energy_operators.py

# This program is free software: you can redistribute it and/or modify
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# the Free Software Foundation, either version 3 of the License, or
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
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# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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# Copyright(C) 2013-2019 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.

import numpy as np

from .. import utilities
from ..domain_tuple import DomainTuple
from ..field import Field
from ..multi_domain import MultiDomain
from ..multi_field import MultiField
from ..sugar import makeDomain, makeOp
from .linear_operator import LinearOperator
from .operator import Operator
from .sampling_enabler import SamplingEnabler
from .scaling_operator import ScalingOperator
from .simple_linear_operators import VdotOperator


class EnergyOperator(Operator):
    """Operator which has a scalar domain as target domain.

    It is intended as an objective function for field inference.

    Examples
    --------
     - Information Hamiltonian, i.e. negative-log-probabilities.
     - Gibbs free energy, i.e. an averaged Hamiltonian, aka Kullback-Leibler
       divergence.
    """
    _target = DomainTuple.scalar_domain()


class Squared2NormOperator(EnergyOperator):
    """Computes the square of the L2-norm of the output of an operator.

    Parameters
    ----------
    domain : Domain, DomainTuple or tuple of Domain
        Domain of the operator in which the L2-norm shall be computed.
    """

    def __init__(self, domain):
        self._domain = domain

    def apply(self, x):
        self._check_input(x)
        if x.jac is None:
            return x.vdot(x)
        res = x.val.vdot(x.val)
        return x.new(res, VdotOperator(2*x.val))


class QuadraticFormOperator(EnergyOperator):
    """Computes the L2-norm of a Field or MultiField with respect to a
    specific kernel given by `endo`.

    .. math ::
        E(f) = \\frac12 f^\\dagger \\text{endo}(f)

    Parameters
    ----------
    endo : EndomorphicOperator
         Kernel of the quadratic form
    """

    def __init__(self, endo):
        from .endomorphic_operator import EndomorphicOperator
        if not isinstance(endo, EndomorphicOperator):
            raise TypeError("op must be an EndomorphicOperator")
        self._op = endo
        self._domain = endo.domain

    def apply(self, x):
        self._check_input(x)
        if x.jac is None:
            return 0.5*x.vdot(self._op(x))
        res = 0.5*x.val.vdot(self._op(x.val))
        return x.new(res, VdotOperator(self._op(x.val)))


class VariableCovarianceGaussianEnergy(EnergyOperator):
    """Computes the negative log pdf of a Gaussian with unknown covariance.

    The covariance is assumed to be diagonal.

    .. math ::
        E(s,D) = - \\log G(s, D) = 0.5 (s)^\\dagger D^{-1} (s) + 0.5 tr log(D),

    an information energy for a Gaussian distribution with residual s and
    diagonal covariance D.
    The domain of this energy will be a MultiDomain with two keys,
    the target will be the scalar domain.

    Parameters
    ----------
    domain : Domain, DomainTuple, tuple of Domain
        domain of the residual and domain of the covariance diagonal.

    residual : key
        Residual key of the Gaussian.

    inverse_covariance : key
        Inverse covariance diagonal key of the Gaussian.
    """

    def __init__(self, domain, residual_key, inverse_covariance_key):
        self._r = str(residual_key)
        self._icov = str(inverse_covariance_key)
        dom = DomainTuple.make(domain)
        self._domain = MultiDomain.make({self._r: dom, self._icov: dom})

    def apply(self, x):
        self._check_input(x)
        res = 0.5*(x[self._r].vdot(x[self._r]*x[self._icov]).real - x[self._icov].ptw("log").sum())
        if not x.want_metric:
            return res
        mf = {self._r: x.val[self._icov], self._icov: .5*x.val[self._icov]**(-2)}
        return res.add_metric(makeOp(MultiField.from_dict(mf)))


class GaussianEnergy(EnergyOperator):
    """Computes a negative-log Gaussian.

    Represents up to constants in :math:`m`:

    .. math ::
        E(f) = - \\log G(f-m, D) = 0.5 (f-m)^\\dagger D^{-1} (f-m),

    an information energy for a Gaussian distribution with mean m and
    covariance D.

    Parameters
    ----------
    mean : Field
        Mean of the Gaussian. Default is 0.
    inverse_covariance : LinearOperator
        Inverse covariance of the Gaussian. Default is the identity operator.
    domain : Domain, DomainTuple, tuple of Domain or MultiDomain
        Operator domain. By default it is inferred from `mean` or
        `covariance` if specified

    Note
    ----
    At least one of the arguments has to be provided.
    """

    def __init__(self, mean=None, inverse_covariance=None, domain=None):
        if mean is not None and not isinstance(mean, (Field, MultiField)):
            raise TypeError
        if inverse_covariance is not None and not isinstance(inverse_covariance, LinearOperator):
            raise TypeError

        self._domain = None
        if mean is not None:
            self._checkEquivalence(mean.domain)
        if inverse_covariance is not None:
            self._checkEquivalence(inverse_covariance.domain)
        if domain is not None:
            self._checkEquivalence(domain)
        if self._domain is None:
            raise ValueError("no domain given")
        self._mean = mean
        if inverse_covariance is None:
            self._op = Squared2NormOperator(self._domain).scale(0.5)
            self._met = ScalingOperator(self._domain, 1)
        else:
            self._op = QuadraticFormOperator(inverse_covariance)
            self._met = inverse_covariance

    def _checkEquivalence(self, newdom):
        newdom = makeDomain(newdom)
        if self._domain is None:
            self._domain = newdom
        else:
            if self._domain != newdom:
                raise ValueError("domain mismatch")

    def apply(self, x):
        self._check_input(x)
        residual = x if self._mean is None else x - self._mean
        res = self._op(residual).real
        if x.want_metric:
            return res.add_metric(self._met)
        return res


class PoissonianEnergy(EnergyOperator):
    """Computes likelihood Hamiltonians of expected count field constrained by
    Poissonian count data.

    Represents up to an f-independent term :math:`log(d!)`:

    .. math ::
        E(f) = -\\log \\text{Poisson}(d|f) = \\sum f - d^\\dagger \\log(f),

    where f is a :class:`Field` in data space with the expectation values for
    the counts.

    Parameters
    ----------
    d : Field
        Data field with counts. Needs to have integer dtype and all field
        values need to be non-negative.
    """

    def __init__(self, d):
        if not isinstance(d, Field) or not np.issubdtype(d.dtype, np.integer):
            raise TypeError
        if np.any(d.val < 0):
            raise ValueError
        self._d = d
        self._domain = DomainTuple.make(d.domain)

    def apply(self, x):
        self._check_input(x)
        res = x.sum() - x.ptw("log").vdot(self._d)
        if not x.want_metric:
            return res
        return res.add_metric(makeOp(1./x.val))


class InverseGammaLikelihood(EnergyOperator):
    """Computes the negative log-likelihood of the inverse gamma distribution.

    It negative log-pdf(x) is given by

    .. math ::

        \\sum_i (\\alpha_i+1)*\\ln(x_i) + \\beta_i/x_i

    This is the likelihood for the variance :math:`x=S_k` given data
    :math:`\\beta = 0.5 |s_k|^2` where the Field :math:`s` is known to have
    the covariance :math:`S_k`.

    Parameters
    ----------
    beta : Field
        beta parameter of the inverse gamma distribution
    alpha : Scalar, Field, optional
        alpha parameter of the inverse gamma distribution
    """

    def __init__(self, beta, alpha=-0.5):
        if not isinstance(beta, Field):
            raise TypeError
        self._domain = DomainTuple.make(beta.domain)
        self._beta = beta
        if np.isscalar(alpha):
            alpha = Field(beta.domain, np.full(beta.shape, alpha))
        elif not isinstance(alpha, Field):
            raise TypeError
        self._alphap1 = alpha+1

    def apply(self, x):
        self._check_input(x)
        res = x.ptw("log").vdot(self._alphap1) + x.ptw("reciprocal").vdot(self._beta)
        if not x.want_metric:
            return res
        return res.add_metric(makeOp(self._alphap1/(x.val**2)))


class StudentTEnergy(EnergyOperator):
    """Computes likelihood energy corresponding to Student's t-distribution.

    .. math ::
        E_\\theta(f) = -\\log \\text{StudentT}_\\theta(f)
                     = \\frac{\\theta + 1}{2} \\log(1 + \\frac{f^2}{\\theta}),

    where f is a field defined on `domain`.

    Parameters
    ----------
    domain : `Domain` or `DomainTuple`
        Domain of the operator
    theta : Scalar
        Degree of freedom parameter for the student t distribution
    """

    def __init__(self, domain, theta):
        self._domain = DomainTuple.make(domain)
        self._theta = theta

    def apply(self, x):
        self._check_input(x)
        res = (((self._theta+1)/2)*(x**2/self._theta).ptw("log1p")).sum()
        if not x.want_metric:
            return res
        met = ScalingOperator(self.domain, (self._theta+1) / (self._theta+3))
        return res.add_metric(met)


class BernoulliEnergy(EnergyOperator):
    """Computes likelihood energy of expected event frequency constrained by
    event data.

    .. math ::
        E(f) = -\\log \\text{Bernoulli}(d|f)
             = -d^\\dagger \\log f  - (1-d)^\\dagger \\log(1-f),

    where f is a field defined on `d.domain` with the expected
    frequencies of events.

    Parameters
    ----------
    d : Field
        Data field with events (1) or non-events (0).
    """

    def __init__(self, d):
        if not isinstance(d, Field) or not np.issubdtype(d.dtype, np.integer):
            raise TypeError
        if not np.all(np.logical_or(d.val == 0, d.val == 1)):
            raise ValueError
        self._d = d
        self._domain = DomainTuple.make(d.domain)

    def apply(self, x):
        self._check_input(x)
        res = -x.ptw("log").vdot(self._d) + (1.-x).ptw("log").vdot(self._d-1.)
        if not x.want_metric:
            return res
        return res.add_metric(makeOp(1./(x.val*(1. - x.val))))


class StandardHamiltonian(EnergyOperator):
    """Computes an information Hamiltonian in its standard form, i.e. with the
    prior being a Gaussian with unit covariance.

    Let the likelihood energy be :math:`E_{lh}`. Then this operator computes:

    .. math ::
         H(f) = 0.5 f^\\dagger f + E_{lh}(f):

    Other field priors can be represented via transformations of a white
    Gaussian field into a field with the desired prior probability structure.

    By implementing prior information this way, the field prior is represented
    by a generative model, from which NIFTy can draw samples and infer a field
    using the Maximum a Posteriori (MAP) or the Variational Bayes (VB) method.

    The metric of this operator can be used as covariance for drawing Gaussian
    samples.

    Parameters
    ----------
    lh : EnergyOperator
        The likelihood energy.
    ic_samp : IterationController
        Tells an internal :class:`SamplingEnabler` which convergence criterion
        to use to draw Gaussian samples.

    See also
    --------
    `Encoding prior knowledge in the structure of the likelihood`,
    Jakob Knollmüller, Torsten A. Ensslin,
    `<https://arxiv.org/abs/1812.04403>`_
    """

    def __init__(self, lh, ic_samp=None, _c_inp=None):
        self._lh = lh
        self._prior = GaussianEnergy(domain=lh.domain)
        if _c_inp is not None:
            _, self._prior = self._prior.simplify_for_constant_input(_c_inp)
        self._ic_samp = ic_samp
        self._domain = lh.domain

    def apply(self, x):
        self._check_input(x)
        if not x.want_metric or self._ic_samp is None:
            return (self._lh + self._prior)(x)
        lhx, prx = self._lh(x), self._prior(x)
        return (lhx+prx).add_metric(SamplingEnabler(lhx.metric, prx.metric, self._ic_samp))

    def __repr__(self):
        subs = 'Likelihood:\n{}'.format(utilities.indent(self._lh.__repr__()))
        subs += '\nPrior:\n{}'.format(self._prior)
        return 'StandardHamiltonian:\n' + utilities.indent(subs)

    def _simplify_for_constant_input_nontrivial(self, c_inp):
        out, lh1 = self._lh.simplify_for_constant_input(c_inp)
        return out, StandardHamiltonian(lh1, self._ic_samp, _c_inp=c_inp)


class AveragedEnergy(EnergyOperator):
    """Averages an energy over samples.

    Parameters
    ----------
    h: Hamiltonian
       The energy to be averaged.
    res_samples : iterable of Fields
       Set of residual sample points to be added to mean field for
       approximate estimation of the KL.

    Notes
    -----
    - Having symmetrized residual samples, with both :math:`v_i` and
      :math:`-v_i` being present, ensures that the distribution mean is
      exactly represented.

    - :class:`AveragedEnergy(h)` approximates
      :math:`\\left< H(f) \\right>_{G(f-m,D)}` if the residuals :math:`f-m`
      are drawn from a Gaussian distribution with covariance :math:`D`.
    """

    def __init__(self, h, res_samples):
        self._h = h
        self._domain = h.domain
        self._res_samples = tuple(res_samples)

    def apply(self, x):
        self._check_input(x)
        mymap = map(lambda v: self._h(x+v), self._res_samples)
        return utilities.my_sum(mymap)/len(self._res_samples)