Source code for treecorr.ntcorrelation

# Copyright (c) 2003-2024 by Mike Jarvis
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"""
.. module:: ngcorrelation
"""

import numpy as np

from . import _treecorr
from .catalog import calculateVarT
from .nzcorrelation import BaseNZCorrelation
from .util import make_writer, make_reader
from .config import make_minimal_config


[docs]class NTCorrelation(BaseNZCorrelation): r"""This class handles the calculation and storage of a 2-point count-trefoil correlation function, where a trefoil is any field with spin-3 rotational properties. Ojects of this class holds the following attributes: Attributes: nbins: The number of bins in logr bin_size: The size of the bins in logr min_sep: The minimum separation being considered max_sep: The maximum separation being considered In addition, the following attributes are numpy arrays of length (nbins): Attributes: logr: The nominal center of the bin in log(r) (the natural logarithm of r). rnom: The nominal center of the bin converted to regular distance. i.e. r = exp(logr). meanr: The (weighted) mean value of r for the pairs in each bin. If there are no pairs in a bin, then exp(logr) will be used instead. meanlogr: The (weighted) mean value of log(r) for the pairs in each bin. If there are no pairs in a bin, then logr will be used instead. xi: The correlation function, :math:`\xi(r) = \langle t_R\rangle`. xi_im: The imaginary part of :math:`\xi(r)`. varxi: An estimate of the variance of :math:`\xi` weight: The total weight in each bin. npairs: The number of pairs going into each bin (including pairs where one or both objects have w=0). cov: An estimate of the full covariance matrix. raw_xi: The raw value of xi, uncorrected by an RT calculation. cf. `calculateXi` raw_xi_im: The raw value of xi_im, uncorrected by an RT calculation. cf. `calculateXi` raw_varxi: The raw value of varxi, uncorrected by an RT calculation. cf. `calculateXi` .. note:: The default method for estimating the variance and covariance attributes (``varxi``, and ``cov``) is 'shot', which only includes the shape noise propagated into the final correlation. This does not include sample variance, so it is always an underestimate of the actual variance. To get better estimates, you need to set ``var_method`` to something else and use patches in the input catalog(s). cf. `Covariance Estimates`. If ``sep_units`` are given (either in the config dict or as a named kwarg) then the distances will all be in these units. .. note:: If you separate out the steps of the `Corr2.process` command and use `Corr2.process_cross`, then the units will not be applied to ``meanr`` or ``meanlogr`` until the `finalize` function is called. The typical usage pattern is as follows: >>> nt = treecorr.NTCorrelation(config) >>> nt.process(cat1,cat2) # Compute the cross-correlation. >>> nt.write(file_name) # Write out to a file. >>> xi = nt.xi # Or access the correlation function directly. Parameters: config (dict): A configuration dict that can be used to pass in kwargs if desired. This dict is allowed to have addition entries besides those listed in `Corr2`, which are ignored here. (default: None) logger: If desired, a logger object for logging. (default: None, in which case one will be built according to the config dict's verbose level.) Keyword Arguments: **kwargs: See the documentation for `Corr2` for the list of allowed keyword arguments, which may be passed either directly or in the config dict. """ _cls = 'NTCorrelation' _letter1 = 'N' _letter2 = 'T' _letters = 'NT' _builder = _treecorr.NTCorr _calculateVar1 = lambda *args, **kwargs: None _calculateVar2 = staticmethod(calculateVarT) _zreal = 'tR' _zimag = 'tR_im'
[docs] def __init__(self, config=None, *, logger=None, **kwargs): """Initialize `NTCorrelation`. See class doc for details. """ super().__init__(config, logger=logger, **kwargs)
[docs] def finalize(self, vart): """Finalize the calculation of the correlation function. The `Corr2.process_cross` command accumulates values in each bin, so it can be called multiple times if appropriate. Afterwards, this command finishes the calculation by dividing each column by the total weight. Parameters: vart (float): The variance per component of the trefoil field. """ super().finalize(vart)
[docs] def calculateXi(self, *, rt=None): r"""Calculate the correlation function possibly given another correlation function that uses random points for the foreground objects. - If rt is None, the simple correlation function :math:`\langle t_R\rangle` is returned. - If rt is not None, then a compensated calculation is done: :math:`\langle t_R\rangle = (DT - RT)`, where DT represents the mean radial trefoil field around the data points and RT represents the mean radial trefoil field around random points. After calling this function, the attributes ``xi``, ``xi_im``, ``varxi``, and ``cov`` will correspond to the compensated values (if rt is provided). The raw, uncompensated values are available as ``rawxi``, ``raw_xi_im``, and ``raw_varxi``. Parameters: rt (NTCorrelation): The cross-correlation using random locations as the lenses (RT), if desired. (default: None) Returns: Tuple containing - xi = array of the real part of :math:`\xi(R)` - xi_im = array of the imaginary part of :math:`\xi(R)` - varxi = array of the variance estimates of the above values """ return super().calculateXi(rz=rt)
[docs] def write(self, file_name, *, rt=None, file_type=None, precision=None, write_patch_results=False, write_cov=False): r"""Write the correlation function to the file, file_name. - If rt is None, the simple correlation function :math:`\langle t_R\rangle` is used. - If rt is not None, then a compensated calculation is done: :math:`\langle t_R\rangle = (DT - RT)`, where DT represents the mean trefoil field around the data points and RT represents the mean trefoil field around random points. The output file will include the following columns: ========== ============================================================= Column Description ========== ============================================================= r_nom The nominal center of the bin in r meanr The mean value :math:`\langle r \rangle` of pairs that fell into each bin meanlogr The mean value :math:`\langle \log(r) \rangle` of pairs that fell into each bin tR The mean real part of the trefoil field relative to the center points. tR_im The mean imaginary part of the trefoil field relative to the center points. sigma The sqrt of the variance estimate of either of these weight The total weight contributing to each bin npairs The total number of pairs in each bin ========== ============================================================= If ``sep_units`` was given at construction, then the distances will all be in these units. Otherwise, they will be in either the same units as x,y,z (for flat or 3d coordinates) or radians (for spherical coordinates). Parameters: file_name (str): The name of the file to write to. rt (NTCorrelation): The cross-correlation using random locations as the lenses (RT), if desired. (default: None) file_type (str): The type of file to write ('ASCII' or 'FITS'). (default: determine the type automatically from the extension of file_name.) precision (int): For ASCII output catalogs, the desired precision. (default: 4; this value can also be given in the constructor in the config dict.) write_patch_results (bool): Whether to write the patch-based results as well. (default: False) write_cov (bool): Whether to write the covariance matrix as well. (default: False) """ super().write(file_name, rt, file_type, precision, write_patch_results, write_cov)