Source code for pycbc.distributions.arbitrary

# Copyright (C) 2016 Miriam Cabero Mueller, Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# Public License for more details.
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
This modules provides classes for evaluating arbitrary distributions from
a file.
import logging
import numpy
import scipy.stats

from pycbc.distributions import bounded
import pycbc.transforms
from import HFile

logger = logging.getLogger('pycbc.distributions.arbitrary')

[docs]class Arbitrary(bounded.BoundedDist): r"""A distribution constructed from a set of parameter values using a kde. Bounds may be optionally provided to limit the range. Parameters ---------- bounds : dict, optional Independent bounds on one or more parameters may be provided to limit the range of the kde. bandwidth : str, optional Set the bandwidth method for the KDE. See :py:func:`scipy.stats.gaussian_kde` for details. Default is "scott". \**params : The keyword arguments should provide the names of the parameters and a list of their parameter values. If multiple parameters are provided, a single kde will be produced with dimension equal to the number of parameters. """ name = 'arbitrary' def __init__(self, bounds=None, bandwidth="scott", **kwargs): # initialize the bounds if bounds is None: bounds = {} bounds.update({p: None for p in kwargs if p not in bounds}) super(Arbitrary, self).__init__(**bounds) # check that all parameters specified in bounds have samples if set(self.params) != set(kwargs.keys()): raise ValueError("Must provide samples for all parameters given " "in the bounds dictionary") # if bounds are provided use logit transform to move the points # to +/- inifinity self._transforms = {} self._tparams = {} for param,bnds in self.bounds.items(): if numpy.isfinite(bnds[1] - bnds[0]): tparam = 'logit'+param samples = kwargs[param] t = pycbc.transforms.Logit(param, tparam, domain=bnds) self._transforms[tparam] = t self._tparams[param] = tparam # remove any sample points that fall out side of the bounds outside = bnds.__contains__(samples) if outside.any(): samples = samples[outside] # transform the sample points kwargs[param] = t.transform({param: samples})[tparam] elif not (~numpy.isfinite(bnds[0]) and ~numpy.isfinite(bnds[1])): raise ValueError("if specifying bounds, both bounds must " "be finite") # build the kde self._kde = self.get_kde_from_arrays(*[kwargs[p] for p in self.params]) self.set_bandwidth(bandwidth) @property def params(self): return self._params @property def kde(self): return self._kde def _pdf(self, **kwargs): """Returns the pdf at the given values. The keyword arguments must contain all of parameters in self's params. Unrecognized arguments are ignored. """ for p in self._params: if p not in kwargs.keys(): raise ValueError('Missing parameter {} to construct pdf.' .format(p)) if kwargs in self: # transform into the kde space jacobian = 1. for param, tparam in self._tparams.items(): t = self._transforms[tparam] try: samples = t.transform({param: kwargs[param]}) except ValueError as e: # can get a value error if the value is exactly == to # the bounds, in which case, just return 0. if kwargs[param] in self.bounds[param]: return 0. else: raise ValueError(e) kwargs[param] = samples[tparam] # update the jacobian for the transform; if p is the pdf # in the params frame (the one we want) and p' is the pdf # in the transformed frame (the one that's calculated) then: # p = J * p', where J is the Jacobian of going from p to p' jacobian *= t.jacobian(samples) # for scipy < 0.15.0, gaussian_kde.pdf = gaussian_kde.evaluate this_pdf = jacobian * self._kde.evaluate([kwargs[p] for p in self._params]) if len(this_pdf) == 1: return float(this_pdf) else: return this_pdf else: return 0. def _logpdf(self, **kwargs): """Returns the log of the pdf at the given values. The keyword arguments must contain all of parameters in self's params. Unrecognized arguments are ignored. """ if kwargs not in self: return -numpy.inf else: return numpy.log(self._pdf(**kwargs))
[docs] def set_bandwidth(self, set_bw="scott"): self._kde.set_bandwidth(set_bw)
[docs] def rvs(self, size=1, param=None): """Gives a set of random values drawn from the kde. Parameters ---------- size : {1, int} The number of values to generate; default is 1. param : {None, string} If provided, will just return values for the given parameter. Otherwise, returns random values for each parameter. Returns ------- structured array The random values in a numpy structured array. If a param was specified, the array will only have an element corresponding to the given parameter. Otherwise, the array will have an element for each parameter in self's params. """ if param is not None: dtype = [(param, float)] else: dtype = [(p, float) for p in self.params] size = int(size) arr = numpy.zeros(size, dtype=dtype) draws = self._kde.resample(size) draws = {param: draws[ii,:] for ii,param in enumerate(self.params)} for (param,_) in dtype: try: # transform back to param space tparam = self._tparams[param] tdraws = {tparam: draws[param]} draws[param] = self._transforms[tparam].inverse_transform( tdraws)[param] except KeyError: pass arr[param] = draws[param] return arr
[docs] @staticmethod def get_kde_from_arrays(*arrays): """Constructs a KDE from the given arrays. \*arrays : Each argument should be a 1D numpy array to construct the kde from. The resulting KDE will have dimension given by the number of parameters. """ return scipy.stats.gaussian_kde(numpy.vstack(arrays))
[docs] @classmethod def from_config(cls, cp, section, variable_args): """Raises a NotImplementedError; to load from a config file, use `FromFile`. """ raise NotImplementedError("This class does not support loading from a " "config file. Use `FromFile` instead.")
[docs]class FromFile(Arbitrary): r"""A distribution that reads the values of the parameter(s) from an hdf file, computes the kde to construct the pdf, and draws random variables from it. Parameters ---------- filename : str The path to an hdf file containing the values of the parameters that want to be used to construct the distribution. Each parameter should be a separate dataset in the hdf file, and all datasets should have the same size. For example, to give a prior for mass1 and mass2 from file f, f['mass1'] and f['mass2'] contain the n values for each parameter. datagroup : str, optional The name of the group to look in for the samples. For example, if ``datagroup = 'samples'``, then parameter ``param`` will be retrived from ``f['samples'][param]``. If none provided (the default) the data sets will be assumed to be in the top level directory of the file. \**params : The keyword arguments should provide the names of the parameters to be read from the file and (optionally) their bounds. If no parameters are provided, it will use all the parameters found in the file. To provide bounds, specify e.g. mass1=[10,100]. Otherwise, mass1=None. Attributes ---------- norm : float The normalization of the multi-dimensional pdf. lognorm : float The log of the normalization. kde : The kde obtained from the values in the file. """ name = 'fromfile' def __init__(self, filename=None, datagroup=None, **params): if filename is None: raise ValueError('A file must be specified for this distribution.') self._filename = filename self.datagroup = datagroup # Get the parameter names to pass to get_kde_from_file if len(params) == 0: ps = None else: ps = list(params.keys()) param_vals, bw = self.get_arrays_from_file(filename, params=ps) super(FromFile, self).__init__(bounds=params, bandwidth=bw, **param_vals) @property def filename(self): """str: The path to the file containing values for the parameter(s). """ return self._filename
[docs] def get_arrays_from_file(self, params_file, params=None): """Reads the values of one or more parameters from an hdf file and returns as a dictionary. Parameters ---------- params_file : str The hdf file that contains the values of the parameters. params : {None, list} If provided, will just retrieve the given parameter names. Returns ------- dict A dictionary of the parameters mapping `param_name -> array`. """ try: f = HFile(params_file, 'r') except: raise ValueError('File not found.') if self.datagroup is not None: get = f[self.datagroup] else: get = f if params is not None: if not isinstance(params, list): params = [params] for p in params: if p not in get.keys(): raise ValueError('Parameter {} is not in {}' .format(p, params_file)) else: params = [str(k) for k in get.keys()] params_values = {p: get[p][()] for p in params} try: bandwidth = f.attrs["bandwidth"] except KeyError: bandwidth = "scott" f.close() return params_values, bandwidth
[docs] @classmethod def from_config(cls, cp, section, variable_args): """Returns a distribution based on a configuration file. The parameters for the distribution are retrieved from the section titled "[`section`-`variable_args`]" in the config file. The file to construct the distribution from must be provided by setting `filename`. Boundary arguments can be provided in the same way as described in `get_param_bounds_from_config`. .. code-block:: ini [{section}-{tag}] name = fromfile filename = ra_prior.hdf min-ra = 0 max-ra = 6.28 Parameters ---------- cp : pycbc.workflow.WorkflowConfigParser A parsed configuration file that contains the distribution options. section : str Name of the section in the configuration file. variable_args : str The names of the parameters for this distribution, separated by `prior.VARARGS_DELIM`. These must appear in the "tag" part of the section header. Returns ------- BoundedDist A distribution instance from the pycbc.inference.prior module. """ return bounded.bounded_from_config(cls, cp, section, variable_args, bounds_required=False)
__all__ = ['Arbitrary', 'FromFile']