Source code for halotools.mock_observables.ia_correlations.ii_minus_3d

r"""
Module containing the `~halotools.mock_observables.alignments.ii_minus_3d` function used to
calculate the intrinsic ellipticity-ellipticity (II) correlation
"""

from __future__ import absolute_import, division, print_function, unicode_literals

import numpy as np
from math import pi, gamma

from .alignment_helpers import process_3d_alignment_args
from ..mock_observables_helpers import (enforce_sample_has_correct_shape,
    get_separation_bins_array, get_line_of_sight_bins_array, get_period, get_num_threads)
from ..pair_counters.mesh_helpers import _enforce_maximum_search_length
from ..pair_counters import positional_marked_npairs_3d, marked_npairs_3d

__all__ = ['ii_plus_3d']
__author__ = ['Duncan Campbell']


np.seterr(divide='ignore', invalid='ignore')  # ignore divide by zero in e.g. DD/RR


[docs] def ii_minus_3d(sample1, orientations1, ellipticities1, sample2, orientations2, ellipticities2, rbins, randoms1=None, randoms2=None, weights1=None, weights2=None, ran_weights1=None, ran_weights2=None, estimator='Natural', period=None, num_threads=1, approx_cell1_size=None, approx_cell2_size=None): r""" Calculate the intrinsic ellipticity-ellipticity correlation function (II), :math:`\xi_{--}(r)`. See the 'Notes' section for details of this calculation. Parameters ---------- sample1 : array_like Npts1 x 3 numpy array containing 3-D positions of points with associated orientations and ellipticities. See the :ref:`mock_obs_pos_formatting` documentation page, or the Examples section below, for instructions on how to transform your coordinate position arrays into the format accepted by the ``sample1`` and ``sample2`` arguments. Length units are comoving and assumed to be in Mpc/h, here and throughout Halotools. orientations1 : array_like Npts1 x 3 numpy array containing projected orientation vectors for each point in ``sample1``. these will be normalized if not already. ellipticities1: array_like Npts1 x 1 numpy array containing ellipticities for each point in ``sample1``. sample2 : array_like, optional Npts2 x 3 array containing 3-D positions of points with associated orientations and ellipticities. orientations2 : array_like Npts1 x 3 numpy array containing projected orientation vectors for each point in ``sample2``. these will be normalized if not already. ellipticities2: array_like Npts1 x 1 numpy array containing ellipticities for each point in ``sample2``. rbins : array_like array of boundaries defining the radial bins in which pairs are counted. Length units are comoving and assumed to be in Mpc/h, here and throughout Halotools. randoms1 : array_like, optional Nran1 x 3 array containing 3-D positions of randomly distributed points corresponding to ``sample1``. If no randoms are provided (the default option), the calculation can proceed using analytical randoms (only valid for periodic boundary conditions). randoms2 : array_like, optional Nran2 x 3 array containing 3-D positions of randomly distributed points corresponding to ``sample2``. If no randoms are provided (the default option), the calculation can proceed using analytical randoms (only valid for periodic boundary conditions). weights1 : array_like, optional Npts1 array of weghts. If this parameter is not specified, it is set to numpy.ones(Npts1). weights2 : array_like, optional Npts2 array of weghts. If this parameter is not specified, it is set to numpy.ones(Npts2). ran_weights1 : array_like, optional Npran1 array of weghts. If this parameter is not specified, it is set to numpy.ones(Nran1). ran_weights2 : array_like, optional Nran2 array of weghts. If this parameter is not specified, it is set to numpy.ones(Nran2). estimator : string, optional string indicating which estimator to use period : array_like, optional Length-3 sequence defining the periodic boundary conditions in each dimension. If you instead provide a single scalar, Lbox, period is assumed to be the same in all Cartesian directions. If set to None (the default option), PBCs are set to infinity, in which case ``randoms`` must be provided. Length units are comoving and assumed to be in Mpc/h, here and throughout Halotools. num_threads : int, optional Number of threads to use in calculation, where parallelization is performed using the python ``multiprocessing`` module. Default is 1 for a purely serial calculation, in which case a multiprocessing Pool object will never be instantiated. A string 'max' may be used to indicate that the pair counters should use all available cores on the machine. approx_cell1_size : array_like, optional Length-3 array serving as a guess for the optimal manner by how points will be apportioned into subvolumes of the simulation box. The optimum choice unavoidably depends on the specs of your machine. Default choice is to use Lbox/10 in each dimension, which will return reasonable result performance for most use-cases. Performance can vary sensitively with this parameter, so it is highly recommended that you experiment with this parameter when carrying out performance-critical calculations. approx_cell2_size : array_like, optional Analogous to ``approx_cell1_size``, but for sample2. See comments for ``approx_cell1_size`` for details. Returns ------- correlation_function : numpy.array *len(rbins)-1* length array containing the correlation function :math:`w_{g+}(r)` computed in each of the bins defined by input ``rbins``. Notes ----- The II-correlation function is calculated as: .. math:: \xi_{--}(r) = \frac{S_{-}S_{-}}{R_sR_s} where .. math:: S_{-}S_{-} = \sum_{i \neq j} w_jw_i e_{-}(j|i)e_{-}(i|j) :math:`w_j` and :math:`w_j` are weights. Weights are set to 1 for all galaxies by default. The alingment of the :math:`j`-th galaxy relative to the direction to the :math:`i`-th galaxy is given by: .. math:: e_{-}(j|i) = e_j\sin(2\phi) where :math:`e_j` is the ellipticity of the :math:`j`-th galaxy. :math:`\phi` is the angle between the orientation vector, :math:`\vec{o}_j`, and the direction between the :math:`j`-th and :math:`i`-th galaxy, :math:`\vec{r}_{i,j}`. .. math:: \cos(\phi) = \vec{o}_j \cdot \vec{r}_{i,j} :math:`R_sR_s` are random pair counts, Examples -------- For demonstration purposes we create a randomly distributed set of points within a periodic cube of Lbox = 250 Mpc/h. >>> Npts = 1000 >>> Lbox = 250 >>> x = np.random.uniform(0, Lbox, Npts) >>> y = np.random.uniform(0, Lbox, Npts) >>> z = np.random.uniform(0, Lbox, Npts) We transform our *x, y, z* points into the array shape used by the pair-counter by taking the transpose of the result of `numpy.vstack`. This boilerplate transformation is used throughout the `~halotools.mock_observables` sub-package: >>> sample1 = np.vstack((x,y,z)).T Alternatively, you may use the `~halotools.mock_observables.return_xyz_formatted_array` convenience function for this same purpose, which provides additional wrapper behavior around `numpy.vstack` such as placing points into redshift-space. We then create a set of random orientation vectors and ellipticities for each point >>> random_orientations = np.random.random((Npts,3)) >>> random_ellipticities = np.random.random(Npts) We can the calculate the projected auto-GI correlation between these points: >>> rbins = np.logspace(-1,1,10) >>> w = ii_minus_3d(sample1, random_orientations, random_ellipticities, sample1, random_orientations, random_ellipticities, rbins, period=Lbox) """ # process arguments alignment_args = (sample1, orientations1, ellipticities1, weights1, sample2, orientations2, ellipticities2, weights2, randoms1, ran_weights1, randoms2, ran_weights2) sample1, orientations1, ellipticities1, weights1, sample2,\ orientations2, ellipticities2, weights2, randoms1, ran_weights1,\ randoms2, ran_weights2 = process_3d_alignment_args(*alignment_args) function_args = (sample1, rbins, sample2, randoms1, randoms2, period, num_threads, approx_cell1_size, approx_cell2_size) sample1, rbins, sample2, randoms1, randoms2,\ period, num_threads, PBCs, no_randoms = _ii_minus_3d_process_args(*function_args) # How many points are there (for normalization purposes)? N1 = len(sample1) N2 = len(sample2) if no_randoms: # set random density the the same as the sampels NR1 = N1 NR2 = N2 else: NR1 = len(randoms1) NR2 = len(randoms2) #define merk vectors to use in pair counting # sample 1 marks1 = np.ones((N1, 4)) marks1[:, 0] = ellipticities1 * weights1 marks1[:, 1] = orientations1[:, 0] marks1[:, 2] = orientations1[:, 1] marks1[:, 3] = orientations1[:, 2] # sample 2 marks2 = np.ones((N2, 4)) marks2[:, 0] = ellipticities2 * weights2 marks2[:, 1] = orientations2[:, 0] marks2[:, 2] = orientations2[:, 1] marks2[:, 3] = orientations2[:, 2] # randoms 1 ran_marks1 = np.ones((NR1, 4)) ran_marks1[:, 0] = ran_weights1 ran_marks1[:, 1] = 0 # dummy ran_marks1[:, 2] = 0 # dummy ran_marks1[:, 3] = 0 # dummy # randoms 2 ran_marks2 = np.ones((NR2, 4)) ran_marks2[:, 0] = ran_weights2 ran_marks2[:, 1] = 0 # dummy ran_marks2[:, 2] = 0 # dummy ran_marks2[:, 3] = 0 # dummy do_SS, do_RR = II_estimator_requirements(estimator) # count marked pairs if do_SS: SS = marked_pair_counts(sample1, sample2, marks1, marks2, rbins, period, num_threads, approx_cell1_size, approx_cell2_size) else: SS = None # count random pairs if do_RR: RR = random_counts(randoms1, randoms2, ran_weights1, ran_weights2, rbins, N1, N2, no_randoms, period, PBCs, num_threads, approx_cell1_size, approx_cell2_size) else: RR = None result = II_estimator(SS, RR, N1, N2, NR1, NR2, estimator) return result # factor of 2pi_max accounts for integration
def II_estimator(SS, RR, N1, N2, NR1, NR2, estimator='Natural'): r""" apply the supplied GI estimator to calculate the correlation function. """ if estimator == 'Natural': factor = (NR1*NR2)/(N1*N2) return factor*(SS/RR) else: msg = ('The estimator provided is not supported.') raise ValueError(msg) def II_estimator_requirements(estimator): r""" Return the requirments for the supplied GI estimator. """ do_RR = False do_SS = False if estimator == 'Natural': do_SS = True do_RR = True return do_SS, do_RR else: msg = ('The estimator provided is not supported.') raise ValueError(msg) def marked_pair_counts(sample1, sample2, weights1, weights2, rbins, period, num_threads, approx_cell1_size, approx_cell2_size): r""" Count marked pairs. """ weight_func_id = 6 SS = positional_marked_npairs_3d(sample1, sample2, rbins, period=period, weights1=weights1, weights2=weights2, weight_func_id=weight_func_id, num_threads=num_threads, approx_cell1_size=approx_cell1_size, approx_cell2_size=approx_cell1_size)[0] SS = np.diff(SS, axis=0) return SS def random_counts(randoms1, randoms2, ran_weights1, ran_weights2, rbins, N1, N2, no_randoms, period, PBCs, num_threads, approx_cell1_size, approx_cell2_size): r""" Count random pairs. """ if no_randoms is False: RR = marked_npairs_3d(randoms1, randoms2, rbins, period=period, num_threads=num_threads, weight_func_id=1, weights1=ran_weights1, weights2=ran_weights2, approx_cell1_size=approx_cell1_size, approx_cell2_size=approx_cell2_size) RR = np.diff(RR, axis=0) return RR else: # set 'number' or randoms # setting Nran to Ndata makes normalization simple NR1 = N1 NR2 = N2 # do volume calculations v = nball_volume(rbins) dv = np.diff(v, axis=0) global_volume = period.prod() # calculate the random-random pairs. rhor = (NR1*NR2)/global_volume RR = (dv*rhor) return RR.flatten() def nball_volume(R, k=3): """ Calculate the volume of a n-shpere. This is used for the analytical randoms. """ return (np.pi**(k/2.0)/gamma(k/2.0+1.0))*R**k def _ii_minus_3d_process_args(sample1, rbins, sample2, randoms1, randoms2, period, num_threads, approx_cell1_size, approx_cell2_size): r""" Private method to do bounds-checking on the arguments passed to `~halotools.mock_observables.alignments.alignments.ii_plus_projected`. """ sample1 = enforce_sample_has_correct_shape(sample1) if randoms1 is not None: randoms1 = np.atleast_1d(randoms1) no_randoms1 = False else: no_randoms1 = True if randoms2 is not None: randoms2 = np.atleast_1d(randoms2) no_randoms2 = False else: no_randoms2 = True #if one of the randoms is missing, raise an error no_randoms = True if no_randoms1: if no_randoms2 is False: msg = "if one set of randoms is provided, both randoms must be provided.\n" raise ValueError(msg) elif no_randoms2: if no_randoms1 is False: msg = "if one set of randoms is provided, both randoms must be provided.\n" raise ValueError(msg) else: no_randoms = False rbins = get_separation_bins_array(rbins) rmax = np.amax(rbins) period, PBCs = get_period(period) _enforce_maximum_search_length([rmax, rmax, rmax], period) if (randoms1 is None) & (PBCs is False): msg = "If no PBCs are specified, both randoms must be provided.\n" raise ValueError(msg) num_threads = get_num_threads(num_threads) return sample1, rbins, sample2, randoms1, randoms2, period, num_threads, PBCs, no_randoms