition at line 2243 of file Catalogue.h.

◆ Order()

void cbl::catalogue::Catalogue::Order ( const std::vector< int > vv )

order the catalogue according to the input vector

Parameters

vv	vector used to order the catalogue

Definition at line 1710 of file Catalogue.cpp.

◆ part()

std::vector<unsigned int> cbl::catalogue::Catalogue::part ( const int index ) const

inline

get the private member Catalogue::m_object[index]->m_part of ChainMeshCell

Parameters

index the object index

Returns: the vector of particles of the i-th object

Definition at line 2170 of file Catalogue.h.

◆ ra()

double cbl::catalogue::Catalogue::ra ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_ra

Parameters

i	the object index

Returns: the Right Ascension of the i-th object

Definition at line 1856 of file Catalogue.h.

◆ ra_tile()

double cbl::catalogue::Catalogue::ra_tile ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_ra_tile

Parameters

i	the object index

Returns: the Right Ascension of the i-th object

Definition at line 1870 of file Catalogue.h.

◆ radius()

double cbl::catalogue::Catalogue::radius ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_radius

Parameters

i	the object index

Returns: radius of the i-th object

Definition at line 2065 of file Catalogue.h.

◆ redshift()

double cbl::catalogue::Catalogue::redshift ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_redshift

Parameters

i	the object index

Returns: the redshift of the i-th object

Definition at line 1891 of file Catalogue.h.

◆ redshiftMax()

double cbl::catalogue::Catalogue::redshiftMax ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_redshiftMax

Parameters

i	the object index

Returns: the maximum redshift of the i-th object

Definition at line 1905 of file Catalogue.h.

◆ redshiftMin()

double cbl::catalogue::Catalogue::redshiftMin ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_redshiftMin

Parameters

i	the object index

Returns: the minimum redshift of the i-th object

Definition at line 1898 of file Catalogue.h.

◆ region() [1/2]

std::vector< long > cbl::catalogue::Catalogue::region ( ) const

get the values of the object regions

Returns: the object regions

Definition at line 423 of file Catalogue.cpp.

◆ region() [2/2]

long cbl::catalogue::Catalogue::region ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_region

Parameters

i	the object index

Returns: the index of the region of the i-th object

Definition at line 1954 of file Catalogue.h.

◆ region_list()

std::vector< long > cbl::catalogue::Catalogue::region_list ( ) const

get the list of regions in which the catalogue is divided

Returns: the list of regions

Definition at line 411 of file Catalogue.cpp.

◆ remove_object()

void cbl::catalogue::Catalogue::remove_object ( const int index )

inline

remove an existing object

Parameters

index the index of the object to be removed

Definition at line 2699 of file Catalogue.h.

◆ remove_objects()

void cbl::catalogue::Catalogue::remove_objects ( const std::vector< bool > index )

remove a set of existing objects

Parameters

index vector of boolean variables

Definition at line 2494 of file Catalogue.cpp.

◆ replace_objects() [1/2]

void cbl::catalogue::Catalogue::replace_objects ( std::vector< std::shared_ptr< Object > > sample )

inline

replace existing objects with new ones

Parameters

sample vector of pointers to objects of type Object

Definition at line 2683 of file Catalogue.h.

◆ replace_objects() [2/2]

template<typename T >

void cbl::catalogue::Catalogue::replace_objects ( std::vector< T > sample )

inline

replace existing objects with new ones

Parameters

sample vector of objects of type T

Definition at line 2674 of file Catalogue.h.

◆ restoreComovingCoordinates()

void cbl::catalogue::Catalogue::restoreComovingCoordinates ( )

restore comoving coordinates

function to normalize comoving coordinates, that is it transforms (x/dc, y/dc, z/dc)) into (x, y, z)

Definition at line 1697 of file Catalogue.cpp.

◆ sample()

std::vector<std::shared_ptr<Object> > cbl::catalogue::Catalogue::sample ( ) const

inline

get the private member Catalogue::m_object

Returns: the vector containing the objects of the catalogue

Definition at line 1800 of file Catalogue.h.

◆ satellites()

std::vector<std::shared_ptr<Object> > cbl::catalogue::Catalogue::satellites ( const int index ) const

inline

get the private member Catalogue::m_object[ii]->m_satellites

Parameters

index the object index

Returns: the vector of pointers to the satellite objects of the i-th object

Definition at line 2163 of file Catalogue.h.

◆ set_field()

void cbl::catalogue::Catalogue::set_field ( const std::vector< std::string > field )

set a private variable

Parameters

field vector containing the object fields

Definition at line 969 of file Catalogue.cpp.

◆ set_nearCells()

void cbl::catalogue::Catalogue::set_nearCells	(	const int	index,
		const std::vector< std::vector< unsigned int >>	nearCells = `{}`
	)

inline

set the private member ChainMeshCell::m_nearCells

Parameters

index	index of the variable to set
nearCells	the matrix of the cells near the i-th object

Definition at line 2537 of file Catalogue.h.

◆ set_part()

void cbl::catalogue::Catalogue::set_part	(	const int	index,
		const std::vector< unsigned int >	part = `{}`
	)

inline

set the private member ChainMeshCell::m_part

Parameters

index	index of the variable to set
part	the vector of particles of the i-th object

Definition at line 2529 of file Catalogue.h.

◆ set_ra_dec_tile()

void cbl::catalogue::Catalogue::set_ra_dec_tile	(	const std::vector< double >	RA_tile,
		const std::vector< double >	Dec_tile,
		const CoordinateUnits	inputUnits = `CoordinateUnits::_degrees_`
	)

set the central R.A. and Dec of the tiles

Parameters

RA_tile	tile central R.A.
Dec_tile	tile central Dec
inputUnits	input units of R.A. and Dec

Definition at line 957 of file Catalogue.cpp.

◆ set_region()

void cbl::catalogue::Catalogue::set_region	(	const std::vector< long >	region,
		const int	nRegions = `-1`
	)

set a private variable

Parameters

region	vector containing the object regions
nRegions	the total number of regions; if this parameter is $<0$, its value will be set to the size of the region vector

Definition at line 933 of file Catalogue.cpp.

◆ set_region_number()

void cbl::catalogue::Catalogue::set_region_number ( const size_t nRegions )

set the private variable m_nRegion

Parameters

nRegions the total number of regions

Definition at line 944 of file Catalogue.cpp.

◆ set_satellite()

void cbl::catalogue::Catalogue::set_satellite	(	const int	index,
		const std::shared_ptr< Object >	satellite = `{}`
	)

inline

set the private member HostHalo::m_satellites

Parameters

index	index of the variable to set
satellite	the vector of shared pointers to satellite objects

Definition at line 2509 of file Catalogue.h.

◆ set_satellites()

void cbl::catalogue::Catalogue::set_satellites	(	const int	index,
		const std::vector< std::shared_ptr< Object >>	satellites = `{}`
	)

inline

set the private member HostHalo::m_satellites

Parameters

index	index of the variable to set
satellites	the vector of shared pointers to satellite objects

Definition at line 2519 of file Catalogue.h.

◆ set_var() [1/4]

void cbl::catalogue::Catalogue::set_var	(	const int	index,
		const Var	var_name,
		const double	value,
		const cosmology::Cosmology	cosmology = `{}`,
		const bool	update_coordinates = `true`
	)

set a private variable

Parameters

index	index of the variable to set
var_name	name of the variable
value	variable value
cosmology	object of class Cosmology, used to estimate the comoving distance from the given redshift
update_coordinates	if true the function cbl::catalogue::Object::set_redshift update the coordinates according to the redshift value

Definition at line 978 of file Catalogue.cpp.

◆ set_var() [2/4]

void cbl::catalogue::Catalogue::set_var	(	const int	index,
		const Var	var_name,
		const int	value,
		const cosmology::Cosmology	cosmology = `{}`
	)

set a private variable

Parameters

index	index of the variable to set
var_name	name of the variable
value	variable value
cosmology	object of class Cosmology

Definition at line 1204 of file Catalogue.cpp.

◆ set_var() [3/4]

void cbl::catalogue::Catalogue::set_var	(	const Var	var_name,
		const std::vector< double >	var,
		const cosmology::Cosmology	cosmology = `{}`,
		const bool	update_coordinates = `true`
	)

set a private variable

Parameters

var_name	name of the variable
var	vector of variables
cosmology	object of class Cosmology, used to estimate the comoving distance from the given redshift
update_coordinates	if true the function cbl::catalogue::Object::set_redshift update the coordinates according to the redshift value

Definition at line 1246 of file Catalogue.cpp.

◆ set_var() [4/4]

void cbl::catalogue::Catalogue::set_var	(	const Var	var_name,
		const std::vector< int >	var,
		const cosmology::Cosmology	cosmology = `{}`
	)

set a private variable

Parameters

var_name	name of the variable
var	vector of variables
cosmology	object of class Cosmology

Definition at line 1477 of file Catalogue.cpp.

◆ shear1()

double cbl::catalogue::Catalogue::shear1 ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_shear1

Parameters

i	the object index

Returns: the first shear component of the i-th object

Definition at line 1912 of file Catalogue.h.

◆ shear2()

double cbl::catalogue::Catalogue::shear2 ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_shear2

Parameters

i	the object index

Returns: the second shear component of the i-th object

Definition at line 1919 of file Catalogue.h.

◆ shuffle()

void cbl::catalogue::Catalogue::shuffle ( const int seed )

shuffle objects in the catalogue

Parameters

seed	the seed for random number generation

pseudo-random numbers generator

Definition at line 2556 of file Catalogue.cpp.

◆ smooth()

shared_ptr< Catalogue > cbl::catalogue::Catalogue::smooth	(	const double	gridsize,
		const cosmology::Cosmology	cosmology,
		const std::vector< Var >	vars = `{}`,
		const int	SUB = `1`
	)

create a smoothed version of the catalogue averaging quantities on a X, Y, Z grid

defalut averaged quantities are X, Y, Z, RA, DEC, REDSHIFT, WEIGHT; others quantities must be passed trough a vector

Parameters

gridsize	the cell size
cosmology	object of class Cosmology, used to estimate the comoving distance from the given redshift
vars	the vector of variable to average on
SUB	the number of sub-catalogue used to create the chain-mesh (use SUB>1 when there could be memory problems)

Returns: pointer to an object of class Catalogue

Definition at line 2125 of file Catalogue.cpp.

◆ sn()

double cbl::catalogue::Catalogue::sn ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_sn

Parameters

i	the object index

Returns: the signal-to-noise ratio of the i-th object

Definition at line 1884 of file Catalogue.h.

◆ sort()

void cbl::catalogue::Catalogue::sort	(	const Var	var_name,
		const bool	increasing = `false`
	)

bubble sort of a catalogue wrt a variable

Parameters

var_name	the name of the variable to use in order to sort the catalogue
increasing	if true order from lower to higher, if false from higher to lower

Definition at line 2521 of file Catalogue.cpp.

◆ stats_var() [1/2]

std::vector< std::vector< double > > cbl::catalogue::Catalogue::stats_var ( const std::vector< Var > var_name ) const

get the mean, the median, the standard deviation, and the difference between the third and first quartiles of a vector of variables

Parameters

var_name the variable name

Returns: vector of vectors containing the mean, the median, the standard deviation and the difference between the third and first quartiles of the input vector of variables

Definition at line 1530 of file Catalogue.cpp.

◆ stats_var() [2/2]

std::vector< double > cbl::catalogue::Catalogue::stats_var ( const Var var_name ) const

get the mean, the median, the standard deviation, and the difference between the third and first quartiles of a variable

Parameters

var_name the variable name

Returns: vector containing the mean, the median, the standard deviation and the difference between the third and first quartiles of the variable

Definition at line 1521 of file Catalogue.cpp.

◆ sub_catalogue() [1/4]

Catalogue cbl::catalogue::Catalogue::sub_catalogue	(	catalogue::Catalogue &	data,
		const double	tile_width_RA,
		const double	tile_width_Dec,
		const bool	write_tiles = `false`,
		const std::string	dir_tiles = `"./"`,
		const std::string	file_tiles = `"tiles_coordinates.txt"`
	)

find the Catalogue objects falling in the tiles of an input data catalogue, given the R.A.-Dec centres of the tiles.

The user must set in the input data catalogue the identification number of the tiles (cbl::catalogue::Var::_Region_) with cbl::catalogue::Catalogue::set_region() and the central R.A. and Dec (cbl::catalogue::Var::_TileRA_ / _TileDec_) of the tiles with cbl::catalogue::Catalogue::set_ra_dec_tile().

If requested, this function writes on file the coordinates of the edges of the tiles (in degrees). The tiles can be easily plotted with the plot function of matplotlib, e.g.:

import matplotlib.pyplot as plt
 
fig, ax = plt.subplots() 
 
for i in range(len(ra_min)):
  ax.plot([ra_min[i],ra_min[i]], [dec_min[i],dec_max[i]], color="k")
  ax.plot([ra_max[i],ra_max[i]], [dec_min[i],dec_max[i]], color="k")
  
  if (ra_min[i] < ra_max[i]):
    ax.plot([ra_min[i],ra_max[i]], [dec_min[i],dec_min[i]], color="k")
    ax.plot([ra_min[i],ra_max[i]], [dec_max[i],dec_max[i]], color="k")
  else:
    ax.plot([ra_max[i],0], [dec_min[i],dec_min[i]], color="k")
    ax.plot([ra_max[i],0], [dec_max[i],dec_max[i]], color="k")
    ax.plot([360,ra_min[i]], [dec_min[i],dec_min[i]], color="k")
    ax.plot([360,ra_min[i]], [dec_max[i],dec_max[i]], color="k")

Author: Giorgio Lesci (giorg.nosp@m.io.l.nosp@m.esci2.nosp@m.@uni.nosp@m.bo.it)

Parameters

data	input catalogue
tile_width_RA	the width of each tile, in degrees (from side to side), along R.A. direction
tile_width_Dec	the width of each tile, in degrees (from side to side), along Dec direction
write_tiles	if true, write RA and Dec edges of the tiles on file (in degrees)
dir_tiles	directory of the tile edges file
file_tiles	tile edges file

Returns: object of class Catalogue

Warning: This function cannot manage the situations in which a tile crosses one of the poles, i.e. if it has a side after the pole and the opposite side in the other side.

Definition at line 1913 of file Catalogue.cpp.

◆ sub_catalogue() [2/4]

Catalogue cbl::catalogue::Catalogue::sub_catalogue	(	const mask_function	mask,
		const bool	excl = `false`
	)		const

create a sub-catalogue

Parameters

mask	function of type std::function<bool(shared_ptr<Object>)> to flag objects
excl	false → create a subcatalogue inside down-up; true → create a subcatalogue outside down-up

Returns: object of class Catalogue

Definition at line 1848 of file Catalogue.cpp.

◆ sub_catalogue() [3/4]

Catalogue cbl::catalogue::Catalogue::sub_catalogue	(	const MaskObject &	mask,
		const bool	excl = `false`
	)		const

create a sub-catalogue

Parameters

mask	object of type cbl::catalogue::MaskObject
excl	false → create a subcatalogue inside down-up; true → create a subcatalogue outside down-up

Returns: object of class Catalogue

Definition at line 1869 of file Catalogue.cpp.

◆ sub_catalogue() [4/4]

Catalogue cbl::catalogue::Catalogue::sub_catalogue	(	const Var	var_name,
		const double	down,
		const double	up,
		const bool	excl = `false`
	)		const

create a sub-catalogue

Parameters

var_name	the variable name
down	minimum variable used to cut the catalogue
up	maximum variable used to cut the catalogue
excl	false → create a subcatalogue inside down-up; true → create a subcatalogue outside down-up

Returns: object of class Catalogue

Examples: catalogue.cpp.

Definition at line 1890 of file Catalogue.cpp.

◆ swap_objects()

void cbl::catalogue::Catalogue::swap_objects	(	const int	ind1,
		const int	ind2
	)

swap two existing objects

Parameters

ind1	the index of the first object to swap
ind2	the index of the second object to swap

Definition at line 2510 of file Catalogue.cpp.

◆ tot_mass()

double cbl::catalogue::Catalogue::tot_mass ( const int i ) const

inline

get the private member Catalogue::m_object[ii]->m_tot_mass

Parameters

i	the object index

Returns: the total mass of the i-th object (sum over all contributions)

Definition at line 2144 of file Catalogue.h.

◆ var() [1/2]

double cbl::catalogue::Catalogue::var	(	const int	index,
		const Var	var_name
	)		const

get the value of the i-th object variable

Parameters

index	the index of the object
var_name	the variable name

Returns: i-th variable Var

Examples: cleanVoidCatalogue.cpp.

Definition at line 449 of file Catalogue.cpp.

◆ var() [2/2]

std::vector< double > cbl::catalogue::Catalogue::var ( const Var var_name ) const

get the values of the object variables

Parameters

var_name the variable name

Returns: the vector of the variable Var

Definition at line 727 of file Catalogue.cpp.

◆ var_distr()

void cbl::catalogue::Catalogue::var_distr	(	const Var	var_name,
		std::vector< double > &	_var,
		std::vector< double > &	dist,
		std::vector< double > &	err,
		const int	nbin,
		const bool	linear = `true`,
		const std::string	file_out = `par::defaultString`,
		const double	Volume = `1.`,
		const bool	norm = `false`,
		const double	V1 = `par::defaultDouble`,
		const double	V2 = `par::defaultDouble`,
		const std::string	bin_type = `"Linear"`,
		const bool	convolution = `false`,
		const double	sigma = `0.`
	)		const

get the distribution of a variable

Parameters

[in]	var_name	the variable name
[out]	_var	vector of variables
[out]	dist	vector of values of f(varibles)
[out]	err	vector of Poissonian errors of f(varibles)
[in]	nbin	number of bins
[in]	linear	true → linear binning; false → logarithmic binning
[in]	file_out	the output file where the distribution is stored
[in]	Volume	the volume of the catalogue
[in]	norm	true → normalize to the number of objects; false → do not normalize
[in]	V1	the minimum limit of the distribution
[in]	V2	the maximum limit of the distribution
[in]	bin_type	"Linear" → dn/dvar; "Log10" → dn/dlog(var); "Log" → dn/dln(var)
[in]	convolution	false → don't convolve the distribution; true → convolve the distribution with a gaussian function
[in]	sigma	σ: the standard deviation of the gaussian function used to convolve the distribution

Definition at line 1544 of file Catalogue.cpp.

◆ var_int() [1/2]

int cbl::catalogue::Catalogue::var_int	(	const int	index,
		const Var	var_name
	)		const

get the value of the i-th object integer variable

Parameters

index	the index of the object
var_name	the variable name

Returns: i-th variable Var

Definition at line 697 of file Catalogue.cpp.

◆ var_int() [2/2]

std::vector< int > cbl::catalogue::Catalogue::var_int ( const Var var_name ) const

get the values of the object integer variables

Parameters

var_name the variable name

Returns: the vector of the variable Var

Definition at line 716 of file Catalogue.cpp.

◆ volume()

double cbl::catalogue::Catalogue::volume ( const double boxside = par::defaultDouble ) const

inline

compute the catalogue's comoving volume

Parameters

boxside length of the side of the box

Returns: volume of the box

Definition at line 2359 of file Catalogue.h.

◆ vx()

double cbl::catalogue::Catalogue::vx ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_vx

Parameters

i	the object index

Returns: the velocity along the x direction of the i-th object

Definition at line 1828 of file Catalogue.h.

◆ vy()

double cbl::catalogue::Catalogue::vy ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_vy

Parameters

i	the object index

Returns: the velocity along the y direction of the i-th object

Definition at line 1835 of file Catalogue.h.

◆ vz()

double cbl::catalogue::Catalogue::vz ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_vz

Parameters

i	the object index

Returns: the velocity along the z direction of the i-th object

Definition at line 1842 of file Catalogue.h.

◆ weight()

double cbl::catalogue::Catalogue::weight ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_weight

Parameters

i	the object index

Returns: the weight of the i-th object

Definition at line 1947 of file Catalogue.h.

◆ weightedN()

double cbl::catalogue::Catalogue::weightedN ( ) const

get the total weight of the objects of the catalogue

Returns: the total weight

Definition at line 1753 of file Catalogue.cpp.

◆ weightedN_condition()

double cbl::catalogue::Catalogue::weightedN_condition	(	const Var	var_name,
		const double	down,
		const double	up,
		const bool	excl = `false`
	)

return the weighted number of objectes following a condition on the variable VAR

Parameters

var_name	the variable name
down	minimum variable used to cut the catalogue
up	maximum variable used to cut the catalogue
excl	false → count objects inside down-up; true → count objects outside down-up;

Returns: weighted number of objects following the condition

Definition at line 2248 of file Catalogue.cpp.

◆ write_comoving_coordinates()

void cbl::catalogue::Catalogue::write_comoving_coordinates ( const std::string outputFile ) const

write the comoving coordinates of the catalogue to an output file

Parameters

outputFile the name of the output file

Definition at line 1765 of file Catalogue.cpp.

◆ write_data()

void cbl::catalogue::Catalogue::write_data	(	const std::string	outputFile,
		const std::vector< Var >	var_name = `{}`,
		const std::string	sep = `" "`,
		const std::string	header = `""`
	)		const

write both the comoving and polar coordinates, and the regions (if present) of the catalogue to an output file

Parameters

outputFile	the name of the output file
var_name	vector containing the variable names to be written
sep	[optional parameter] specifies the file separator, default is " " for retrocompatibility. Is strongly raccomanded to use standard values like: "\t" or ",".
header	[optional parameter] string with the header of the file. Default is "".

Examples: cleanVoidCatalogue.cpp.

Definition at line 1804 of file Catalogue.cpp.

◆ write_obs_coordinates()

void cbl::catalogue::Catalogue::write_obs_coordinates ( const std::string outputFile ) const

write the polar coordinates of the catalogue to an output file

Parameters

outputFile the name of the output file

Definition at line 1783 of file Catalogue.cpp.

◆ x_displacement()

double cbl::catalogue::Catalogue::x_displacement ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_x_displacement

Parameters

i	the object index

Returns: the displacement of the i-th object along the x-axis

Definition at line 1969 of file Catalogue.h.

◆ xx()

double cbl::catalogue::Catalogue::xx ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_xx

Parameters

i	the object index

Returns: the coordinate x of the i-th object

Definition at line 1807 of file Catalogue.h.

◆ y_displacement()

double cbl::catalogue::Catalogue::y_displacement ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_y_displacement

Parameters

i	the object index

Returns: the displacement of the i-th object along the x-axis

Definition at line 1977 of file Catalogue.h.

◆ yy()

double cbl::catalogue::Catalogue::yy ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_yy

Parameters

i	the object index

Returns: the coordinate y of the i-th object

Definition at line 1814 of file Catalogue.h.

◆ z_bins()

std::vector<double> cbl::catalogue::Catalogue::z_bins ( const int nbin ) const

inline

get the catalogue's redshift bins

Parameters

nbin	number of bins on which to fit the redshift

Returns: private variable z_bins

Definition at line 2412 of file Catalogue.h.

◆ z_displacement()

double cbl::catalogue::Catalogue::z_displacement ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_z_displacement

Parameters

i	the object index

Returns: the displacement of the i-th object along the x-axis

Definition at line 1985 of file Catalogue.h.

◆ zz()

double cbl::catalogue::Catalogue::zz ( const int i ) const

inline

get the private member Catalogue::m_object[i]->m_zz

Parameters

i	the object index

Returns: the coordinate z of the i-th object

Definition at line 1821 of file Catalogue.h.

The documentation for this class was generated from the following files:

Headers/Catalogue.h
Catalogue/Catalogue.cpp
Catalogue/FITSCatalogue.cpp
Catalogue/GadgetCatalogue.cpp
Catalogue/HODCatalogue.cpp
Catalogue/RandomCatalogue.cpp
Catalogue/VoidCatalogue.cpp

Public Member Functions

Private Attributes

private variables and functions used to read catalogues from standard GADGET files

Detailed Description

Constructor & Destructor Documentation

◆ Catalogue() [1/26]

◆ Catalogue() [2/26]

◆ Catalogue() [3/26]

◆ Catalogue() [4/26]

◆ Catalogue() [5/26]

◆ Catalogue() [6/26]

◆ Catalogue() [7/26]

◆ Catalogue() [8/26]

◆ Catalogue() [9/26]

◆ Catalogue() [10/26]

◆ Catalogue() [11/26]

◆ Catalogue() [12/26]

◆ Catalogue() [13/26]

◆ Catalogue() [14/26]

◆ Catalogue() [15/26]

◆ Catalogue() [16/26]

◆ Catalogue() [17/26]

◆ Catalogue() [18/26]

◆ Catalogue() [19/26]

◆ Catalogue() [20/26]

◆ Catalogue() [21/26]

◆ Catalogue() [22/26]

◆ Catalogue() [23/26]

◆ Catalogue() [24/26]

◆ Catalogue() [25/26]

◆ Catalogue() [26/26]

Member Function Documentation

◆ add_object() [1/2]

◆ add_object() [2/2]

◆ add_objects() [1/2]

◆ add_objects() [2/2]

◆ angsep_xyz()

◆ catalogue_object() [1/2]

◆ catalogue_object() [2/2]

◆ centralDensity()

◆ clean_void_catalogue() [1/3]

◆ clean_void_catalogue() [2/3]

◆ clean_void_catalogue() [3/3]

◆ compute_catalogueProperties_box()

◆ compute_catalogueProperties_lightCone()

◆ compute_centralDensity() [1/3]

◆ compute_centralDensity() [2/3]

◆ compute_centralDensity() [3/3]

◆ compute_densityContrast()

◆ computeComovingCoordinates()

◆ computePolarCoordinates() [1/2]

◆ computePolarCoordinates() [2/2]

◆ coordinate()

◆ counts_in_cell()

◆ dc()

◆ dec()

◆ dec_tile()

◆ density_field()

◆ densityContrast()

◆ diluted_catalogue()

◆ distance()

◆ equalize_random_box()

◆ equalize_random_lightCone()

◆ field() [1/2]

◆ field() [2/2]

◆ field_list()

◆ galaxyTag()

◆ generic()

◆ ID()

◆ IDHost()

◆ isSetVar() [1/2]

◆ isSetVar() [2/2]

◆ lensingCalib()

◆ lensingWeight()

◆ m_check_it_in()

◆ m_check_it_out()

◆ m_read_header()

◆ m_swap_header() [1/2]

◆ m_swap_header() [2/2]

◆ magnitude()